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| { | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "view-in-github", | |
| "colab_type": "text" | |
| }, | |
| "source": [ | |
| "<a href=\"https://colab.research.google.com/gist/tonigi/c573598b2fec20dff248f6381247a77a/copy-of-welcome-to-colab.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!nvidia-smi" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "-F7CukjoGx6H", | |
| "outputId": "2791a51e-f40f-410e-8079-cdd1a555870b" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "Tue Jul 9 15:27:25 2024 \n", | |
| "+---------------------------------------------------------------------------------------+\n", | |
| "| NVIDIA-SMI 535.104.05 Driver Version: 535.104.05 CUDA Version: 12.2 |\n", | |
| "|-----------------------------------------+----------------------+----------------------+\n", | |
| "| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |\n", | |
| "| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |\n", | |
| "| | | MIG M. |\n", | |
| "|=========================================+======================+======================|\n", | |
| "| 0 Tesla T4 Off | 00000000:00:04.0 Off | 0 |\n", | |
| "| N/A 57C P8 10W / 70W | 0MiB / 15360MiB | 0% Default |\n", | |
| "| | | N/A |\n", | |
| "+-----------------------------------------+----------------------+----------------------+\n", | |
| " \n", | |
| "+---------------------------------------------------------------------------------------+\n", | |
| "| Processes: |\n", | |
| "| GPU GI CI PID Type Process name GPU Memory |\n", | |
| "| ID ID Usage |\n", | |
| "|=======================================================================================|\n", | |
| "| No running processes found |\n", | |
| "+---------------------------------------------------------------------------------------+\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "LAZ11nESX6qt", | |
| "outputId": "bec3835f-af7a-443c-a06a-625f1dedc8de" | |
| }, | |
| "source": [ | |
| "!pip install -q condacolab\n", | |
| "import condacolab\n", | |
| "condacolab.install()" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "⏬ Downloading https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-Linux-x86_64.sh...\n", | |
| "📦 Installing...\n", | |
| "📌 Adjusting configuration...\n", | |
| "🩹 Patching environment...\n", | |
| "⏲ Done in 0:00:11\n", | |
| "🔁 Restarting kernel...\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!conda install gromacs=2024.2=nompi_cuda*" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "Ze7vK6GUG_xG", | |
| "outputId": "57bcbdea-cd51-4649-b846-3e65a76b39b5" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "Channels:\n", | |
| " - conda-forge\n", | |
| "Platform: linux-64\n", | |
| "Collecting package metadata (repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n", | |
| "Solving environment: \\ \b\b| \b\b/ \b\bdone\n", | |
| "\n", | |
| "\n", | |
| "==> WARNING: A newer version of conda exists. <==\n", | |
| " current version: 23.11.0\n", | |
| " latest version: 24.5.0\n", | |
| "\n", | |
| "Please update conda by running\n", | |
| "\n", | |
| " $ conda update -n base -c conda-forge conda\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "## Package Plan ##\n", | |
| "\n", | |
| " environment location: /usr/local\n", | |
| "\n", | |
| " added / updated specs:\n", | |
| " - gromacs==2024.2[build=nompi_cuda*]\n", | |
| "\n", | |
| "\n", | |
| "The following packages will be downloaded:\n", | |
| "\n", | |
| " package | build\n", | |
| " ---------------------------|-----------------\n", | |
| " ca-certificates-2024.7.4 | hbcca054_0 151 KB conda-forge\n", | |
| " certifi-2024.7.4 | pyhd8ed1ab_0 156 KB conda-forge\n", | |
| " cudatoolkit-11.8.0 | h4ba93d1_13 682.5 MB conda-forge\n", | |
| " fftw-3.3.10 |nompi_hf1063bd_110 2.0 MB conda-forge\n", | |
| " gromacs-2024.2 |nompi_cuda_h40ca9ac_3 40.6 MB conda-forge\n", | |
| " libgfortran-ng-13.2.0 | h69a702a_13 47 KB conda-forge\n", | |
| " libgfortran5-13.2.0 | h3d2ce59_13 1.4 MB conda-forge\n", | |
| " libhwloc-2.11.0 |default_h5622ce7_1000 2.3 MB conda-forge\n", | |
| " libxml2-2.12.7 | hc051c1a_1 688 KB conda-forge\n", | |
| " openssl-3.3.1 | h4ab18f5_1 2.8 MB conda-forge\n", | |
| " ------------------------------------------------------------\n", | |
| " Total: 732.5 MB\n", | |
| "\n", | |
| "The following NEW packages will be INSTALLED:\n", | |
| "\n", | |
| " cudatoolkit conda-forge/linux-64::cudatoolkit-11.8.0-h4ba93d1_13 \n", | |
| " fftw conda-forge/linux-64::fftw-3.3.10-nompi_hf1063bd_110 \n", | |
| " gromacs conda-forge/linux-64::gromacs-2024.2-nompi_cuda_h40ca9ac_3 \n", | |
| " libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_13 \n", | |
| " libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_13 \n", | |
| " libhwloc conda-forge/linux-64::libhwloc-2.11.0-default_h5622ce7_1000 \n", | |
| "\n", | |
| "The following packages will be UPDATED:\n", | |
| "\n", | |
| " ca-certificates 2023.11.17-hbcca054_0 --> 2024.7.4-hbcca054_0 \n", | |
| " certifi 2023.11.17-pyhd8ed1ab_0 --> 2024.7.4-pyhd8ed1ab_0 \n", | |
| " libxml2 2.12.3-h232c23b_0 --> 2.12.7-hc051c1a_1 \n", | |
| " openssl 3.2.0-hd590300_1 --> 3.3.1-h4ab18f5_1 \n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "Downloading and Extracting Packages:\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 0% 0/1 [00:00<?, ?it/s]\n", | |
| "gromacs-2024.2 | 40.6 MB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\n", | |
| "\n", | |
| "openssl-3.3.1 | 2.8 MB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "libhwloc-2.11.0 | 2.3 MB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "fftw-3.3.10 | 2.0 MB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran5-13.2.0 | 1.4 MB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libxml2-2.12.7 | 688 KB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "certifi-2024.7.4 | 156 KB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "ca-certificates-2024 | 151 KB | : 0% 0/1 [00:00<?, ?it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 0% 2.289529124182724e-05/1 [00:00<1:13:04, 4384.14s/it]\n", | |
| "\n", | |
| "openssl-3.3.1 | 2.8 MB | : 1% 0.005656267153672742/1 [00:00<00:19, 19.20s/it]\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "libhwloc-2.11.0 | 2.3 MB | : 1% 0.006782150327454835/1 [00:00<00:18, 18.17s/it]\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 1% 0.007051749702482789/1 [00:00<00:24, 24.20s/it] \n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran5-13.2.0 | 1.4 MB | : 1% 0.011226654533693668/1 [00:00<00:18, 18.98s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libxml2-2.12.7 | 688 KB | : 2% 0.02324024375021277/1 [00:00<00:10, 10.24s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 1% 0.012661096056730462/1 [00:00<00:20, 20.92s/it]\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "ca-certificates-2024 | 151 KB | : 11% 0.10580356854565297/1 [00:00<00:02, 2.93s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 2% 0.024818495706140725/1 [00:00<00:12, 13.02s/it]\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "fftw-3.3.10 | 2.0 MB | : 100% 1.0/1 [00:00<00:00, 2.25it/s] \u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 5% 0.04645454592966747/1 [00:00<00:10, 10.88s/it]\n", | |
| "gromacs-2024.2 | 40.6 MB | : 0% 0.00038500124989114266/1 [00:00<27:42, 1663.05s/it]\u001b[A\n", | |
| "\n", | |
| "openssl-3.3.1 | 2.8 MB | : 100% 1.0/1 [00:00<00:00, 1.62it/s] \u001b[A\u001b[A\n", | |
| "\n", | |
| "openssl-3.3.1 | 2.8 MB | : 100% 1.0/1 [00:00<00:00, 1.62it/s]\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "certifi-2024.7.4 | 156 KB | : 100% 1.0/1 [00:00<00:00, 1.53it/s] \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "certifi-2024.7.4 | 156 KB | : 100% 1.0/1 [00:00<00:00, 1.53it/s]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 6% 0.055635557717640186/1 [00:00<00:12, 13.28s/it]\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libxml2-2.12.7 | 688 KB | : 100% 1.0/1 [00:00<00:00, 1.25it/s] \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 6% 0.06390075785593982/1 [00:00<00:12, 12.97s/it] \n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 7% 0.07193700508182119/1 [00:00<00:12, 13.39s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 8% 0.07962982293907513/1 [00:01<00:12, 13.31s/it]\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran5-13.2.0 | 1.4 MB | : 100% 1.0/1 [00:01<00:00, 1.05s/it] \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran5-13.2.0 | 1.4 MB | : 100% 1.0/1 [00:01<00:00, 1.05s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "ca-certificates-2024 | 151 KB | : 100% 1.0/1 [00:01<00:00, 1.08s/it] \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 9% 0.08729974550508726/1 [00:01<00:12, 13.24s/it]\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran-ng-13.2. | 47 KB | : 100% 1.0/1 [00:01<00:00, 1.27s/it] \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "\n", | |
| "libgfortran-ng-13.2. | 47 KB | : 100% 1.0/1 [00:01<00:00, 1.27s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "libhwloc-2.11.0 | 2.3 MB | : 100% 1.0/1 [00:01<00:00, 1.25s/it] \u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 10% 0.09874739112600088/1 [00:01<00:10, 11.53s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 11% 0.11321721519083569/1 [00:01<00:08, 9.65s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 12% 0.12473354668547479/1 [00:01<00:08, 9.38s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 16% 0.15958017995553583/1 [00:01<00:06, 7.20s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 17% 0.17356920290429229/1 [00:01<00:05, 7.25s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 19% 0.19195412177147955/1 [00:01<00:05, 6.60s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 22% 0.21537600471186882/1 [00:02<00:04, 5.68s/it]\n", | |
| "cudatoolkit-11.8.0 | 682.5 MB | : 67% 0.6651768964488067/1 [00:09<00:16, 48.46s/it]\n", | |
| "gromacs-2024.2 | 40.6 MB | : 100% 1.0/1 [00:09<00:00, 24.15s/it] \u001b[A\n", | |
| " \n", | |
| " \u001b[A\n", | |
| "\n", | |
| " \u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
| " \u001b[A\u001b[A\u001b[A\n", | |
| "\n", | |
| "\n", | |
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| " \u001b[A\u001b[A\u001b[A\u001b[A\n", | |
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| "Preparing transaction: \\ \b\bdone\n", | |
| "Verifying transaction: / \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n", | |
| "Executing transaction: \\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html\n", | |
| "\n", | |
| "\b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\bdone\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!gmx" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "7uAcHoJGHGs5", | |
| "outputId": "706e3e43-2833-48a6-c865-331ebfa4d72a" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| " :-) GROMACS - gmx, 2024.2-conda_forge (-:\n", | |
| "\n", | |
| "Executable: /usr/local/bin.AVX2_256/gmx\n", | |
| "Data prefix: /usr/local\n", | |
| "Working dir: /content\n", | |
| "Command line:\n", | |
| " gmx\n", | |
| "\n", | |
| "SYNOPSIS\n", | |
| "\n", | |
| "gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]\n", | |
| " [-[no]backup]\n", | |
| "\n", | |
| "OPTIONS\n", | |
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| "Other options:\n", | |
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| " -[no]h (no)\n", | |
| " Print help and quit\n", | |
| " -[no]quiet (no)\n", | |
| " Do not print common startup info or quotes\n", | |
| " -[no]version (no)\n", | |
| " Print extended version information and quit\n", | |
| " -[no]copyright (no)\n", | |
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| " -nice <int> (19)\n", | |
| " Set the nicelevel (default depends on command)\n", | |
| " -[no]backup (yes)\n", | |
| " Write backups if output files exist\n", | |
| "\n", | |
| "Additional help is available on the following topics:\n", | |
| " commands List of available commands\n", | |
| " selections Selection syntax and usage\n", | |
| "To access the help, use 'gmx help <topic>'.\n", | |
| "For help on a command, use 'gmx help <command>'.\n", | |
| "\n", | |
| "GROMACS reminds you: \"A programmer's spouse says 'While you're at the grocery store, buy some eggs.' The programmer never comes back.\" (Anonymous)\n", | |
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| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!wget -O- https://ftp.gromacs.org/regressiontests/regressiontests-2024.2.tar.gz|tar -zxvf-" | |
| ], | |
| "metadata": { | |
| "colab": { | |
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| "execution_count": null, | |
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| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
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| "--2024-07-09 15:32:42-- https://ftp.gromacs.org/regressiontests/regressiontests-2024.2.tar.gz\n", | |
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| "HTTP request sent, awaiting response... 200 OK\n", | |
| "Length: 48131919 (46M) [application/x-gzip]\n", | |
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| "regressiontests-2024.2/freeenergy/transformAtoB/reference_s.trr\n", | |
| "regressiontests-2024.2/freeenergy/transformAtoB/reference_s.warn\n", | |
| "regressiontests-2024.2/freeenergy/transformAtoB/topol.top\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/conf.gro\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/grompp.mdp\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_d.edr\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_d.log\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_d.tpr\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_d.trr\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_d.warn\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_s.edr\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_s.log\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_s.tpr\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_s.trr\n", | |
| "- 100%[===================>] 45.90M 15.0MB/s in 3.6s \n", | |
| "\n", | |
| "2024-07-09 15:32:47 (12.8 MB/s) - written to stdout [48131919/48131919]\n", | |
| "\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/reference_s.warn\n", | |
| "regressiontests-2024.2/freeenergy/vdwalone/topol.top\n", | |
| "regressiontests-2024.2/gmxFile/\n", | |
| "regressiontests-2024.2/gmxFile/Path.pm\n", | |
| "regressiontests-2024.2/gmxtest.pl\n", | |
| "regressiontests-2024.2/scripts/\n", | |
| "regressiontests-2024.2/scripts/CTest2JUnit.xsl\n", | |
| "regressiontests-2024.2/tools/\n", | |
| "regressiontests-2024.2/tools/aminoacids.tpr\n", | |
| "regressiontests-2024.2/tools/aminoacids.trr\n", | |
| "regressiontests-2024.2/tools/g_rms.cfg\n", | |
| "regressiontests-2024.2/tools/g_rms/\n", | |
| "regressiontests-2024.2/tools/g_rms/1/\n", | |
| "regressiontests-2024.2/tools/g_rms/1/rmsd.xvg.ref\n", | |
| "regressiontests-2024.2/tools/g_rms/2/\n", | |
| "regressiontests-2024.2/tools/g_rms/2/aver.xvg.ref\n", | |
| "regressiontests-2024.2/tools/g_rms/2/avgrp.xvg.ref\n", | |
| "regressiontests-2024.2/tools/g_rmsdist.cfg\n", | |
| "regressiontests-2024.2/tools/g_rmsdist/\n", | |
| "regressiontests-2024.2/tools/g_rmsdist/1/\n", | |
| "regressiontests-2024.2/tools/g_rmsdist/1/distrmsd.xvg.ref\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "%cd regressiontests-2024.2" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "1LSfCqMUICWU", | |
| "outputId": "7b43c812-4cd4-4ff0-dd66-422597297d80" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "/content/regressiontests-2024.2\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!find /usr/local -name GMXRC" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "06eojkOcIFBz", | |
| "outputId": "1e0d91f2-5c15-4027-afaa-6dfc0747b484" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "/usr/local/bin.AVX2_256/GMXRC\n", | |
| "/usr/local/bin.SSE2/GMXRC\n", | |
| "/usr/local/pkgs/gromacs-2024.2-nompi_cuda_h40ca9ac_3/bin.AVX2_256/GMXRC\n", | |
| "/usr/local/pkgs/gromacs-2024.2-nompi_cuda_h40ca9ac_3/bin.SSE2/GMXRC\n", | |
| "/usr/local/pkgs/gromacs-2024.2-nompi_cuda_h40ca9ac_3/bin.AVX_256/GMXRC\n", | |
| "/usr/local/bin.AVX_256/GMXRC\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [ | |
| "!./gmxtest.pl all" | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "v4r1DT9-IJaz", | |
| "outputId": "df16966c-8ab8-45ee-ca2a-110cc9a8f802" | |
| }, | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "Testing acetonitrilRF . . . gmx grompp -f /content/regressiontests-2024.2/complex/acetonitrilRF/grompp.mdp -c /content/regressiontests-2024.2/complex/acetonitrilRF/conf -r /content/regressiontests-2024.2/complex/acetonitrilRF/conf -p /content/regressiontests-2024.2/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/acetonitrilRF/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/acetonitrilRF/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/acetonitrilRF/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing aminoacids . . . gmx grompp -f /content/regressiontests-2024.2/complex/aminoacids/grompp.mdp -c /content/regressiontests-2024.2/complex/aminoacids/conf -r /content/regressiontests-2024.2/complex/aminoacids/conf -p /content/regressiontests-2024.2/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/aminoacids/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/aminoacids/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running aminoacids using only CPU-based non-bonded kernels\n", | |
| "Testing aminoacids-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/aminoacids/grompp.mdp -c /content/regressiontests-2024.2/complex/aminoacids/conf -r /content/regressiontests-2024.2/complex/aminoacids/conf -p /content/regressiontests-2024.2/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/aminoacids/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/aminoacids/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running aminoacids using CPU-based update\n", | |
| "Testing aminoacids-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/aminoacids/grompp.mdp -c /content/regressiontests-2024.2/complex/aminoacids/conf -r /content/regressiontests-2024.2/complex/aminoacids/conf -p /content/regressiontests-2024.2/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/aminoacids/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/aminoacids/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing argon . . . gmx grompp -f /content/regressiontests-2024.2/complex/argon/grompp.mdp -c /content/regressiontests-2024.2/complex/argon/conf -r /content/regressiontests-2024.2/complex/argon/conf -p /content/regressiontests-2024.2/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing awh_multibias . . . gmx grompp -f /content/regressiontests-2024.2/complex/awh_multibias/grompp.mdp -c /content/regressiontests-2024.2/complex/awh_multibias/conf -r /content/regressiontests-2024.2/complex/awh_multibias/conf -p /content/regressiontests-2024.2/complex/awh_multibias/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/awh_multibias/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/awh_multibias/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -cpi /content/regressiontests-2024.2/complex/awh_multibias/continue -noappend >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/awh_multibias/reference_s.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/awh_multibias/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing awh_multidim . . . gmx grompp -f /content/regressiontests-2024.2/complex/awh_multidim/grompp.mdp -c /content/regressiontests-2024.2/complex/awh_multidim/conf -r /content/regressiontests-2024.2/complex/awh_multidim/conf -p /content/regressiontests-2024.2/complex/awh_multidim/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/awh_multidim/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/awh_multidim/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/awh_multidim/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running awh_multidim using only CPU-based non-bonded kernels\n", | |
| "Testing awh_multidim-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/awh_multidim/grompp.mdp -c /content/regressiontests-2024.2/complex/awh_multidim/conf -r /content/regressiontests-2024.2/complex/awh_multidim/conf -p /content/regressiontests-2024.2/complex/awh_multidim/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/awh_multidim/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/awh_multidim/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/awh_multidim/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running awh_multidim using CPU-based update\n", | |
| "Testing awh_multidim-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/awh_multidim/grompp.mdp -c /content/regressiontests-2024.2/complex/awh_multidim/conf -r /content/regressiontests-2024.2/complex/awh_multidim/conf -p /content/regressiontests-2024.2/complex/awh_multidim/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/awh_multidim/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/awh_multidim/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/awh_multidim/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing butane . . . gmx grompp -f /content/regressiontests-2024.2/complex/butane/grompp.mdp -c /content/regressiontests-2024.2/complex/butane/conf -r /content/regressiontests-2024.2/complex/butane/conf -p /content/regressiontests-2024.2/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/butane/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/butane/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running butane using only CPU-based non-bonded kernels\n", | |
| "Testing butane-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/butane/grompp.mdp -c /content/regressiontests-2024.2/complex/butane/conf -r /content/regressiontests-2024.2/complex/butane/conf -p /content/regressiontests-2024.2/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/butane/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/butane/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running butane using CPU-based update\n", | |
| "Testing butane-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/butane/grompp.mdp -c /content/regressiontests-2024.2/complex/butane/conf -r /content/regressiontests-2024.2/complex/butane/conf -p /content/regressiontests-2024.2/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/butane/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/butane/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing cbt . . . gmx grompp -f /content/regressiontests-2024.2/complex/cbt/grompp.mdp -c /content/regressiontests-2024.2/complex/cbt/conf -r /content/regressiontests-2024.2/complex/cbt/conf -p /content/regressiontests-2024.2/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/cbt/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/cbt/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/cbt/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing dd121 . . . gmx grompp -f /content/regressiontests-2024.2/complex/dd121/grompp.mdp -c /content/regressiontests-2024.2/complex/dd121/conf -r /content/regressiontests-2024.2/complex/dd121/conf -p /content/regressiontests-2024.2/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/dd121/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/dd121/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running dd121 using only CPU-based non-bonded kernels\n", | |
| "Testing dd121-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/dd121/grompp.mdp -c /content/regressiontests-2024.2/complex/dd121/conf -r /content/regressiontests-2024.2/complex/dd121/conf -p /content/regressiontests-2024.2/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 12 -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/dd121/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/dd121/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing dec+water . . . gmx grompp -f /content/regressiontests-2024.2/complex/dec+water/grompp.mdp -c /content/regressiontests-2024.2/complex/dec+water/conf -r /content/regressiontests-2024.2/complex/dec+water/conf -p /content/regressiontests-2024.2/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/dec+water/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/dec+water/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/dec+water/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing distance_restraints . . . gmx grompp -f /content/regressiontests-2024.2/complex/distance_restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/distance_restraints/conf -r /content/regressiontests-2024.2/complex/distance_restraints/conf -p /content/regressiontests-2024.2/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running distance_restraints using only CPU-based non-bonded kernels\n", | |
| "Testing distance_restraints-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/distance_restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/distance_restraints/conf -r /content/regressiontests-2024.2/complex/distance_restraints/conf -p /content/regressiontests-2024.2/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running distance_restraints using CPU-based update\n", | |
| "Testing distance_restraints-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/distance_restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/distance_restraints/conf -r /content/regressiontests-2024.2/complex/distance_restraints/conf -p /content/regressiontests-2024.2/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing ethyleenglycol . . . gmx grompp -f /content/regressiontests-2024.2/complex/ethyleenglycol/grompp.mdp -c /content/regressiontests-2024.2/complex/ethyleenglycol/conf -r /content/regressiontests-2024.2/complex/ethyleenglycol/conf -p /content/regressiontests-2024.2/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running ethyleenglycol using only CPU-based non-bonded kernels\n", | |
| "Testing ethyleenglycol-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/ethyleenglycol/grompp.mdp -c /content/regressiontests-2024.2/complex/ethyleenglycol/conf -r /content/regressiontests-2024.2/complex/ethyleenglycol/conf -p /content/regressiontests-2024.2/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running ethyleenglycol using CPU-based update\n", | |
| "Testing ethyleenglycol-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/ethyleenglycol/grompp.mdp -c /content/regressiontests-2024.2/complex/ethyleenglycol/conf -r /content/regressiontests-2024.2/complex/ethyleenglycol/conf -p /content/regressiontests-2024.2/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/ethyleenglycol/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing field . . . gmx grompp -f /content/regressiontests-2024.2/complex/field/grompp.mdp -c /content/regressiontests-2024.2/complex/field/conf -r /content/regressiontests-2024.2/complex/field/conf -p /content/regressiontests-2024.2/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/field/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/field/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running field using only CPU-based non-bonded kernels\n", | |
| "Testing field-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/field/grompp.mdp -c /content/regressiontests-2024.2/complex/field/conf -r /content/regressiontests-2024.2/complex/field/conf -p /content/regressiontests-2024.2/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/field/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/field/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running field using CPU-based update\n", | |
| "Testing field-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/field/grompp.mdp -c /content/regressiontests-2024.2/complex/field/conf -r /content/regressiontests-2024.2/complex/field/conf -p /content/regressiontests-2024.2/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/field/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/field/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nacl . . . gmx grompp -f /content/regressiontests-2024.2/complex/nacl/grompp.mdp -c /content/regressiontests-2024.2/complex/nacl/conf -r /content/regressiontests-2024.2/complex/nacl/conf -p /content/regressiontests-2024.2/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nacl/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nacl/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nacl using only CPU-based non-bonded kernels\n", | |
| "Testing nacl-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nacl/grompp.mdp -c /content/regressiontests-2024.2/complex/nacl/conf -r /content/regressiontests-2024.2/complex/nacl/conf -p /content/regressiontests-2024.2/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nacl/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nacl/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nacl using CPU-based update\n", | |
| "Testing nacl-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nacl/grompp.mdp -c /content/regressiontests-2024.2/complex/nacl/conf -r /content/regressiontests-2024.2/complex/nacl/conf -p /content/regressiontests-2024.2/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nacl/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nacl/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-energy-groups . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-energy-groups/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-energy-groups/conf -r /content/regressiontests-2024.2/complex/nbnxn-energy-groups/conf -p /content/regressiontests-2024.2/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-energy-groups/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-energy-groups/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-energy-groups/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-free-energy . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -r /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -p /content/regressiontests-2024.2/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-free-energy using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-free-energy-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -r /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -p /content/regressiontests-2024.2/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-free-energy using CPU-based update\n", | |
| "Testing nbnxn-free-energy-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -r /content/regressiontests-2024.2/complex/nbnxn-free-energy/conf -p /content/regressiontests-2024.2/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-free-energy/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-free-energy-vv . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/conf -r /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/conf -p /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-free-energy-vv using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-free-energy-vv-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/conf -r /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/conf -p /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-free-energy-vv/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-ljpme-geometric . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-ljpme-geometric using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-ljpme-geometric-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-ljpme-geometric using CPU-based update\n", | |
| "Testing nbnxn-ljpme-geometric-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-ljpme-LB . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-ljpme-LB using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-ljpme-LB-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-ljpme-LB-geometric . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-ljpme-LB-geometric using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-ljpme-LB-geometric-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/conf -r /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/conf -p /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-ljpme-LB-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-vdw-force-switch . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-force-switch using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-vdw-force-switch-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-force-switch using CPU-based update\n", | |
| "Testing nbnxn-vdw-force-switch-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-force-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-vdw-potential-switch . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-potential-switch using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-vdw-potential-switch-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-potential-switch using CPU-based PME\n", | |
| "Testing nbnxn-vdw-potential-switch-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-potential-switch using CPU-based update\n", | |
| "Testing nbnxn-vdw-potential-switch-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn-vdw-potential-switch-argon . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-potential-switch-argon using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn-vdw-potential-switch-argon-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn-vdw-potential-switch-argon using CPU-based update\n", | |
| "Testing nbnxn-vdw-potential-switch-argon-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -r /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/conf -p /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn-vdw-potential-switch-argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_pme . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_pme-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme using CPU-based PME\n", | |
| "Testing nbnxn_pme-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme using CPU-based update\n", | |
| "Testing nbnxn_pme-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_pme_order5 . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme_order5 using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_pme_order5-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme_order5 using CPU-based update\n", | |
| "Testing nbnxn_pme_order5-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order5/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order5/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_pme_order6 . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme_order6 using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_pme_order6-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_pme_order6 using CPU-based update\n", | |
| "Testing nbnxn_pme_order6-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -r /content/regressiontests-2024.2/complex/nbnxn_pme_order6/conf -p /content/regressiontests-2024.2/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_pme_order6/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_rf . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rf/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rf/conf -r /content/regressiontests-2024.2/complex/nbnxn_rf/conf -p /content/regressiontests-2024.2/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_rf using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_rf-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rf/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rf/conf -r /content/regressiontests-2024.2/complex/nbnxn_rf/conf -p /content/regressiontests-2024.2/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_rf using CPU-based update\n", | |
| "Testing nbnxn_rf-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rf/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rf/conf -r /content/regressiontests-2024.2/complex/nbnxn_rf/conf -p /content/regressiontests-2024.2/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rf/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_rzero . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rzero/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -r /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -p /content/regressiontests-2024.2/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_rzero using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_rzero-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rzero/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -r /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -p /content/regressiontests-2024.2/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_rzero using CPU-based update\n", | |
| "Testing nbnxn_rzero-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_rzero/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -r /content/regressiontests-2024.2/complex/nbnxn_rzero/conf -p /content/regressiontests-2024.2/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_rzero/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nbnxn_vsite . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_vsite/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_vsite/conf -r /content/regressiontests-2024.2/complex/nbnxn_vsite/conf -p /content/regressiontests-2024.2/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nbnxn_vsite using only CPU-based non-bonded kernels\n", | |
| "Testing nbnxn_vsite-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nbnxn_vsite/grompp.mdp -c /content/regressiontests-2024.2/complex/nbnxn_vsite/conf -r /content/regressiontests-2024.2/complex/nbnxn_vsite/conf -p /content/regressiontests-2024.2/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 6 -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nbnxn_vsite/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing nst_mismatch . . . gmx grompp -f /content/regressiontests-2024.2/complex/nst_mismatch/grompp.mdp -c /content/regressiontests-2024.2/complex/nst_mismatch/conf -r /content/regressiontests-2024.2/complex/nst_mismatch/conf -p /content/regressiontests-2024.2/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nst_mismatch using only CPU-based non-bonded kernels\n", | |
| "Testing nst_mismatch-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nst_mismatch/grompp.mdp -c /content/regressiontests-2024.2/complex/nst_mismatch/conf -r /content/regressiontests-2024.2/complex/nst_mismatch/conf -p /content/regressiontests-2024.2/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running nst_mismatch using CPU-based update\n", | |
| "Testing nst_mismatch-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/nst_mismatch/grompp.mdp -c /content/regressiontests-2024.2/complex/nst_mismatch/conf -r /content/regressiontests-2024.2/complex/nst_mismatch/conf -p /content/regressiontests-2024.2/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/nst_mismatch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing octahedron . . . gmx grompp -f /content/regressiontests-2024.2/complex/octahedron/grompp.mdp -c /content/regressiontests-2024.2/complex/octahedron/conf -r /content/regressiontests-2024.2/complex/octahedron/conf -p /content/regressiontests-2024.2/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running octahedron using only CPU-based non-bonded kernels\n", | |
| "Testing octahedron-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/octahedron/grompp.mdp -c /content/regressiontests-2024.2/complex/octahedron/conf -r /content/regressiontests-2024.2/complex/octahedron/conf -p /content/regressiontests-2024.2/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running octahedron using CPU-based PME\n", | |
| "Testing octahedron-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/octahedron/grompp.mdp -c /content/regressiontests-2024.2/complex/octahedron/conf -r /content/regressiontests-2024.2/complex/octahedron/conf -p /content/regressiontests-2024.2/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running octahedron using CPU-based update\n", | |
| "Testing octahedron-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/octahedron/grompp.mdp -c /content/regressiontests-2024.2/complex/octahedron/conf -r /content/regressiontests-2024.2/complex/octahedron/conf -p /content/regressiontests-2024.2/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing orientation-restraints . . . gmx grompp -f /content/regressiontests-2024.2/complex/orientation-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/orientation-restraints/conf -r /content/regressiontests-2024.2/complex/orientation-restraints/conf -p /content/regressiontests-2024.2/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running orientation-restraints using only CPU-based non-bonded kernels\n", | |
| "Testing orientation-restraints-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/orientation-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/orientation-restraints/conf -r /content/regressiontests-2024.2/complex/orientation-restraints/conf -p /content/regressiontests-2024.2/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running orientation-restraints using CPU-based PME\n", | |
| "Testing orientation-restraints-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/orientation-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/orientation-restraints/conf -r /content/regressiontests-2024.2/complex/orientation-restraints/conf -p /content/regressiontests-2024.2/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing position-restraints . . . gmx grompp -f /content/regressiontests-2024.2/complex/position-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/position-restraints/conf -r /content/regressiontests-2024.2/complex/position-restraints/conf -p /content/regressiontests-2024.2/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running position-restraints using only CPU-based non-bonded kernels\n", | |
| "Testing position-restraints-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/position-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/position-restraints/conf -r /content/regressiontests-2024.2/complex/position-restraints/conf -p /content/regressiontests-2024.2/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running position-restraints using CPU-based update\n", | |
| "Testing position-restraints-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/position-restraints/grompp.mdp -c /content/regressiontests-2024.2/complex/position-restraints/conf -r /content/regressiontests-2024.2/complex/position-restraints/conf -p /content/regressiontests-2024.2/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pr-vrescale . . . gmx grompp -f /content/regressiontests-2024.2/complex/pr-vrescale/grompp.mdp -c /content/regressiontests-2024.2/complex/pr-vrescale/conf -r /content/regressiontests-2024.2/complex/pr-vrescale/conf -p /content/regressiontests-2024.2/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pr-vrescale using only CPU-based non-bonded kernels\n", | |
| "Testing pr-vrescale-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pr-vrescale/grompp.mdp -c /content/regressiontests-2024.2/complex/pr-vrescale/conf -r /content/regressiontests-2024.2/complex/pr-vrescale/conf -p /content/regressiontests-2024.2/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pr-vrescale using CPU-based update\n", | |
| "Testing pr-vrescale-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pr-vrescale/grompp.mdp -c /content/regressiontests-2024.2/complex/pr-vrescale/conf -r /content/regressiontests-2024.2/complex/pr-vrescale/conf -p /content/regressiontests-2024.2/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pr-vrescale/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pull_constraint . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_constraint/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_constraint/conf -r /content/regressiontests-2024.2/complex/pull_constraint/conf -p /content/regressiontests-2024.2/complex/pull_constraint/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_constraint/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_constraint/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_constraint/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_constraint using only CPU-based non-bonded kernels\n", | |
| "Testing pull_constraint-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_constraint/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_constraint/conf -r /content/regressiontests-2024.2/complex/pull_constraint/conf -p /content/regressiontests-2024.2/complex/pull_constraint/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_constraint/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_constraint/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_constraint/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pull_cylinder . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_cylinder/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_cylinder/conf -r /content/regressiontests-2024.2/complex/pull_cylinder/conf -p /content/regressiontests-2024.2/complex/pull_cylinder/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_cylinder/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_cylinder using only CPU-based non-bonded kernels\n", | |
| "Testing pull_cylinder-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_cylinder/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_cylinder/conf -r /content/regressiontests-2024.2/complex/pull_cylinder/conf -p /content/regressiontests-2024.2/complex/pull_cylinder/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_cylinder/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_cylinder using CPU-based update\n", | |
| "Testing pull_cylinder-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_cylinder/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_cylinder/conf -r /content/regressiontests-2024.2/complex/pull_cylinder/conf -p /content/regressiontests-2024.2/complex/pull_cylinder/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_cylinder/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_cylinder/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pull_geometry_angle . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle using only CPU-based non-bonded kernels\n", | |
| "Testing pull_geometry_angle-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle using CPU-based PME\n", | |
| "Testing pull_geometry_angle-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle using CPU-based update\n", | |
| "Testing pull_geometry_angle-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pull_geometry_angle-axis . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle-axis using only CPU-based non-bonded kernels\n", | |
| "Testing pull_geometry_angle-axis-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle-axis using CPU-based PME\n", | |
| "Testing pull_geometry_angle-axis-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_angle-axis using CPU-based update\n", | |
| "Testing pull_geometry_angle-axis-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -r /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/conf -p /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing pull_geometry_dihedral . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -r /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -p /content/regressiontests-2024.2/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_dihedral using only CPU-based non-bonded kernels\n", | |
| "Testing pull_geometry_dihedral-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -r /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -p /content/regressiontests-2024.2/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_dihedral using CPU-based PME\n", | |
| "Testing pull_geometry_dihedral-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -r /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -p /content/regressiontests-2024.2/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running pull_geometry_dihedral using CPU-based update\n", | |
| "Testing pull_geometry_dihedral-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/grompp.mdp -c /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -r /content/regressiontests-2024.2/complex/pull_geometry_dihedral/conf -p /content/regressiontests-2024.2/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing reb . . . gmx grompp -f /content/regressiontests-2024.2/complex/reb/grompp.mdp -c /content/regressiontests-2024.2/complex/reb/conf -r /content/regressiontests-2024.2/complex/reb/conf -p /content/regressiontests-2024.2/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/reb/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/reb/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/reb/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing sw . . . gmx grompp -f /content/regressiontests-2024.2/complex/sw/grompp.mdp -c /content/regressiontests-2024.2/complex/sw/conf -r /content/regressiontests-2024.2/complex/sw/conf -p /content/regressiontests-2024.2/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running sw using only CPU-based non-bonded kernels\n", | |
| "Testing sw-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/sw/grompp.mdp -c /content/regressiontests-2024.2/complex/sw/conf -r /content/regressiontests-2024.2/complex/sw/conf -p /content/regressiontests-2024.2/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -ntmpi 1 -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing swap_x . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_x/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_x/conf -r /content/regressiontests-2024.2/complex/swap_x/conf -p /content/regressiontests-2024.2/complex/swap_x/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_x/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_x/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_x/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_x using only CPU-based non-bonded kernels\n", | |
| "Testing swap_x-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_x/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_x/conf -r /content/regressiontests-2024.2/complex/swap_x/conf -p /content/regressiontests-2024.2/complex/swap_x/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_x/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_x/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_x/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_x using CPU-based PME\n", | |
| "Testing swap_x-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_x/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_x/conf -r /content/regressiontests-2024.2/complex/swap_x/conf -p /content/regressiontests-2024.2/complex/swap_x/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_x/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_x/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_x/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing swap_y . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_y/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_y/conf -r /content/regressiontests-2024.2/complex/swap_y/conf -p /content/regressiontests-2024.2/complex/swap_y/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_y/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_y/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_y/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_y using only CPU-based non-bonded kernels\n", | |
| "Testing swap_y-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_y/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_y/conf -r /content/regressiontests-2024.2/complex/swap_y/conf -p /content/regressiontests-2024.2/complex/swap_y/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_y/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_y/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_y/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_y using CPU-based PME\n", | |
| "Testing swap_y-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_y/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_y/conf -r /content/regressiontests-2024.2/complex/swap_y/conf -p /content/regressiontests-2024.2/complex/swap_y/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_y/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_y/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_y/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing swap_z . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_z/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_z/conf -r /content/regressiontests-2024.2/complex/swap_z/conf -p /content/regressiontests-2024.2/complex/swap_z/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_z/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_z/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_z/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_z using only CPU-based non-bonded kernels\n", | |
| "Testing swap_z-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_z/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_z/conf -r /content/regressiontests-2024.2/complex/swap_z/conf -p /content/regressiontests-2024.2/complex/swap_z/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_z/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_z/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_z/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running swap_z using CPU-based PME\n", | |
| "Testing swap_z-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/swap_z/grompp.mdp -c /content/regressiontests-2024.2/complex/swap_z/conf -r /content/regressiontests-2024.2/complex/swap_z/conf -p /content/regressiontests-2024.2/complex/swap_z/topol -maxwarn 10 -n /content/regressiontests-2024.2/complex/swap_z/index >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/swap_z/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/swap_z/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing tip4p . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4p/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4p/conf -r /content/regressiontests-2024.2/complex/tip4p/conf -p /content/regressiontests-2024.2/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4p/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4p/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running tip4p using only CPU-based non-bonded kernels\n", | |
| "Testing tip4p-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4p/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4p/conf -r /content/regressiontests-2024.2/complex/tip4p/conf -p /content/regressiontests-2024.2/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4p/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4p/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running tip4p using CPU-based PME\n", | |
| "Testing tip4p-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4p/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4p/conf -r /content/regressiontests-2024.2/complex/tip4p/conf -p /content/regressiontests-2024.2/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4p/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4p/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing tip4p_continue . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4p_continue/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4p_continue/conf -r /content/regressiontests-2024.2/complex/tip4p_continue/conf -p /content/regressiontests-2024.2/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4p_continue/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -cpi /content/regressiontests-2024.2/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4p_continue/reference_s.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4p_continue/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing tip4pflex . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4pflex/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4pflex/conf -r /content/regressiontests-2024.2/complex/tip4pflex/conf -p /content/regressiontests-2024.2/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4pflex/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4pflex/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running tip4pflex using only CPU-based non-bonded kernels\n", | |
| "Testing tip4pflex-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4pflex/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4pflex/conf -r /content/regressiontests-2024.2/complex/tip4pflex/conf -p /content/regressiontests-2024.2/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4pflex/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4pflex/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running tip4pflex using CPU-based PME\n", | |
| "Testing tip4pflex-pme-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/tip4pflex/grompp.mdp -c /content/regressiontests-2024.2/complex/tip4pflex/conf -r /content/regressiontests-2024.2/complex/tip4pflex/conf -p /content/regressiontests-2024.2/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -pme cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/tip4pflex/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/tip4pflex/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing urea . . . gmx grompp -f /content/regressiontests-2024.2/complex/urea/grompp.mdp -c /content/regressiontests-2024.2/complex/urea/conf -r /content/regressiontests-2024.2/complex/urea/conf -p /content/regressiontests-2024.2/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/urea/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/urea/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running urea using only CPU-based non-bonded kernels\n", | |
| "Testing urea-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/urea/grompp.mdp -c /content/regressiontests-2024.2/complex/urea/conf -r /content/regressiontests-2024.2/complex/urea/conf -p /content/regressiontests-2024.2/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/urea/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/urea/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running urea using CPU-based update\n", | |
| "Testing urea-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/urea/grompp.mdp -c /content/regressiontests-2024.2/complex/urea/conf -r /content/regressiontests-2024.2/complex/urea/conf -p /content/regressiontests-2024.2/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/urea/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/urea/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing walls . . . gmx grompp -f /content/regressiontests-2024.2/complex/walls/grompp.mdp -c /content/regressiontests-2024.2/complex/walls/conf -r /content/regressiontests-2024.2/complex/walls/conf -p /content/regressiontests-2024.2/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/walls/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/walls/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running walls using only CPU-based non-bonded kernels\n", | |
| "Testing walls-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/walls/grompp.mdp -c /content/regressiontests-2024.2/complex/walls/conf -r /content/regressiontests-2024.2/complex/walls/conf -p /content/regressiontests-2024.2/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/walls/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/walls/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running walls using CPU-based update\n", | |
| "Testing walls-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/complex/walls/grompp.mdp -c /content/regressiontests-2024.2/complex/walls/conf -r /content/regressiontests-2024.2/complex/walls/conf -p /content/regressiontests-2024.2/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/complex/walls/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/complex/walls/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "All 127 complex tests PASSED\n", | |
| "Testing coulandvdwsequential_coul . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwsequential_coul using only CPU-based non-bonded kernels\n", | |
| "Testing coulandvdwsequential_coul-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwsequential_coul using CPU-based update\n", | |
| "Testing coulandvdwsequential_coul-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_coul/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing coulandvdwsequential_vdw . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwsequential_vdw using only CPU-based non-bonded kernels\n", | |
| "Testing coulandvdwsequential_vdw-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwsequential_vdw using CPU-based update\n", | |
| "Testing coulandvdwsequential_vdw-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwsequential_vdw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing coulandvdwtogether . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwtogether using only CPU-based non-bonded kernels\n", | |
| "Testing coulandvdwtogether-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running coulandvdwtogether using CPU-based update\n", | |
| "Testing coulandvdwtogether-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -r /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/conf -p /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/coulandvdwtogether/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing expanded . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/expanded/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/expanded/conf -r /content/regressiontests-2024.2/freeenergy/expanded/conf -p /content/regressiontests-2024.2/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/expanded/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/expanded/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running expanded using only CPU-based non-bonded kernels\n", | |
| "Testing expanded-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/expanded/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/expanded/conf -r /content/regressiontests-2024.2/freeenergy/expanded/conf -p /content/regressiontests-2024.2/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/expanded/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/expanded/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing relative . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/relative/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/relative/conf -r /content/regressiontests-2024.2/freeenergy/relative/conf -p /content/regressiontests-2024.2/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/relative/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/relative/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running relative using only CPU-based non-bonded kernels\n", | |
| "Testing relative-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/relative/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/relative/conf -r /content/regressiontests-2024.2/freeenergy/relative/conf -p /content/regressiontests-2024.2/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/relative/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/relative/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing relative-position-restraints . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/relative-position-restraints/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/relative-position-restraints/conf -r /content/regressiontests-2024.2/freeenergy/relative-position-restraints/conf -p /content/regressiontests-2024.2/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running relative-position-restraints using only CPU-based non-bonded kernels\n", | |
| "Testing relative-position-restraints-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/relative-position-restraints/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/relative-position-restraints/conf -r /content/regressiontests-2024.2/freeenergy/relative-position-restraints/conf -p /content/regressiontests-2024.2/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/relative-position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing restraints . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/restraints/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/restraints/conf -r /content/regressiontests-2024.2/freeenergy/restraints/conf -p /content/regressiontests-2024.2/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running restraints using only CPU-based non-bonded kernels\n", | |
| "Testing restraints-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/restraints/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/restraints/conf -r /content/regressiontests-2024.2/freeenergy/restraints/conf -p /content/regressiontests-2024.2/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing simtemp . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/simtemp/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/simtemp/conf -r /content/regressiontests-2024.2/freeenergy/simtemp/conf -p /content/regressiontests-2024.2/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running simtemp using only CPU-based non-bonded kernels\n", | |
| "Testing simtemp-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/simtemp/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/simtemp/conf -r /content/regressiontests-2024.2/freeenergy/simtemp/conf -p /content/regressiontests-2024.2/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/simtemp/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing transformAtoB . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/transformAtoB/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/transformAtoB/conf -r /content/regressiontests-2024.2/freeenergy/transformAtoB/conf -p /content/regressiontests-2024.2/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running transformAtoB using only CPU-based non-bonded kernels\n", | |
| "Testing transformAtoB-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/transformAtoB/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/transformAtoB/conf -r /content/regressiontests-2024.2/freeenergy/transformAtoB/conf -p /content/regressiontests-2024.2/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/transformAtoB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Testing vdwalone . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/vdwalone/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/vdwalone/conf -r /content/regressiontests-2024.2/freeenergy/vdwalone/conf -p /content/regressiontests-2024.2/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running vdwalone using only CPU-based non-bonded kernels\n", | |
| "Testing vdwalone-nb-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/vdwalone/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/vdwalone/conf -r /content/regressiontests-2024.2/freeenergy/vdwalone/conf -p /content/regressiontests-2024.2/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -notunepme -nb cpu >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "Re-running vdwalone using CPU-based update\n", | |
| "Testing vdwalone-update-cpu . . . gmx grompp -f /content/regressiontests-2024.2/freeenergy/vdwalone/grompp.mdp -c /content/regressiontests-2024.2/freeenergy/vdwalone/conf -r /content/regressiontests-2024.2/freeenergy/vdwalone/conf -p /content/regressiontests-2024.2/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err\n", | |
| "gmx check -s1 /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err\n", | |
| " gmx mdrun -update cpu -notunepme >mdrun.out 2>&1\n", | |
| "gmx check -e /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err\n", | |
| "gmx check -f /content/regressiontests-2024.2/freeenergy/vdwalone/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err\n", | |
| "PASSED but check mdp file differences\n", | |
| "All 24 freeenergy tests PASSED\n", | |
| "All 0 extra tests PASSED\n", | |
| "Testing linfix . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/linfix/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/linfix/conf -r /content/regressiontests-2024.2/essentialdynamics/linfix/conf -p /content/regressiontests-2024.2/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| "echo 0 | gmx make_edi -f /content/regressiontests-2024.2/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err\n", | |
| " gmx mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0.05\n", | |
| "Comparing column #2 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 1e-06\n", | |
| "Testing linacc . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/linacc/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/linacc/conf -r /content/regressiontests-2024.2/essentialdynamics/linacc/conf -p /content/regressiontests-2024.2/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| "echo 0 | gmx make_edi -f /content/regressiontests-2024.2/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err\n", | |
| " gmx mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.005\n", | |
| "Comparing column #2 of .xvg files /content/regressiontests-2024.2/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.001\n", | |
| "Checking monotonicity for column 2 of file linacc.xvg ... values of column 2 are increasing monotonically.\n", | |
| "Testing radfix . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/radfix/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/radfix/conf -r /content/regressiontests-2024.2/essentialdynamics/radfix/conf -p /content/regressiontests-2024.2/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| "echo 0 | gmx make_edi -f /content/regressiontests-2024.2/essentialdynamics/radfix/eigenvec.trr -outfrq 1 -radfix 1-2 -radstep 0.002 -o sam.edi 1>make_edi.out 2>make_edi.err\n", | |
| " gmx mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0.05\n", | |
| "Comparing column #4 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0\n", | |
| "Checking radius for file radfix.xvg ... all values within tolerance of 1e-05\n", | |
| "Testing radacc . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/radacc/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/radacc/conf -r /content/regressiontests-2024.2/essentialdynamics/radacc/conf -p /content/regressiontests-2024.2/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| "echo 0 | gmx make_edi -f /content/regressiontests-2024.2/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err\n", | |
| " gmx mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0.05\n", | |
| "Checking radius for file radacc.xvg ... all values within tolerance of 1e-05\n", | |
| "Checking monotonicity for column 4 of file radacc.xvg ... values of column 4 are increasing monotonically.\n", | |
| "Testing radcon . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/radcon/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/radcon/conf -r /content/regressiontests-2024.2/essentialdynamics/radcon/conf -p /content/regressiontests-2024.2/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| "echo 0 0 | gmx make_edi -f /content/regressiontests-2024.2/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /content/regressiontests-2024.2/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err\n", | |
| " gmx mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0.05\n", | |
| "Checking radius for file radcon.xvg ... all values within tolerance of 1e-05\n", | |
| "Checking monotonicity for column 4 of file radcon.xvg ... values of column 4 are decreasing monotonically.\n", | |
| "Testing flooding1 . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/flooding1/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/flooding1/conf -r /content/regressiontests-2024.2/essentialdynamics/flooding1/conf -p /content/regressiontests-2024.2/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| " gmx mdrun -ei /content/regressiontests-2024.2/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05\n", | |
| "Comparing column #2 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05\n", | |
| "Comparing column #3 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1\n", | |
| "Comparing column #4 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1\n", | |
| "Comparing column #5 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05\n", | |
| "Comparing column #6 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1\n", | |
| "Comparing column #7 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1\n", | |
| "Testing flooding2 . . .\n", | |
| "gmx grompp -f /content/regressiontests-2024.2/essentialdynamics/flooding2/grompp.mdp -c /content/regressiontests-2024.2/essentialdynamics/flooding2/conf -r /content/regressiontests-2024.2/essentialdynamics/flooding2/conf -p /content/regressiontests-2024.2/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err\n", | |
| " gmx mdrun -ei /content/regressiontests-2024.2/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1\n", | |
| "Comparing column #0 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0\n", | |
| "Comparing column #1 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.05\n", | |
| "Comparing column #2 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025\n", | |
| "Comparing column #3 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250\n", | |
| "Comparing column #4 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000\n", | |
| "Comparing column #5 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025\n", | |
| "Comparing column #6 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250\n", | |
| "Comparing column #7 of .xvg files /content/regressiontests-2024.2/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000\n", | |
| "All 7 essential dynamics tests PASSED\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "source": [], | |
| "metadata": { | |
| "id": "9Zr_CCRGIgRQ" | |
| }, | |
| "execution_count": null, | |
| "outputs": [] | |
| } | |
| ], | |
| "metadata": { | |
| "colab": { | |
| "toc_visible": true, | |
| "provenance": [], | |
| "gpuType": "T4", | |
| "include_colab_link": true | |
| }, | |
| "kernelspec": { | |
| "display_name": "Python 3", | |
| "name": "python3" | |
| }, | |
| "accelerator": "GPU" | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 0 | |
| } |
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