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@marcc-hpc
marcc-hpc / Makefile
Created January 31, 2018 03:36
Building FastQTL on MARCC - Makefile
#PLEASE SPECIFY THE R path here where you built the R math library standalone
RMATH=/cm/shared/apps/R/3.4.3/gcc/5.4/lib
#compiler
CXX=g++ -std=c++11
#internal paths
VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
PATH_TABX=lib/Tabix
PATH_EIGN=lib/Eigen
@marcc-hpc
marcc-hpc / pyrosetta_job.sh
Last active April 26, 2018 22:43
Singularity PyRosetta Script
#!/bin/bash
#SBATCH -p shared
#SBATCH --reservation=t-jgray21
#SBATCH -t 4:0:0
#SBATCH -N 1
#SBATCH -n 20
#SBATCH -J pyrosetta_job
# important presets for pyrosetta
export AMINO_SURFACE_CALL="--job_title HAp_FEP --surface_type HAp_010 --aa_type A --batches 500 --batch_size 100"
@marcc-hpc
marcc-hpc / singularity_pyrosetta
Last active August 12, 2023 18:56
PyRosetta Singularity File with Anaconda and OpenMPI
Bootstrap: docker
From: centos:centos7
%environment
PATH="/opt/software/bin:$PATH"
export PATH
LD_LIBRARY_PATH="/opt/software/lib/openmpi:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
%files
@marcc-hpc
marcc-hpc / install_run_sircel.sh
Last active May 6, 2018 08:54
Installing Sircel on MARCC
#!/bin/bash
# this module is specific to MARCC
module load anaconda-python/3.6
# create anaconda environment and use it
conda create -y -n sircel python
source activate sircel
# install kallisto, redis
@marcc-hpc
marcc-hpc / .vimrc
Created May 1, 2018 15:46
YAML vimrc
set autoindent
set tabstop=2
set shiftwidth=2
autocmd FileType yaml setlocal ai ts=2 sw=2 et
autocmd FileType yml setlocal ai ts=2 sw=2 et
#include <iostream>
#include <fstream>
using namespace std;
// dgeev_ is a symbol in the LAPACK library files
extern "C" {
extern int dgeev_(char*,char*,int*,double*,int*,double*, double*, double*, int*, double*, int*, double*, int*, int*);
}
@marcc-hpc
marcc-hpc / test_lapack_matrix.txt
Created July 13, 2018 17:26
Matching test matrix for test_lapack.cpp
3 3
-1.0 -8.0 0.0
-1.0 1.0 -5.0
3.0 0.0 2.0
@marcc-hpc
marcc-hpc / example_lapack.py
Created August 7, 2018 14:03
An example of generating a random matrix solver on MARCC
"""
Running LAPACK with Anaconda Python
Copyright 2016 Ohio Supercomputer Center (OSC)
Copyright 2017 Maryland Advanced Research Computing Center (MARCC)
Attributions:
This example was inspired by
"Numerical Computing with Modern Fortran" (SIAM, 2013) by Hanson & Hopkins
"""
@marcc-hpc
marcc-hpc / example_lapack.job
Created August 7, 2018 14:05
Matching job script for example_lapack.py
#!/bin/bash -l
#SBATCH --job-name=test_with_gnu_parallel
#SBATCH --partition=parallel
#SBATCH --time=1:0:0
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cores=6
# in this example we are using multithreading via MKL threads
# if you have single core tasks set ntasks=24