# git clone ...ecflow
# git checkout 5.8.4
ln -s /home/kinow/Development/python/workspace/ecflow/ /tmp/ecflow_build/ecFlow-5.8.4-Source
export WK=/tmp/ecflow_build/ecFlow-5.8.4-Source
export BOOST_ROOT=/tmp/ecflow_build/boost_1_71_0
cd $BOOST_ROOT
./bootstrap.sh --prefix=/home/kinow/Development/python/workspace/ecflow/boost
./b2 install
# boost_build.sh failed to locate /usr/bin/libcrypt.so ?
# A multi-stage image with Cypress and Java+Maven for Jena... ALv2... | |
# To build it: | |
# `docker build -t jena/build:latest .` | |
# | |
# To run it: | |
# `docker run --entrypoint "" --rm -ti jena/build:latest /bin/bash` | |
FROM 'maven:3.9.8-eclipse-temurin-21-jammy' AS maven | |
# The Maven stage. Nothing to see here, we simply copy artefacts |
# What I modified | |
EXPERIMENT: | |
DATELIST: '20000101 20000102' |
#!Jinja2 | |
{% if MEMBERS is not defined %} | |
{% set MEMBERS = 4 %} | |
{% endif %} | |
[scheduler] | |
UTC mode = true | |
allow implicit tasks = True | |
[scheduling] |
<?xml version="1.0" ?> | |
<coverage version="7.2.5" timestamp="1684529350876" lines-valid="23787" lines-covered="17741" line-rate="0.7458" branches-valid="10117" branches-covered="6379" branch-rate="0.6305" complexity="0"> | |
<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.2.5 --> | |
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd --> | |
<sources> | |
<source>/home/kinow/Development/python/workspace/cylc-flow/cylc</source> | |
</sources> | |
<packages> | |
<package name="flow" line-rate="0.7415" branch-rate="0.6293" complexity="0"> | |
<classes> |
--- | |
Apache Maven 3.8.5 (3599d3414f046de2324203b78ddcf9b5e4388aa0) | |
Maven home: /opt/apache-maven-3.8.5 | |
Java version: 17.0.6, vendor: Private Build, runtime: /usr/lib/jvm/java-17-openjdk-amd64 | |
Default locale: en_US, platform encoding: UTF-8 | |
OS name: "linux", version: "5.15.0-69-generic", arch: "amd64", family: "unix" | |
--- | |
[INFO] Scanning for projects... | |
[INFO] ------------------------------------------------------------------------ |
Managed to complete a run of an Autosubmit workflow today for the first time, running the commands that I wanted. Here's where I was erring, and what I did to fix it.
When you use the PS
platform type, you also need to enable an SSH server.
Autosubmit reads the SSH config
file to load the host configuration.
Install Autosubmit with pip install autosubmit==3.*
. Follow their tutorial to set up the workflow engine (basically
autosubmit configure
and autosubmit install
to create the directories, files, and databases).
Create an experiment with autosubmit expid --HPC local --description "autosubmit-fl..."
, and edit the files
expdef_a000.conf
and jobs_a000.conf
in the ~/autosubmit/a000/
directory. The important entries to add or
modify in expdef_a000.conf
are:
Here's the step by step that I used to have a running workflow.
- Synced
master
branch - Re-installed dependencies in venv,
pip install -U -e .
- Removed old files,
rm -rf ~/.autosubmit*
andrm -rf ~/autosubmit
- Configured and installed Autosubmit,
autosubmit configure
, followed byautosubmit install
- Created a new dummy experiment with
autosubmit expid -H local --dummy -d DummyExp
- Updated my experiment's platform file
version 1.0 | |
workflow blast { | |
input { | |
String? blast_docker_override | |
String blast_docker= select_first([blast_docker_override,"swr.cn-south-1.myhuaweicloud.com/cngbdb/blast:1.2"]) | |
File queryfa | |
String fname = '/sfs/blastdb/2019_ncov/nucl/v6/ncov' | |
String method = 'blastn' | |
Int outfmt = 7 |