kinow

<?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">

kinow

---
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...

kinow

# 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 ?

kinow

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.

Ubuntu sshd configurations

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.

kinow

Autosubmit

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:

kinow

Here's the step by step that I used to have a running workflow.

1. Synced master branch
2. Re-installed dependencies in venv, pip install -U -e .
3. Removed old files, rm -rf ~/.autosubmit* and rm -rf ~/autosubmit
4. Configured and installed Autosubmit, autosubmit configure, followed by autosubmit install
5. Created a new dummy experiment with autosubmit expid -H local --dummy -d DummyExp
6. Updated my experiment's platform file

kinow

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

kinow

def hello():
  print("hello")


__version__ = '0.1'

kinow

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow

label: "Hello World"
doc: "Outputs a message using echo"

inputs: []

outputs:

kinow

package org.apache.commons.geometry.examples.tutorials;

import java.util.Map;

import org.apache.commons.geometry.core.collection.PointMap;
import org.apache.commons.geometry.core.internal.PointMapAsSetAdapter;
import org.apache.commons.geometry.euclidean.EuclideanCollections;
import org.apache.commons.geometry.euclidean.oned.Vector1D;
import org.apache.commons.numbers.core.Precision;