cwltool 3.2.20260720092025 ran successfully on RIKEN Fugaku 🇯🇵🎉🥳
It ran the CWL v1.0 conformance tests successfully, and also ran a small MPI workflow compiling (mpifcc) and running (mpiexec) on PJM.
github.com/kinow/cwl-mp...
#RIKEN #Fugaku #hpc #cwltool #commonwl #sciworkflows #workflows #japan
It ran the CWL v1.0 conformance tests successfully, and also ran a small MPI workflow compiling (mpifcc) and running (mpiexec) on PJM.
github.com/kinow/cwl-mp...
#RIKEN #Fugaku #hpc #cwltool #commonwl #sciworkflows #workflows #japan
September 24, 2026 at 9:06 AM
cwltool 3.2.20260720092025 ran successfully on RIKEN Fugaku 🇯🇵🎉🥳
It ran the CWL v1.0 conformance tests successfully, and also ran a small MPI workflow compiling (mpifcc) and running (mpiexec) on PJM.
github.com/kinow/cwl-mp...
#RIKEN #Fugaku #hpc #cwltool #commonwl #sciworkflows #workflows #japan
It ran the CWL v1.0 conformance tests successfully, and also ran a small MPI workflow compiling (mpifcc) and running (mpiexec) on PJM.
github.com/kinow/cwl-mp...
#RIKEN #Fugaku #hpc #cwltool #commonwl #sciworkflows #workflows #japan
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
F1000Research Article: Sustainable data analysis with Snakemake.
Read the latest article version by Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vi...
f1000research.com
September 23, 2025 at 10:18 AM
Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-...
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
cwltool CWL v1.0 conformance tests passed on RIKEN Fugaku HPC login node! Unfortunately, it's failing when using PJM (due to login / compute nodes using different CPU architectures). An interesting workflow problem 🤓
github.com/kinow/cwl-mp...
#sciworkflows #cwl #commonwl #hpc #Fugaku #RIKEN
github.com/kinow/cwl-mp...
#sciworkflows #cwl #commonwl #hpc #Fugaku #RIKEN
cwl-mpi/cwl-conformance-tests/output/cwltool/fugaku at master · kinow/cwl-mpi
Repository for research artefacts produced in the thesis “CWL workflows with MPI in bare-metal, containers, cloud, and HPC” - kinow/cwl-mpi
github.com
September 20, 2026 at 8:12 PM
cwltool CWL v1.0 conformance tests passed on RIKEN Fugaku HPC login node! Unfortunately, it's failing when using PJM (due to login / compute nodes using different CPU architectures). An interesting workflow problem 🤓
github.com/kinow/cwl-mp...
#sciworkflows #cwl #commonwl #hpc #Fugaku #RIKEN
github.com/kinow/cwl-mp...
#sciworkflows #cwl #commonwl #hpc #Fugaku #RIKEN
#Snakemake has recently reached 1 million downloads on #Bioconda! snakemake.github.io
#sciworkflows #reproducibility
#sciworkflows #reproducibility
April 3, 2024 at 7:02 AM
#Snakemake has recently reached 1 million downloads on #Bioconda! snakemake.github.io
#sciworkflows #reproducibility
#sciworkflows #reproducibility
#Snakemake 8.25.4 has been released with lots of little bug fixes: snakemake.readthedocs.io/en/stable/pr... #sciworkflows #reproducibility
Changelog | Snakemake 8.25.4 documentation
snakemake.readthedocs.io
November 28, 2024 at 8:22 AM
#Snakemake 8.25.4 has been released with lots of little bug fixes: snakemake.readthedocs.io/en/stable/pr... #sciworkflows #reproducibility
Visualizing an RO-Crate archive with Describo and NovaCrate #OpenSource #Provenance #Metadata #rocrate #graph #UI #dataviz #workflows #sciworkflows
July 24, 2025 at 3:43 PM
Visualizing an RO-Crate archive with Describo and NovaCrate #OpenSource #Provenance #Metadata #rocrate #graph #UI #dataviz #workflows #sciworkflows
New paper out in Nature Scientific Data: “Applying the FAIR Principles to computational workflows”, Wilkinson, S.R., Aloqalaa, M., Belhajjame, K. et al., 2025 (open access): www.nature.com/articles/s41... #workflows #sciworkflows #fair #fairness #rocrate #reproducibility #fdo #provenance
Applying the FAIR Principles to computational workflows - Scientific Data
Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access t...
www.nature.com
February 27, 2025 at 9:05 PM
New paper out in Nature Scientific Data: “Applying the FAIR Principles to computational workflows”, Wilkinson, S.R., Aloqalaa, M., Belhajjame, K. et al., 2025 (open access): www.nature.com/articles/s41... #workflows #sciworkflows #fair #fairness #rocrate #reproducibility #fdo #provenance
Fixed an annoying “operator does not exist: jsonb = bytea” Hibernate/SpringBoot bug in CWLViewer before it turned 6 months! 😅 Now pending a test and confirmation that it's working by OP of the issue github.com/common-workf... #OpenSource #Java #SpringBoot #CWL #SciWorkflows #hibernate #postgresql
March 31, 2025 at 8:16 AM
Fixed an annoying “operator does not exist: jsonb = bytea” Hibernate/SpringBoot bug in CWLViewer before it turned 6 months! 😅 Now pending a test and confirmation that it's working by OP of the issue github.com/common-workf... #OpenSource #Java #SpringBoot #CWL #SciWorkflows #hibernate #postgresql
#snakemake 8.14 has been released. It supports setting the shell to use per rule if needed (e.g. if your analysis step runs in a container that does not have bash shell).
#sciworkflows #reproducibility
snakemake.github.io
#sciworkflows #reproducibility
snakemake.github.io
Snakemake
snakemake.github.io
June 11, 2024 at 11:07 AM
#snakemake 8.14 has been released. It supports setting the shell to use per rule if needed (e.g. if your analysis step runs in a container that does not have bash shell).
#sciworkflows #reproducibility
snakemake.github.io
#sciworkflows #reproducibility
snakemake.github.io
Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...
#sciworkflows #reproducibility
#sciworkflows #reproducibility
Snakemake Hackathon March 2026
We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...
indico.cern.ch
October 17, 2025 at 4:49 PM
Want to help shaping the future of #Snakemake? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here: indico.cern.ch/e/snakemake-...
#sciworkflows #reproducibility
#sciworkflows #reproducibility
Finished preparing the pull request to add support to MPI and Singularity in cwltool. Already tested on BSC MareNostrum5 🎉! github.com/common-workf... #cwl #mpi #opensource #sciworkflows #workflows
Detect MPI with Singularity by kinow · Pull Request #2216 · common-workflow-language/cwltool
Related to #2208 (not sure if this is enough to close that issue)
@mr-c, I started some tests yesterday, and completed them today after work. Once I managed to run the workflow on my machine reprod...
github.com
April 28, 2026 at 10:10 PM
Finished preparing the pull request to add support to MPI and Singularity in cwltool. Already tested on BSC MareNostrum5 🎉! github.com/common-workf... #cwl #mpi #opensource #sciworkflows #workflows
Executed my first Cylc Flow 8 workflow on BSC MareNostrum5 🚀🧑🚀 It works if you enable the polling mode & intervals 😀 cylc.github.io/cylc-doc/sta... #OpenSource #Workflows #SciWorkflows #Cylc #BSC #MareNostrum5 #HPC #Slurm #EuroHPC
May 9, 2025 at 8:48 PM
Executed my first Cylc Flow 8 workflow on BSC MareNostrum5 🚀🧑🚀 It works if you enable the polling mode & intervals 😀 cylc.github.io/cylc-doc/sta... #OpenSource #Workflows #SciWorkflows #Cylc #BSC #MareNostrum5 #HPC #Slurm #EuroHPC
Better workflow graph (more compact for long commands and paths by auto-folding), coming up in the next release of #scicommander ... #sciworkflows
February 27, 2026 at 11:56 AM
Better workflow graph (more compact for long commands and paths by auto-folding), coming up in the next release of #scicommander ... #sciworkflows
The Destination Earth Climate Digital Twin workflow is now open source! It's available from Destination Earth's GitHub org, soon with RO-Crate and uploaded to WorkflowHub.
github.com/DestinE-Clim... & github.com/DestinE-Clim...
#OpenSource #workflow #SciWorkflows #HPC
github.com/DestinE-Clim... & github.com/DestinE-Clim...
#OpenSource #workflow #SciWorkflows #HPC
GitHub - DestinE-Climate-DT/Workflow: Development of the workflow in charge of evolving the ModelSV and periodically extracting the OutputSV, to produce the GSV, already projected to the observation space. This workflow, together with the one developed in DE_34080 (WP8) for the consumption of the GSV by the applications, will constitute the greater climate DT workflow.
Development of the workflow in charge of evolving the ModelSV and periodically extracting the OutputSV, to produce the GSV, already projected to the observation space. This workflow, together with ...
github.com
June 6, 2025 at 3:14 PM
The Destination Earth Climate Digital Twin workflow is now open source! It's available from Destination Earth's GitHub org, soon with RO-Crate and uploaded to WorkflowHub.
github.com/DestinE-Clim... & github.com/DestinE-Clim...
#OpenSource #workflow #SciWorkflows #HPC
github.com/DestinE-Clim... & github.com/DestinE-Clim...
#OpenSource #workflow #SciWorkflows #HPC
CWLViewer PR to updated SpringBoot from 3->4 done, ready for review. Now time to go back to writing about CWL and MPI 🤓 github.com/common-workf... #cwl #sciworkflows #opensource
Bump org.springframework.boot:spring-boot-starter-parent from 3.1.4 to 4.1.0-RC1 by dependabot[bot] · Pull Request #751 · common-workflow-language/cwlviewer
Bumps org.springframework.boot:spring-boot-starter-parent from 3.1.4 to 4.0.0.
Release notes
Sourced from org.springframework.boot:spring-boot-starter-parent's releases.
v4.0.0
⭐ New Features...
github.com
May 13, 2026 at 11:12 PM
CWLViewer PR to updated SpringBoot from 3->4 done, ready for review. Now time to go back to writing about CWL and MPI 🤓 github.com/common-workf... #cwl #sciworkflows #opensource
Soon workflows written with CWL that use Singularity should be able to run with Toil in the offline nodes of BSC MareNostrum 5 🎉 Thanks to the maintainer of Toil Adam Novak github.com/DataBiospher... #opensource #cwl #sciworkflows
Error running toil-cwl-runner in BSC MareNostrum 5 compute nodes (offline) · Issue #5529 · DataBiosphere/toil
Hi, I chose one of the CWL Conformance tests that used CWL v1.0 and failed with Toil 9.4.1 on BSC MareNostrum 5. From the list at https://github.com/kinow/cwl-mpi/blob/master/cwl-conformance-tests/...
github.com
June 4, 2026 at 6:40 PM
Soon workflows written with CWL that use Singularity should be able to run with Toil in the offline nodes of BSC MareNostrum 5 🎉 Thanks to the maintainer of Toil Adam Novak github.com/DataBiospher... #opensource #cwl #sciworkflows
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
November 13, 2025 at 8:45 PM
I might be biased (as they mention scipipe.org), but a recommended related paper:
www.nature.com/articles/s41... #sciworkflows
www.nature.com/articles/s41... #sciworkflows
I am now a codechecker 🎉🤓⚗️🤖 Will talk within my group to recruit others and verify a few HPC & workflows & earth sciences & climate papers #FAIR #reproducibility #sciworkflows
github.com/codecheckers...
github.com/codecheckers...
Register as codechecker · Issue #81 · codecheckers/codecheckers
Your data: Bruno P. Kinoshita,@kinow,0000-0001-8250-4074,kinow@apache.org,"Workflows, Software Engineering, HPC, Earth Sciences, CWL, Cylc, ecFlow, Autosubmit","Java, Python, PHP, Shell, Prolog, Ja...
github.com
August 15, 2026 at 10:03 AM
I am now a codechecker 🎉🤓⚗️🤖 Will talk within my group to recruit others and verify a few HPC & workflows & earth sciences & climate papers #FAIR #reproducibility #sciworkflows
github.com/codecheckers...
github.com/codecheckers...
New blog post “Running Cylc workflows on BSC MareNostrum5” kinoshita.eti.br/2025/05/25/r... #cylc #sciworkflows #workflows #graph #hpc #autosubmit #ecflow #networking
Running Cylc workflows on BSC MareNostrum5
TL;DR: Using the communication method = poll of Cylc 8 you can easily run Cylc 8 workflows on BSC MareNostrum5 HPC.
A couple of years ago I gave a talk about “HPC workflows for climate models” at an E...
kinoshita.eti.br
May 25, 2025 at 2:29 PM
New blog post “Running Cylc workflows on BSC MareNostrum5” kinoshita.eti.br/2025/05/25/r... #cylc #sciworkflows #workflows #graph #hpc #autosubmit #ecflow #networking
Testing today how cwltool and toil-cwl-runner behave with --preserve-environment, checking MPI environment variables for CWL workflows runs on BSC MareNostrum 5
github.com/DataBiospher...
#python #sciworkflows #toil #cwl #cwltool #hpc
github.com/DataBiospher...
#python #sciworkflows #toil #cwl #cwltool #hpc
Allow loading HPC module system modules for Toil CWL jobs, possibly by preamble script · Issue #1938 · DataBiosphere/toil
Dear All, I want to use toil/CWL to implement a pipeline to run on our SLURM cluster. It turned out that for proper working some modules should be loaded before toil.worker is called. Jobs are subm...
github.com
September 6, 2026 at 10:21 AM
Testing today how cwltool and toil-cwl-runner behave with --preserve-environment, checking MPI environment variables for CWL workflows runs on BSC MareNostrum 5
github.com/DataBiospher...
#python #sciworkflows #toil #cwl #cwltool #hpc
github.com/DataBiospher...
#python #sciworkflows #toil #cwl #cwltool #hpc
Postgres support coming to Autosubmit soon 🚀 code & unit tests finished, we are now starting the manual testing & final adjustments to test it on EDITO Model Lab 🤓 github.com/BSC-ES/autos... #autosubmit #SciWorkflows #workflows #postgres #sqlalchemy #python #OpenSource #BSC #EDITO
Add Postgres support to Autosubmit by LuiggiTenorioK · Pull Request #2187 · BSC-ES/autosubmit
Closes #1285
Supersedes #1914
PR to enable Postgres support in Autosubmit
Tasks
Enable CI job to test using a Postgres instance
Migrate db_structure
Check if there are any columns or tables mis...
github.com
May 21, 2025 at 3:04 PM
Postgres support coming to Autosubmit soon 🚀 code & unit tests finished, we are now starting the manual testing & final adjustments to test it on EDITO Model Lab 🤓 github.com/BSC-ES/autos... #autosubmit #SciWorkflows #workflows #postgres #sqlalchemy #python #OpenSource #BSC #EDITO
There's still time for more CWL + MPI tests on HPCs. This time CESGA FinisTerrae III. First, fixing an annoying issue where CWLTest silently fails when the YAML file given does not exist 😅 github.com/common-workf... #cwl #sciworkflows #CESGA #FT3 #hpc
Print an error if the test file is invalid by kinow · Pull Request #336 · common-workflow-language/cwltest
A user running conformance tests may accidentally point to the wrong file in --test. Right now, cwltest quietly exits with 1.
After this PR:
(venv) kinow@ranma:~/Development/python/workspace/common...
github.com
September 6, 2026 at 2:35 PM
There's still time for more CWL + MPI tests on HPCs. This time CESGA FinisTerrae III. First, fixing an annoying issue where CWLTest silently fails when the YAML file given does not exist 😅 github.com/common-workf... #cwl #sciworkflows #CESGA #FT3 #hpc
Finished the pull request, it's being reviewed now. Since the new code was better organised, managed to easily add Bash autocomplete (via ) and helpful messages "Did you mean 'run'" for users that mistyped commands like "rum". #python #autosubmit #Sciworkflows
August 26, 2026 at 1:35 PM
Finished the pull request, it's being reviewed now. Since the new code was better organised, managed to easily add Bash autocomplete (via ) and helpful messages "Did you mean 'run'" for users that mistyped commands like "rum". #python #autosubmit #Sciworkflows
New CLI help and argument parsing in Autosubmit 🎉🚀 Showing the before & after here (not in this order) #Python #SciWorkflows #Autosubmit #workflows
August 21, 2026 at 6:44 AM
New CLI help and argument parsing in Autosubmit 🎉🚀 Showing the before & after here (not in this order) #Python #SciWorkflows #Autosubmit #workflows
We are looking for a Workflows Engineer for AI processes (RE2) to join my team at the Barcelona Supercomputing Center (BSC), in Barcelona, Catalonia, Spain www.bsc.es/join-us/job-... #sciworkflows #jobs #spain #catalonia #python #autosubmit #hpc
Workflows Engineer for AI processes (RE2)
Reference: 382_26_ES_EMW_RE2 Job title: Workflows Engineer for AI processes (RE2) About BSC The Barcelona Supercomputing Center - Centro Nacional de Supercomputación
www.bsc.es
August 17, 2026 at 7:13 AM
We are looking for a Workflows Engineer for AI processes (RE2) to join my team at the Barcelona Supercomputing Center (BSC), in Barcelona, Catalonia, Spain www.bsc.es/join-us/job-... #sciworkflows #jobs #spain #catalonia #python #autosubmit #hpc