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My understanding was that the main problem (i.e. the slow down) comes from the NFS usage (not related to singularity in the end).
Hi again, Does anyone know how to set temporary-directory per step in the cromwell-config file? Because as I would have expected from previous experience with picard ... when I run multiple subject on our server the /tmp dir got full by one of…
I found the issue that was actually in plain sight of my first post and not related to the use of singularity but to the temporary directory set by cromwell on an NFS system that apparently saturates (quote at 400MB/s in both directions), as oppose…
Using cromwell with singularity on my own desktop the process run at normal speed (i.e. 4 to 6s per million read). So, I will probably contact my IT to know if they can find the issue causing this slow down ..
Actually I noticed that this issue is probably exactly the same as wdl/discussion/23788/cromwell-slow-when-running-markduplicates which was unanswered However, I can add that running with slurm (our cluster) or not (our server) makes no differenc…
Hi, To answer my own question, As mentioned I followed the insights from discussion/11897/support-for-singularity and also how to configure cromwell that I had not seen before posting cromwell.readthedocs.io/en/stable/backends/SLURM/ The main…
Hi, Has a solution been found or posted somewhere to replace the use of docker by singularity in the wdl workflow? To give a bit more details: I saw this post in discussion/11897/support-for-singularity with someone posting a full configuration…