No Output when using snakemake on slurm #2
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Hi @linkmonica,
If (1) is true but (2) is not, my guess is the failure is happening in DRMAA. (This is consistent with the core dump file.) To use Snakemake on the SLURM cluster at my institution, I had to use a non-standard library for the SLURM-DRMAA interface (https://anaconda.org/jluquette/natefoo-slurm-drmaa). I believe this should be installed by default with SCAN-SNV, although I have no idea if it is portable. Could you try running without using |
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Hi @jluquette Traceback (most recent call last): I am also trying to install SLURM-DRMAA interface (https://anaconda.org/jluquette/natefoo-slurm-drmaa) but no luck! |
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Ok, thanks for the bug report. I just updated the script to fix that error. Could you clone the newest version of the private branch to see if it works for you? Re: SLURM-DRMAA: I think this should be installed by default. Can you post the output of |
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Output shows python-drmaa installed but not slurm-drmaa and I tried installing it from SLURM-DRMAA interface (https://anaconda.org/jluquette/natefoo-slurm-drmaa) but no luck! conda list -n scansnv |
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Hi @linkmonica, It looks like you do have the correct library installed. From your output: What issue are you running into now? Are you still getting the |
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Hi,
I am still getting core dump!
On Wed, 20 Nov 2019 at 21:15, jluquette ***@***.***> wrote:
Hi @linkmonica <https://github.com/linkmonica>,
It looks like you do have the correct library installed. From your output:
natefoo-slurm-drmaa 1.2.0_dev_deca826 0 jluquette
What issue are you running into now? Are you still getting the str
instance, int found error after downloading the newest commit? Are you
now getting a core dump?
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Monica Valecha, PhD Student
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University of Vigo
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@linkmonica sorry for the late reply. In my experience, DRMAA segfaults have only happened in relationship to specifying a -o parameter in the --drmaa string. This is a shot in the dark, but could you try just adding something like -o %logdir/slurm-%A.log to your --drmaa string? E.g., change
to
Be sure to test this WITHOUT loading your system wide slurm-drmaa (i.e., do not run module load slurm-drmaa/1.2.0-dev.deca826). |
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Hi,
I am trying to run scan-snv for whole chromosome in slurm cluster, I don't get any error or output. The config.yaml seems to be correct and coreXXX binary file is generated, and I don't see any error in ./output_dir/.snakemake./log.
Can you please let me know what can be wrong that no output is generated, demo works fine but as soon as I want to do run it in parallel.
Command:
Thanks in advance!
Monica.
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