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We run custom WDL genomics pipelines and also parts of the BioWDL somaticcalling pipeline (https://biowdl.github.io/) using the broadinstitute/cromwell:64 cromwell container with a gridengine backend.…
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I am running this script:
``` python
with drmaa.Session() as s:
jt = s.createJobTemplate()
jt.remoteCommand = "python"
jt.args = ['env.py']
jt.jobEnvironment = {'ALEX':…
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Authorizing on gce with client_id and client_secret fails as the credentials object in
https://github.com/gc3-uzh-ch/elasticluster/blob/b69208a358315183d3f83e5032b4edb18d6ba5d5/elasticluster/provider…
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This script is intended to be used with GPUs but you have not compiled Kaldi with CUDA
If you want to use GPUs (and have them), go to src/, and configure and make on a machine
where "nvcc" is insta…
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Hi,
we need to implement continuous-integration-style MPI-submission tests, eventually;
such as http://centers.hpc.mil/MPI_TESTS/index.html
or @besserox's CDASH-based http://my.cdash.org/index.php?p…
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It seems that the handling of WMS failing to retrieve a job has changed quite a bit. As a result, the HTCondor backend may produce an unneeded traceback:
```
2016-08-22 18:04:01 - wms.condor:ERROR - …
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DrBox-v2-tensorflow >: cat nlp.o2215624
/opt/gridengine/default/spool/sge_execd/node413/job_scripts/2215624: line 1: ge:: command not found
Running on host: node413.
In directory: /home/d/dc593/Dr…
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From https://www.biostars.org/p/344955/
## Expected Behavior
Tell us what should happen
## Actual Behavior
```
openjdk-8.0.12 100% |###########################################################…
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I am unsure based on the documentation whether elasticluster can be set up to support multiple users scheduling jobs to the same set of nodes, clarification in the docs would be helpful, even if the a…
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Hi,
I am in need to reinstall cactus on a gridEngine system without docker. I've created a virtualenv with python 3.6, installed the lastest commit of toil, and cloned the latest version of cactus.
…