When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the following LSF error on Ubuntu:
caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name atac_seq_pipeline
2023-08-22 15:18:59,196|caper.hpc|INFO| Running shell command: bsub -W 2880 -M 4g -env all -J CAPER_atac_seq_pipeline /nfs/users/nfs_s/<userID>/lniu4in7.sh
MEMLIMIT value <4g> is not valid. Limit must be a positive integer. You can use the following units for the limit: KB (or K), MB (or M), GB (or G), TB (or T), PB (or P), EB (or E), ZB (or Z). Job not submitted.
OS/Platform
OS/Platform: Ubuntu 18.04.6 LTS
Conda version: conda 23.3.1
Pipeline version: newest pulled from github
Caper version: caper 2.3.2
Caper configuration file
Paste contents of ~/.caper/default.conf.
backend=lsf
# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=
cromwell=/nfs/users/nfs_s/<userID>/.caper/cromwell_jar/cromwell-82.jar
womtool=/nfs/users/nfs_s/<userID>/.caper/womtool_jar/womtool-82.jar
sbresnahan
commented
3 weeks ago
Invalid MEMLIMIT value with LSF on Linux
When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the following LSF error on Ubuntu:
OS/Platform
Caper configuration file
Paste contents of
~/.caper/default.conf.Input JSON file
Paste contents of your input JSON file.