probléme singularity : montage du $pwd pas automatique sous migale
Le $PWD ne se monte pas automatiquement; ça semble lié au lien symb de work
et save
(base) mba@migale:/work_home/mba/formation-alvisnlp/exercices/1-projection$ singularity run alvisnlp.sif project-on-txt.plan
Container was created
Arguments received: project-on-txt.plan
[2021-07-22 14:19:27.208][alvisnlp] build version: 0.8.1
[2021-07-22 14:19:27.213][alvisnlp] tag: 0.8.1 +0
[2021-07-22 14:19:27.213][alvisnlp] commit id: 32762cc4660bcac61c08fc12565581795aff872f
[2021-07-22 14:19:27.218][alvisnlp] commit time: Thu Aug 06 14:12:27 UTC 2020
[2021-07-22 14:19:27.219][alvisnlp] branch: 32762cc4660bcac61c08fc12565581795aff872f
[2021-07-22 14:19:27.219][alvisnlp] build host: jj-1404-129
[2021-07-22 14:19:27.219][alvisnlp] build time: Thu Aug 06 14:31:02 UTC 2020
[2021-07-22 14:19:27.223][alvisnlp] host: migale
[2021-07-22 14:19:27.224][alvisnlp] java home: /usr/local/public/jdk-11.0.9
[2021-07-22 14:19:27.224][alvisnlp] user: mba
[2021-07-22 14:19:27.224][alvisnlp] class path: /alvisnlp/lib/*:
[2021-07-22 14:19:27.224][alvisnlp] java version: 1.8.0_252
[Fatal Error] :-1:-1: Premature end of file.
[2021-07-22 14:19:27.275][alvisnlp] SEVERE XML error at null:-1: Premature end of file.
[2021-07-22 14:19:27.275][alvisnlp] use -verbose option to get debug info
(base) mba@migale:/work_home/mba/formation-alvisnlp/exercices/1-projection$ singularity run -B $PWD alvisnlp.sif project-on-txt.plan
Container was created
Arguments received: project-on-txt.plan
[2021-07-22 14:20:49.370][alvisnlp] build version: 0.8.1
[2021-07-22 14:20:49.375][alvisnlp] tag: 0.8.1 +0
[2021-07-22 14:20:49.375][alvisnlp] commit id: 32762cc4660bcac61c08fc12565581795aff872f
[2021-07-22 14:20:49.381][alvisnlp] commit time: Thu Aug 06 14:12:27 UTC 2020
[2021-07-22 14:20:49.381][alvisnlp] branch: 32762cc4660bcac61c08fc12565581795aff872f
[2021-07-22 14:20:49.381][alvisnlp] build host: jj-1404-129
[2021-07-22 14:20:49.381][alvisnlp] build time: Thu Aug 06 14:31:02 UTC 2020
[2021-07-22 14:20:49.385][alvisnlp] host: migale
[2021-07-22 14:20:49.385][alvisnlp] java home: /usr/local/public/jdk-11.0.9
[2021-07-22 14:20:49.386][alvisnlp] user: mba
[2021-07-22 14:20:49.386][alvisnlp] class path: /alvisnlp/lib/*:
[2021-07-22 14:20:49.386][alvisnlp] java version: 1.8.0_252
[2021-07-22 14:20:49.440][alvisnlp] loading plan from project-on-txt.plan
[2021-07-22 14:20:49.489][alvisnlp] finished loading project-on-txt.plan
[2021-07-22 14:20:49.492][project-on-txt.read] SEVERE /work_home/mba/formation-alvisnlp/exercices/1-projection/../share/BioNLP-ST-2013_Gene_Regulation_Network_train does not exist
[2021-07-22 14:20:49.492][project-on-txt.project] SEVERE /work_home/mba/formation-alvisnlp/exercices/1-projection/../share/subtiwiki-genes_2020-01-27.txt does not exist
[2021-07-22 14:20:49.493][alvisnlp] SEVERE error in plan: some parameter values do not satisfy constraints
[2021-07-22 14:20:49.493][alvisnlp] use -verbose option to get debug info