These are chat archives for nextflow-io/nextflow

22nd
Jul 2017
Anthony Underwood
@aunderwo
Jul 22 2017 05:33
@fmorency I'm getting this error which suggests that it's not mounting home :(
Command error:
  WARNING: Ignoring user bind request: host does not support PR_SET_NO_NEW_PRIVS
  /bin/bash: line 0: cd: /phengs/hpc_storage/home/anthony/software/workflow_execution/work/49/006fab04a6d0104b74f195b23b945d: No such file or directory
  /bin/bash: .command.sh: No such file or directory
Anthony Underwood
@aunderwo
Jul 22 2017 05:55

@pditommaso I think you also experienced similar issues (see https://github.com/singularityware/singularity/issues/256#issuecomment-256909121)

If I set user bind control = no in the singularity config I now get

Command error:
  WARNING: Ignoring user bind request: user bind control is disabled by system administrator
  /bin/bash: line 0: cd: /phengs/hpc_storage/home/anthony/software/workflow_execution/work/d7/7b1cad7ecea15ba51c2e860a45f61d: No such file or directory
  /bin/bash: .command.sh: No such file or directory
However invoking singularity on the shell works fine
singularity shell -w singularity/phenix-2017-05-15-862ad3f0cdad.img
Paolo Di Tommaso
@pditommaso
Jul 22 2017 08:12
@aunderwo the critical message here is WARNING: Ignoring user bind request: host does not support PR_SET_NO_NEW_PRIVS
I think w/o that feature singularity is not able to mount the host path
I would suggest to ask in the singularity forum https://groups.google.com/a/lbl.gov/forum/#!forum/singularity
Anthony Underwood
@aunderwo
Jul 22 2017 08:14
@pditommaso Thanks. Strange that when I access singularity through shell it mounts my home dir. I'll post on forum as you suggest
Paolo Di Tommaso
@pditommaso
Jul 22 2017 08:15
yes, weird
are you using the latest version ?
Anthony Underwood
@aunderwo
Jul 22 2017 08:15
yes - dev branch from git
oooh there's a singularity slack group https://singularity-container.slack.com/
Paolo Di Tommaso
@pditommaso
Jul 22 2017 08:17
yes, you need to request access in the google group :)