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apptainer / singularity

Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.
https://github.com/apptainer/apptainer
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FATAL: while opening capability config file: open /opt/go/src/github.com/sylabs/singularity/builddir/etc/singularity/capability.json: no such file or directory #5432

Closed akshayMpatel closed 4 years ago

akshayMpatel commented 4 years ago

Version of Singularity:

3.5.3

What OS/distro are you running

centos7

How did you install Singularity

rpm

Expected behavior

to run normally

Actual behavior

error message:

FATAL: while opening capability config file: open /opt/go/src/github.com/sylabs/singularity/builddir/etc/singularity/capability.json: no such file or directory

Steps to reproduce this behavior

as non-root with a root-installed singularity:

built container remotely with : singularity build --remote centos7_cat12-standalone.simg centos7_cat12-standalone.def can run it without any user related flags on local machine as my_user@machine1 with :

singularity run \
--cleanenv \
--bind ~/singularity/cat12 \
centos7_cat12-standalone.simg \
-b ~/singularity/cat12/batch_file.txt \
~/singularity/cat12/data/file.nii

then tried to run container within the qlogin interactive environment on our HPC as my_user@machine2 with same command

dtrudg commented 4 years ago

Please could you provide the exact detail of how this rpm packages was built? Is it self-built or is it installed from EPEL? rpm -qa | grep singularity

The path /opt/go/src/github.com/sylabs/singularity/builddir/etc/singularity/capability.json suggests that a prefix was not set correctly for the install location - where is singularity actually installed, i.e. output of which singularity

akshayMpatel commented 4 years ago

yes indeed the problem was that the machine used for qlogin pointed to the old install of singularity not installed with rpm. so we fixed that. sorry for the confusion.