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brainvisa / casa-distro

Unified development environment for BrainVISA projects.
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At the installation bug at the first command "singularity run -B bla bla.." #310

Closed clarafischer closed 1 year ago

clarafischer commented 1 year ago

When we follow the tuto to install a new casa, the first command singularity does not work on a laptop (install CEA and no CEA, Julie had the same problem). The command return : /usr/local/bin/entrypoint: 34: .: cannot open /usr/local/fsl/etc/fslconf/fsl.sh: No such file But /usr/local/fsl/etc/fslconf/fsl.sh exist and I can open it.

I can make it work by putting sudo before but after bv_maker won't work, it return : PermissionError: [Errno 13] Permission denied: '/casa/host/src/bv_maker.cfg' I suppose because of the sudo all my directories where root so I change for me to be the owner of the directories and it worked.

I try with the image casa-dev-5.3.8.sif and my version of singularity is 3.9.5-bionic. I had already a casa with an image casa-dev-5.0.11.sif and I had no problem during the installation.

Any ideas why it is not working any more ? Thanks !

denisri commented 1 year ago

Hi, You mean when installing a new environment using singularity run -B <env_directory>:/casa/setup casa-dev-5.3.8.sif ... ? I don't have this error, and I don't know where this reference to FSL is. Maybe there is a home directory and home config (.bashrc/.bash_profile/.profile). That's probably the clue: by default singularity shares the user and his/her home directory, thus the entrypoint script sources the user host .profile. Later, bv / casa_distro uses a different home dir to avoid this kind of problem, but during setup it's the "raw" singularity which is used. Here /usr/local/fsl is probably used in your host ~/.profile, and this directory exists on the host system, but obviously not in the casa-distro image. Maybe try adding -H /tmp (or another empty directory) to the singularity command, to use a different home directory ?

sapetnioc commented 1 year ago

Instead of using -H /tmp it could be possible to use -c (or --contain) that prevent singularity to mount directory by default.

clarafischer commented 1 year ago

Hello, sorry for the delay. Yes Denis it was when I do singularity run -B <env_directory>:/casa/setup casa-dev-5.3.8.sif .... And yes you are right I have install FSL on may laptop so I have /usr/local/fslin my ~/.profile. I try Yann's solution -c and it works well ! Thanks a lot, may be it should be mention on the tuto because I don't think I am the only one to have stuff in the ~/.profile.

denisri commented 1 year ago

I have added the option in docs and in the website (https://brainvisa.info/web/download.html).