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From: Paul M. <pau...@gm...> - 2021-10-19 15:21:50
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This actually sounds like a bug with singularity - as your singularity session should be isolated from your normal environment. This is like your shell variables affecting the environment in a virtual Linux machine. It seems to be a goal of singularity, that the process under it run under a completely isolated and consistent environment, see: https://singularity.hpcng.org/ On 10/19/2021 9:35 AM, Götz Waschk wrote: > Hi everyone, > > I have noticed a problem with environment-modules since upgrading to CentOS8. The startup file /usr/share/Modules/init/zsh modifies the variable $FPATH that defines the function search path used by zsh. If the variable is modified from its default, it is inherited by singularity when running a container, breaking functionality if this container has a different version of zsh. > > Here's an example of this behaviour: > > [wgs03] ~ % echo $FPATH > /usr/share/Modules/init/zsh-functions:/usr/local/share/zsh/site-functions:/usr/share/zsh/site-functions:/usr/share/zsh/5.5.1/functions > [wgs03] ~ % singularity run /project/singularity/images/SL6.img > ************************************************************************ > * You are now running a shell in a Singularity container providing a * > * Scientific Linux 6 environment. Most things should just work as if * > * you had just logged in to such a system, but there are differences. * > ************************************************************************ > /etc/site/zshrc:72: compinit: function definition file not found > [wgs03:SL6] ~ % echo $FPATH > /usr/share/Modules/init/zsh-functions:/usr/local/share/zsh/site-functions:/usr/share/zsh/site-functions:/usr/share/zsh/5.5.1/functions > > If I remove environment-modules from the system, this problem doesn't occur: > > [wgs03] ~ % echo $FPATH > /usr/local/share/zsh/site-functions:/usr/share/zsh/site-functions:/usr/share/zsh/5.5.1/functions > [wgs03] ~ % singularity run /project/singularity/images/SL6.img > ************************************************************************ > * You are now running a shell in a Singularity container providing a * > * Scientific Linux 6 environment. Most things should just work as if * > * you had just logged in to such a system, but there are differences. * > ************************************************************************ > [wgs03:SL6] ~ % echo $FPATH > /usr/share/zsh/site-functions:/usr/share/zsh/4.3.11/functions > > So every time, $FPATH is modified, it is inherited by the container. I'd prefer it if zsh wouldn't modify $FPATH. Wouldn't it work as well if _module was placed in /usr/share/zsh/site-functions? My test regarding this was fine. > > Regards, > Götz Waschk > > > > _______________________________________________ > Modules-interest mailing list > Mod...@li... > https://lists.sourceforge.net/lists/listinfo/modules-interest > -- -------------------------------------------------------- The views and opinions expressed above are strictly those of the author(s). The content of this message has not been reviewed nor approved by any entity whatsoever. -------------------------------------------------------- Paul FM Info: http://paulfm.com/~paulfm/ -------------------------------------------------------- |
