Commit 8235c48f authored by Richard Berger's avatar Richard Berger
Browse files

Avoid errors due to host Lmod in containers 

These changes ensure that environment variables that are automatically passed
to the container don't interfere with Lmod inside of the container. The previous
implementation would not take care of sticky packages from the outside and Lmod
would try to reload them.

Note that Lmod defines the 'module' bash function, which doesn't propagate to
the final shell when using 'singularity shell'. If the 'module' command is needed
a login shell needs to be launched:

$ singularity exec <CONTAINER> bash -l
parent 82b1fc71

tools/singularity/centos7.def

+17 −2
Original line number Diff line number Diff line
@@ -14,9 +14,24 @@ From: centos:7 
%environment

        LC_ALL=C

        export LC_ALL



        # we need to reset any module variables

        # inherited from the host.

        unset __LMOD_REF_COUNT__LMFILES_

        unset __LMOD_REF_COUNT_PATH

        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH

        unset __LMOD_REF_COUNT_MANPATH

        unset __LMOD_REF_COUNT_MODULEPATH

        unset __LMOD_REF_COUNT_LOADEDMODULES

        unset _LMFILES_

        unset MODULEPATH

        unset MODULESHOME

        unset MODULEPATH_ROOT

        unset LOADEDMODULES

        . /etc/profile.d/z00_lmod.sh

        module purge

        unset LMOD_SYSTEM_DEFAULT_MODULES



        # load MPI by default

        . /etc/profile

        module load mpi



%labels

tools/singularity/centos8.def

+17 −2
Original line number Diff line number Diff line
@@ -19,9 +19,24 @@ From: centos:8 
%environment

        LC_ALL=C

        export LC_ALL



        # we need to reset any module variables

        # inherited from the host.

        unset __LMOD_REF_COUNT__LMFILES_

        unset __LMOD_REF_COUNT_PATH

        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH

        unset __LMOD_REF_COUNT_MANPATH

        unset __LMOD_REF_COUNT_MODULEPATH

        unset __LMOD_REF_COUNT_LOADEDMODULES

        unset _LMFILES_

        unset MODULEPATH

        unset MODULESHOME

        unset MODULEPATH_ROOT

        unset LOADEDMODULES

        . /etc/profile.d/modules.sh

        module purge

        unset LMOD_SYSTEM_DEFAULT_MODULES



        # load MPI by default

        . /etc/profile

        module load mpi



%labels

tools/singularity/fedora30_mingw.def

+16 −3
Original line number Diff line number Diff line
@@ -38,12 +38,25 @@ From: fedora:30 
%environment

        LC_ALL=C

        export LC_ALL



        # we need to reset any module variables

        # inherited from the host.

        unset __LMOD_REF_COUNT__LMFILES_

        unset __LMOD_REF_COUNT_PATH

        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH

        unset __LMOD_REF_COUNT_MANPATH

        unset __LMOD_REF_COUNT_MODULEPATH

        unset __LMOD_REF_COUNT_LOADEDMODULES

        unset _LMFILES_

        unset MODULEPATH

        unset MODULESHOME

        unset MODULEPATH_ROOT

        unset LOADEDMODULES

        . /etc/profile.d/modules.sh

        module purge

        unset LMOD_SYSTEM_DEFAULT_MODULES



        # load MPI by default

        . /etc/profile

        module load mpi



%labels

        Author akohlmey
 
        Author akohlmey, rbberger

tools/singularity/fedora32_mingw.def

+15 −5
Original line number Diff line number Diff line
@@ -36,14 +36,24 @@ From: fedora:32 
               texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng



%environment

        LC_ALL=C

        export LC_ALL

        # we need to reset any module variables

        # inherited from the host.

        unset __LMOD_REF_COUNT__LMFILES_

        unset __LMOD_REF_COUNT_PATH

        unset __LMOD_REF_COUNT_LD_LIBRARY_PATH

        unset __LMOD_REF_COUNT_MANPATH

        unset __LMOD_REF_COUNT_MODULEPATH

        unset __LMOD_REF_COUNT_LOADEDMODULES

        unset _LMFILES_

        unset MODULEPATH

        unset MODULESHOME

        unset MODULEPATH_ROOT

        unset LOADEDMODULES

        . /etc/profile.d/modules.sh

        module purge

        unset LMOD_SYSTEM_DEFAULT_MODULES



        # load MPI by default

        . /etc/profile

        module load mpi



%labels

        Author akohlmey
 
        Author akohlmey, rbberger

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