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

tools/singularity/centos7.def

@@ -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

@@ -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

@@ -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

@@ -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