Merge branch 'master' of gitlab.psi.ch:Pmodules/buildblocks

Compiler/hdf5_serial/files/variants.Linux → Compiler/hdf5_serial/files/variants.rhel6

@@ -46,3 +46,5 @@ hdf5_serial/1.10.4	stable		pgi/18.5
 hdf5_serial/1.10.5	stable		gcc/{5.5.0,6.4.0,6.5.0,7.3.0,7.4.0,8.2.0,8.3.0}
 hdf5_serial/1.10.5	stable		intel/{18.4,19.3}
 hdf5_serial/1.10.5	stable		pgi/18.5
+
+hdf5_serial/1.10.6	unstable	gcc/{7.5.0,8.4.0,9.3.0,10.2.0}

Compiler/openmpi/build

@@ -23,23 +23,39 @@ pbuild::pre_configure() {
 	pbuild::add_configure_args "--enable-shared"
 	pbuild::add_configure_args "--enable-static"
 	pbuild::add_configure_args "--with-sge=yes"
+       	pbuild::add_configure_args "--with-ucx"
+       	pbuild::add_configure_args "--with-hwloc=internal"
 	pbuild::add_configure_args "--with-slurm=yes"
+
+        if pbuild::use_flag slurm ; then
+		pbuild::add_configure_args "--with-pmi"
+		pbuild::add_configure_args "--with-pmi-libdir=/usr/lib64/"
+
+                if pbuild::use_flag "libpmix"; then
+                  pbuild::add_configure_args "--enable-install-libpmix"
+                fi
+        fi
+
 	local version
 	(( version = (${V_MAJOR} * 100 + ${V_MINOR}) * 100 + V_PATCHLVL ))
-	if (( version < 30104 )) ; then
+        if (( V_MAJOR < 4 )); then
 		pbuild::add_configure_args "--enable-mpi-f90"
 		pbuild::add_configure_args "--enable-mpi-profile"
 		pbuild::add_configure_args "--enable-smp-locks"
 	elif (( V_MAJOR >= 4 )); then
 		pbuild::add_configure_args "--enable-mpi-fortran"
+		pbuild::add_configure_args "--without-verbs"
 	fi
 }
 
 pbuild::post_install() {
 	mkdir -p "${PREFIX}/lib/fallback"
 	local -r binary=$(ls "${PREFIX}"/lib/libmpi.so.*.*.*)
-	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/usr/.*/libuc[mpst].so'
-	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/usr/.*/libnuma.so'
-	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/usr/.*/libbverbs.so'
-	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/usr/.*/librdmacm.so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuc[mpst].so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libuct_ib.so.0'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libnuma.so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libibverbs.so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/librdmacm.so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi.so'
+	pbuild::install_shared_libs "${binary}" "${PREFIX}/lib/fallback" '/libpmi2.so'
 }

Compiler/openmpi/files/variants.merlin6

-openmpi/3.1.4_merlin6   stable  gcc/{7.4.0,8.3.0}
-openmpi/3.1.4-1_merlin6   stable  gcc/{7.4.0,8.3.0}
+openmpi/3.1.4_merlin6   deprecated gcc/{7.4.0,8.3.0}
 
+openmpi/3.1.5_merlin6   deprecated gcc/{7.3.0,7.4.0,8.3.0,9.2.0}
+openmpi/3.1.5_merlin6   deprecated intel/{15.2,17.4,18.4}
+
+openmpi/3.1.5-1_merlin6 stable     gcc/{7.3.0,7.4.0,8.3.0,9.2.0}
+openmpi/3.1.5-1_merlin6 stable     intel/{15.2,17.4,18.4}
+
+openmpi/2.1.6_slurm     unstable   gcc/{4.9.4,5.5.0,6.5.0,7.4.0,8.3.0,9.2.0}
+openmpi/2.1.6_slurm     unstable   intel/{15.2,17.4,18.4}
+
+openmpi/3.0.5_slurm     unstable   gcc/{4.9.4,5.5.0,6.5.0,7.4.0,8.3.0,9.2.0}
+openmpi/3.0.5_slurm     unstable   intel/{15.2,17.4,18.4}
+
+openmpi/3.1.6_slurm     stable     gcc/{4.9.4,5.5.0,6.5.0,7.5.0,8.4.0,9.3.0}
+openmpi/3.1.6_slurm     stable     intel/{15.2,17.4,18.4,20.1}
+
+openmpi/4.0.4_slurm     stable     gcc/{4.9.4,5.5.0,6.5.0,7.5.0,8.4.0,9.3.0}
+openmpi/4.0.4_slurm     stable     intel/{15.2,17.4,18.4,20.1}
+
+openmpi/4.0.4_slurm_libpmix unstable gcc/9.3.0

Compiler/openmpi/modulefile

@@ -29,8 +29,10 @@ set libibverbs  [glob -nocomplain /usr/lib{64,}/libibverbs.so.1*]
 set libnuma     [glob -nocomplain /usr/lib{64,}/libnuma.so.1*]
 set librdmacm   [glob -nocomplain /usr/lib{64,}/librdmacm.so.1*]
 set libucx      [glob -nocomplain /usr/lib{64,}/libuc\[mpst\].so.0*]
+set libpmi      [glob -nocomplain /usr/lib{64,}/libpmi.so.0*]
+set libpmi2     [glob -nocomplain /usr/lib{64,}/libpmi2.so.0*]
 
-if { $libibverbs eq "" || $libnuma eq "" || $librdmacm eq "" || $libucx eq "" } {
+if { $libibverbs eq "" || $libnuma eq "" || $librdmacm eq "" || $libucx eq "" || $libpmi eq "" || $libpmi2 eq "" } {
     if { [file isdirectory $PREFIX/lib/fallback] } {
         prepend-path LD_LIBRARY_PATH      $PREFIX/lib/fallback
     }

EM/relion/files/variants

@@ -2,5 +2,5 @@ relion/2.1.b1	stable	gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
 relion/3.0_beta	stable	gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
 relion/3.0.8	stable	gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
 relion/3.1-beta	unstable	gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
-relion/3.1.0	unstable	gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
+relion/3.1.0	stable	gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
 

MPI/gromacs/2020/variants

+gromacs/2020_sp        unstable gcc/7.4.0 openmpi/3.1.5_merlin6 cuda/10.0.130 Python/3.7.4 b:cmake/3.14.0
+gromacs/2020.2_sp      unstable gcc/7.5.0 openmpi/3.1.6_slurm cuda/10.0.130 Python/3.7.4 b:cmake/3.15.5
+gromacs/2020.2_sp_gpu  unstable gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 Python/3.7.4 b:cmake/3.15.5

MPI/gromacs/build

@@ -11,10 +11,6 @@ else
 fi
 
 pbuild::pre_configure() {
-  # For enabling GPU, set to 'yes'
-  local enable_gpu='yes'
-
-  echo here
   pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=RELEASE"
   pbuild::add_configure_args "-DGMX_MPI=on"
 
@@ -24,11 +20,16 @@ pbuild::pre_configure() {
     pbuild::add_configure_args "-DGFMX_DOUBLE=off"
   fi
 
-  if [[ "${enable_gpu}" == 'yes' ]]; then
+  if pbuild::use_flag "gpu"; then
  	pbuild::add_configure_args "-DGMX_GPU=on"
   else
  	pbuild::add_configure_args "-DGMX_GPU=off"
   fi
-  # To remove: pbuild::add_configure_args "-DGMX_SIMD=SSE2"
+
+  # For GMX_SIMD the lowest instruction number you think might work on all nodes
+  #   |- Available numbers: http://manual.gromacs.org/documentation/2020/install-guide/index.html#simd-support
+  #   |- AVX_512 is only for newest Intel processors (Xeon Scalable Gold, Core i9, etc.)
+  #      AVX_512 will not work on old GPUs, this is why we chood AVX2_256 which are processors from 2013
+  pbuild::add_configure_args "-DGMX_SIMD=AVX2_256"
   pbuild::add_configure_args "-DGMX_BUILD_OWN_FFTW=on"
 }

MPI/lammps/2020/variants

+lammps/2020.3_merlin6  unstable    gcc/8.4.0 openmpi/4.0.4_slurm b:cmake/3.15.5

MPI/lammps/README.txt

+[27.08.2020] 
+  * With CMake is necessary to have 'python3-virtualenv' installed. Needed for building documentation.
+  * Compilation for version 2020.3 with OMP, GCC v8, OpenMPI v4.0.4 works without the need of specifying '-D LAMMPS_OMP_COMPAT=4'
+    * More details here: https://lammps.sandia.gov/doc/Build_basics.html)
+    * Problems are seen with GCC v9, so is recommended to use GCC v8 for that. It was compiled with v8.

MPI/lammps/build

@@ -4,80 +4,50 @@
 TARNAME=$(grep -E "^${V_MAJOR}.${V_MINOR}" files/version-to-tarname.txt| awk '{print $2}')
 
 # pbuild::set_download_url "https://gitlab.psi.ch/caubet_m/merlin-software/raw/master/$P/$P-${V_PKG}.tar.gz"
-pbuild::set_download_url "https://github.com/lammps/lammps/archive/${TARNAME}"
+# pbuild::set_download_url "https://github.com/lammps/lammps/archive/${TARNAME}"
+pbuild::set_download_url "https://lammps.sandia.gov/tars/${TARNAME}"
 
 pbuild::add_to_group 'MPI'
 
 pbuild::install_docfiles README LICENSE
 
-pbuild::compile_in_sourcetree
-
-# pbuild::pre_configure() {
-#   pbuild::add_configure_args "-D CMAKE_BUILD_TYPE=RELEASE"
-# 
-#   pbuild::add_configure_args "-D BUILD_MPI=yes"
-#   pbuild::add_configure_args "-D BUILD_OMP=yes"
-#   pbuild::add_configure_args "-D PKG_USER-OMP=yes"
-#   pbuild::add_configure_args "-D PKG_BODY=yes"
-#   pbuild::add_configure_args "-D PKG_DIPOLE=yes"
-#   pbuild::add_configure_args "-D PKG_MOLECULE=yes"
-#   pbuild::add_configure_args "-D PKG_MPIIO=yes"
-#   pbuild::add_configure_args "-D PKG_REPLICA=yes"
-#   # pbuild::add_configure_args "-D PKG_REAX=yes"
-#   pbuild::add_configure_args "-D PKG_RIGID=yes"
-#   pbuild::add_configure_args "-D PKG_USER-REAXC=yes"
-# 
-# }
-
-# pbuild::configure() {
-# 	cp -v "${BUILDBLOCK_DIR}/files/Makefile.PSI" "${BUILD_DIR}/src/MAKE/MINE"
-# }
-#
 pbuild::configure() {
-  sed -i '/^CCFLAGS.*/ s/$/ -fopenmp/' ${BUILD_DIR}/src/MAKE/Makefile.mpi
-  sed -i '/^LINKFLAGS.*/ s/$/ -fopenmp/' ${BUILD_DIR}/src/MAKE/Makefile.mpi
+	cmake -D CMAKE_INSTALL_PREFIX="${PREFIX}" \
+              -D CMAKE_BUILD_TYPE=RELEASE \
+              -D BUILD_MPI=yes \
+              -D BUILD_OMP=yes \
+              -D BUILD_TOOLS=yes \
+              -D BUILD_DOC=yes \
+              -D LAMMPS_MACHINE=mpi \
+              -D PKG_USER-OMP=yes \
+              -D PKG_ASPHERE=yes \
+              -D PKG_BODY=yes \
+              -D PKG_COMPRESS=yes \
+              -D PKG_CORESHELL=yes \
+              -D PKG_DIPOLE=yes \
+              -D PKG_GRANULAR=yes \
+              -D PKG_MANYBODY=yes \
+              -D PKG_KSPACE=yes \
+              -D PKG_MC=yes \
+              -D PKG_MISC=yes \
+              -D PKG_MOLECULE=yes \
+              -D PKG_MPIIO=yes \
+              -D PKG_OPT=yes \
+              -D PKG_PYTHON=yes \
+              -D PKG_REPLICA=yes \
+              -D PKG_RIGID=yes \
+              -D PKG_SNAP=yes \
+              -D PKG_USER-EFF=yes \
+              -D PKG_USER-DRUDE=yes \
+              -D PKG_USER-REAXC=yes \
+              -D BUILD_SHARED_LIBS=on \
+	      ${BUILD_DIR}/../src/cmake
 }
 
 pbuild::compile() {
-  echo BEGIN COMPILE
-  cd src
-  # make clean-all
-  # make no-all
-  make yes-user-omp
-  make yes-asphere
-  make yes-body
-  make yes-compress
-  make yes-coreshell
-  make yes-dipole
-  make yes-granular
-  make yes-manybody
-  make yes-kspace
-  make yes-mc
-  make yes-misc
-  make yes-molecule
-  make yes-mpiio
-  make yes-opt
-  make yes-python
-  make yes-replica
-  make yes-rigid
-  make yes-snap
-  make yes-user-eff
-  make yes-user-drude
-  make yes-user-reaxc
-  make yes-user-reaxc args="-m serial"
-  make yes-user-reaxc args="-m mpi"
-  make mpi
-  echo ENDCOMPILE
+	cmake --build ${BUILD_DIR}
 }
 
 pbuild::install() {
-	install -m 0755 -d "${PREFIX}/bin"
-  # Modify this for installing individual binaries
-	install -m 0755  "${BUILD_DIR}/src/lmp_mpi" "${PREFIX}/bin/"
-
-  # Strip all present binaries
-  for file in $(ls ${PREFIX}/bin/lmp_*)
-  do
-    strip "$file"
-  done
+        make install
 }

MPI/lammps/files/version-to-tarname.txt

 2018.11      patch_15Nov2018.tar.gz
 2019.8       stable_7Aug2019.tar.gz
+2020.3       lammps-3Mar20.tar.gz

MPI/qe/6/variants

 qe/6.3  unstable	gcc/8.2.0 openmpi/3.1.1       b:cmake/3.9.6
+qe/6.5  unstable        gcc/9.3.0 lapack/3.9.0 OpenBLAS/0.3.9 openmpi/4.0.4_slurm b:cmake/3.15.5

MPI/qe/build

 #!/usr/bin/env modbuild
 
 pbuild::set_download_url "https://github.com/QEF/q-e/archive/$P-$V.tar.gz"
-echo "https://github.com/QEF/q-e/archive/$P-$V.tar.gz"
 
 pbuild::add_to_group 'MPI'
 
@@ -9,24 +8,16 @@ pbuild::install_docfiles License README.md CONTRIBUTING.md
 
 pbuild::compile_in_sourcetree
 
-
-pbuild::configure() {
-  mkdir -p ${PREFIX}
-  ./configure -enable-openmp --with-prefix="${PREFIX}/bin" --prefix="${PREFIX}/bin"
+pbuild::pre_configure() {
+        pbuild::add_configure_args "-enable-openmp"
 }
 
 pbuild::compile() {
         make all
+        make install
 }
 
 pbuild::install() {
-   # Due to bug in: https://gitlab.com/QEF/q-e/commit/88e6558646dbbcfcafa5f3fa758217f6062ab91c.diff
-   #   Deploying custom install procedure
-   mkdir -p ${PREFIX}/bin
-   cd ${BUILD_DIR}
-   for x in `find * ! -path "test-suite/*" -name *.x -type f` ; do 
-     cp $x ${PREFIX}/bin/
-   done
-   echo 'Quantum ESPRESSO binaries installed in ${PREFIX}/bin'
-  # make install
+	:
 }
+

Programming/Java/10u44/variants

+Java/10u44   stable
+Java/10.0.44 removed

Programming/Java/12.0.2/variants

-Java/12.0.2   stable

Programming/Java/12u2/variants

+Java/12u2    stable
+Java/12.0.2  deprecated

Programming/Java/15u36/variants

+Java/15u36   stable

Programming/Java/build

 #!/usr/bin/env modbuild 
 
-pbuild::set_download_url "https://download.java.net/java/GA/jdk12.0.2/e482c34c86bd4bf8b56c0b35558996b9/10/GPL/openjdk-12.0.2_linux-x64_bin.tar.gz"
+URL=$(grep -E "^${V_MAJOR}" files/version-to-URL.txt | awk '{print $2}')
+
+echo $URL
+
+pbuild::set_download_url "${URL}"
 
 pbuild::add_to_group 'Programming'
 
@@ -13,33 +17,7 @@ pbuild::compile() {
 }
 
 pbuild::install() {
-  install -m 0755 -d "${PREFIX}/bin"
-  for binary_file in $(ls ${SRC_DIR}/bin/*)
-  do
-    install -m 0755 "${binary_file}" "${PREFIX}/bin"
-  done
-
-  for java_dir in $(echo "lib lib/security lib/jfr lib/server")
-  do
-    mkdir -p "${PREFIX}/${java_dir}"
-    install -m 0755 -d "${PREFIX}/${java_dir}"
-    for library_file in $(find ${SRC_DIR}/${java_dir} -maxdepth 1 -type f)
-    do
-      install -m 0755 "${library_file}" "${PREFIX}/${java_dir}"
-    done
-  done
-
-  for java_dir in $(echo "conf conf/management conf/security conf/security/policy conf/security/policy/unlimited conf/security/policy/limited conf/sdp")
-  do
-    mkdir -p "${PREFIX}/${java_dir}"
-    install -m 0755 -d "${PREFIX}/${java_dir}"
-    for library_file in $(find ${SRC_DIR}/${java_dir} -maxdepth 1 -type f)
-    do
-      install -m 0755 "${library_file}" "${PREFIX}/${java_dir}"
-    done
-  done
-
-  for java_dir in $(echo "jmods")
+  for java_dir in $(find ${SRC_DIR} -type d | sed -n "s|^${SRC_DIR}/||p")
   do
     mkdir -p "${PREFIX}/${java_dir}"
     install -m 0755 -d "${PREFIX}/${java_dir}"

Programming/Java/files/version-to-URL.txt

+10u44  https://download.java.net/openjdk/jdk10/ri/openjdk-10+44_linux-x64_bin_ri.tar.gz
+12u2   https://download.java.net/java/GA/jdk12.0.2/e482c34c86bd4bf8b56c0b35558996b9/10/GPL/openjdk-12.0.2_linux-x64_bin.tar.gz
+15u36  https://download.java.net/java/GA/jdk15/779bf45e88a44cbd9ea6621d33e33db1/36/GPL/openjdk-15_linux-x64_bin.tar.gz

Programming/anaconda/2019.07/conda-env-defs/hep-root/README.md

+ROOT environment created on request from Alexander Skawran

Programming/anaconda/2019.07/conda-env-defs/hep-root/hep-root.yml

+name: hep_root
+channels:
+  - conda-forge
+dependencies:
+  -  python=3.7
+  -  root     
+  -  numpy    
+  -  root_numpy
+  -  pandas   
+  -  matplotlib
+  -  tensorflow
+  -  nb_conda_kernels

Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml

@@ -6,5 +6,15 @@ channels:
 dependencies:
   - python=3.6
   - ldapuserdir
-  - cython  # for pyslurm
+  # python development
   - conda-build
+  - cython  # for pyslurm
+  - black
+  - flake8
+  - mypy
+  - mypy_extensions
+  - typing_extensions
+  - tox
+  - tox-conda
+  - pytest
+  - bpython

Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md

+# scicat-client
+
+The scicat-client environment is used in the datacatalog module. Contact
+Spencer Bliven, Stephan Egli, or Leo Sala for more info.
+
+## Installing
+
+First, create the conda environment
+
+    conda env create -f scicat_client.yml
+
+Next, install scicat_client. Eventually this should be done automatically
+through conda, but for now it needs to be installed from source.
+
+    git clone git@github.com:paulscherrerinstitute/scicat_client.git
+    cd scicat_client
+    conda activate scicat_client-0.1.0
+    python setup.py install
+
+

Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml

+# Clean environment based on pure conda-forge packages
+name: scicat_client-0.1.0
+channels:
+  - conda-forge
+  - http://conda-pkg.intranet.psi.ch
+dependencies:
+  - python=3.8
+  - requests
+  # development tools
+  - conda-build
+  - black
+  - flake8
+  - mypy
+  - mypy_extensions
+  - typing_extensions
+  - tox
+  - tox-conda
+  - pytest

Programming/anaconda/2019.07/conda-env-defs/topaz/README.md

+# Topaz
+
+[Topaz](https://github.com/tbepler/topaz) is a conda-based cryoEM particle
+picker. It is used primarily through cryosparc, but also provides python
+notebooks.
+
+See https://intranet.psi.ch/en/bio/computing-cryosparc
+
+## INSTALLATION
+
+IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
+
+    export TMPDIR=/opt/tmp/$USER
+    export XDG_CACHE_HOME=/opt/tmp/$USER/.cache
+    CONDA_COPY_ALWAYS=1 conda env create --file topaz.yml
+    conda activate topaz-0.2.5
+
+The alternate TMPDIR is required on pmod6 because /tmp is too small for pip to expand all wheel files.
+

Programming/anaconda/2019.07/conda-env-defs/topaz/topaz.yml

+name: topaz-0.2.5
+channels:
+  - tbepler
+  - defaults
+dependencies:
+  - python=3.6
+  - cudatoolkit=9.2
+  - pytorch
+  - topaz
+

Programming/anaconda/README.md

 # Building of an Anaconda release using Pmodules
 
+## Important Note about access permissions
+
+   The central anacoda installations are located below `/afs/psi.ch/sys/psi.merlin/Programming/anaconda`. All administrators
+   of these installations must be members of the AFS group `sys.modules:psi_python` in order to have write permission.
+
 ## Concepts
 
    * The anaconda module just provides the **conda** package management tool together with its directory infrastructure which contains *conda environments* and a cache of downloaded packages
@@ -14,7 +19,7 @@
    
 ## Building a central conda environment
 
-   * **Allways work on the host pmod6**: conda is trying to use hardlinks where it can. There is an issue that can appear if you install from a machine that uses Auristor (which provides hardlinks). This causes whole environments to become corrupt, so that only a PSI AFS admin can fix the problem. Therefore we only install from pmod6 which runs openAFS.
+   * **Allways work on the host pmod6**: conda is trying to use hardlinks where it can. There is an issue that can appear if you install from a machine that uses Auristor (which provides hardlinks within the same AFS volume). Accessing or modifying from an old OpenAFS client can cause problems. This causes whole environments to become corrupt, so that only a PSI AFS admin can fix the problem. Therefore we only install from pmod6 which runs openAFS.
 
 ### installation of a pure conda environment
 
@@ -70,3 +75,48 @@ This works if the python package has a correct setup.py build
      cd /opt/psi/Programming/anaconda/2019.07/xxxx/mypackage
      pip install .
      ```
+     
+## Building for use with jupyter
+
+Jupyter can discover conda environments if the environment contains the **nb_conda_kernels** package.
+Regrettably the environment activation by this package does not run through the full process as compared to the command line functions. The activation scripts that can be placed in an environment do not get executed (q.v. my bug report https://github.com/Anaconda-Platform/nb_conda_kernels/issues/145).
+   
+In order to fix this, we must use a workaround which involves modifying the kernel spec configuration file of the environment to wrap the call to the python kernel like in this example for `.../envs/mpi-test/share/jupyter/kernels/python3/kernel.json`:
+
+```
+     {
+         "argv": [
+      	"/opt/psi/Programming/anaconda/2019.07/admintools/kernelwrapper.sh",
+      	"mpi-test",
+      	"/opt/psi/Programming/anaconda/2019.07/conda/envs/mpi-test/bin/python",
+      	"-m",
+      	"ipykernel_launcher",
+      	"-f",
+      	"{connection_file}"
+      ],
+      "display_name": "Python 3",
+      "language": "python"
+     }
+```
+
+In order to modify an environment easily I wrote a tool found in the `admintools` of this buildblock which you can use as follows:
+
+```
+files/admintools/install-kernelwrapper.py -v /opt/psi/Programming/anaconda/2019.07/conda/envs/hep_root
+```
+
+### Logging of environment activation information
+
+The logging of information for the usage of central environments is
+important, because it allows to do lifetime management of the conda
+environments. We can find out whether a particular environment is used at all
+and by whom, and can so plan the decommissioning.
+
+Logging is currently implemented by an activation hook script that gets placed
+in each environment. This is done by running the script `.../files/admintools/install-env-loggers.sh`
+which will loop over all central environments of this anaconda pmodule.
+
+
+
+
+

Programming/anaconda/files/admintools/conda_setup.sh

-# simulate `conda init` type hook
-# Expects CONDA_EXE and CONDA_PREFIX to be set
-__conda_setup="$("${CONDA_EXE:-conda}" 'shell.bash' 'hook' 2> /dev/null)"
-if [ $? -eq 0 ]; then
-    eval "$__conda_setup"
-else
-    if [ -f "${CONDA_PREFIX:?CONDA_PREFIX not set}/etc/profile.d/conda.sh" ]; then
-        . "${CONDA_PREFIX}/etc/profile.d/conda.sh"
-    else
-        export PATH="${CONDA_PREFIX}/bin:$PATH"
-    fi
-fi
-unset __conda_setup
-

Programming/anaconda/files/admintools/install-env-loggers.sh

+#!/bin/bash
+# Script to install logging into the activation hook directories
+# of environments
+#
+# 2020 - Derek Feichtinger
+
+function envlist() {
+    conda env list --json | jq -r '.envs[]' | grep -E -v 'conda$'
+}
+
+if [[ -z "$CONDA_PREFIX" ]]; then
+    echo "Error: No conda distribution seems active (CONDA_PREFIX)" >&2
+    exit 1
+fi
+
+for env in $(envlist); do
+    if [[ -e "$env/etc" ]]; then
+	echo "Installing into $env"
+	mkdir -p $env/etc/conda/activate.d
+	cat <<'EOF' > $env/etc/conda/activate.d/log-envname.sh
+#!/bin/bash
+logger "activated conda module: ${CONDA_PREFIX}"  
+EOF
+    else
+	echo "WARNING: SKIPPING ENV: $env has no /etc" >&2
+    fi
+done
+

Programming/anaconda/files/admintools/install-kernelwrapper.py

+#!/usr/bin/env python
+# installs a jupyter kernel wrapper solution into the environment's
+# $ENVPATH/share/jupyter/kernels/python3/kernel.json kernel definition
+
+# typical envpath at PSI
+#     "/opt/psi/Programming/anaconda/2019.07/conda/envs/datascience_py37"
+
+import re
+import os
+import sys
+import shutil
+from datetime import datetime
+import argparse
+parser = argparse.ArgumentParser()
+
+# DEFAULTS
+verbose_flag = False
+
+parser.add_argument("envpath", help="conda env path")
+parser.add_argument("-v", "--verbose", help="verbose mode",action="store_true")
+args = parser.parse_args()
+
+if args.verbose:
+    verbose_flag = True
+
+envpath = args.envpath
+envname = os.path.basename(envpath)
+condaroot = re.sub(r'(.*)/conda/envs/.*', r'\1', envpath)
+kwrapper = os.path.join(condaroot, 'admintools/kernelwrapper.sh')
+kfile = os.path.join(envpath,"share/jupyter/kernels/python3/kernel.json")
+
+date_time = datetime.now().strftime("%Y%m%d-%H%M%S")
+
+if verbose_flag:
+    print("env: %s" % envname)
+    print(kwrapper)
+
+if not os.path.isfile(kwrapper):
+    sys.stderr.write("Error: no wrapper found at %s\n" % (kwrapper))
+    sys.exit(1)
+
+searchstr = r'"argv": \[\n( *"/.*python", *)'
+subststr = r'"argv": [\n' + '  "' + kwrapper + '",\n' + '  "' + envname + r'",\n\1'
+
+try:
+    with open(kfile,"r") as fp:
+        filestr = "".join(fp.readlines())
+except IOError:
+    sys.stderr.write("Error: Env has no kernel file: %s\n" % kfile)
+    sys.exit(0)
+
+if re.search(kwrapper, filestr):
+        if verbose_flag:
+            print("env %s already contains kernelwrapper" % envpath)
+            sys.exit(0)
+            
+if re.search(searchstr, filestr):
+    filestr = re.sub(searchstr,
+                     subststr,
+                     filestr)
+    print(filestr)
+
+    bupfile = kfile + "-" + date_time + ".bup"
+    if verbose_flag:
+        print("copying original file to %s" % bupfile)
+    shutil.copyfile(kfile, bupfile)
+    if verbose_flag:
+        print("writing new file %s" % kfile)
+        print(filestr)
+    with open(kfile,"w") as fp:
+        fp.write(filestr)
+else:
+    sys.stderr.write("ERROR: Could not do substitution in %s" % kfile)
+    sys.stderr.write(filestr)

Programming/anaconda/files/admintools/kernelwrapper.sh

 #!/bin/bash
+# kernelwrapper.sh
+# This wrapper is needed to correctly have jupyter activate conda evnironments
+# including the running of the $ENV/etc/conda/activate.d hooks
+# q.v. https://github.com/Anaconda-Platform/nb_conda_kernels/issues/145
+#
+# This script must be called from the config located in an environment
+#   $ENV/share/jupyter/kernels/python3/kernel.jsonshare/jupyter/kernels/python3/kernel.json 
+
+# 2019 - Derek Feichtinger
 dbgecho() {
     DBGLOG=/tmp/kernelwrapper-${USER}.log
     if [[ $DEBUG_JUPYTER_WRAPPER == 1 ]]; then

Programming/anaconda/files/variants

 anaconda/2018.12	unstable	
 anaconda/2019.03	unstable	
-anaconda/2019.07	unstable	
+anaconda/2019.07	stable