consolidate wheel libraries under /opt/nrnwheel

.circleci/config.yml

@@ -25,7 +25,7 @@ jobs:
             docker run --rm \
                 -w /root/nrn \
                 -v $PWD:/root/nrn \
-                -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
+                -v /opt/nrnwheel/mpt:/opt/nrnwheel/mpt \
                 -e NEURON_NIGHTLY_TAG \
                 -e NRN_NIGHTLY_UPLOAD \
                 -e NRN_RELEASE_UPLOAD \

azure-pipelines.yml

@@ -53,15 +53,15 @@ stages:
         inputs:
           secureFile: 'mpt_headears.2.21.tar.gz'
 
-      # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt`
+      # Note that mpt headers must be mounted in the docker imager under `/opt/nrnwheel/mpt`
       # This path is checked by `packaging/python/build_wheels.bash` when run in the image.
       - script: |
           sudo mkdir -p /opt/nrnwheel/mpt
           sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt
           docker run --rm \
             -w /root/nrn \
             -v $PWD:/root/nrn \
-            -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
+            -v /opt/nrnwheel/mpt:/opt/nrnwheel/mpt \
             -e NEURON_NIGHTLY_TAG \
             -e NRN_NIGHTLY_UPLOAD \
             -e NRN_RELEASE_UPLOAD \
@@ -106,15 +106,15 @@ stages:
         inputs:
           secureFile: 'mpt_headears.2.21.tar.gz'
 
-      # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt`
+      # Note that mpt headers must be mounted in the docker imager under `/opt/nrnwheel/mpt`
       # This path is checked by `packaging/python/build_wheels.bash` when run in the image.
       - script: |
           sudo mkdir -p /opt/nrnwheel/mpt
           sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt
           docker run --rm \
             -w /root/nrn \
             -v $PWD:/root/nrn \
-            -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
+            -v /opt/nrnwheel/mpt:/opt/nrnwheel/mpt \
             -e NEURON_NIGHTLY_TAG \
             -e NRN_NIGHTLY_UPLOAD \
             -e NRN_RELEASE_UPLOAD \

cmake/CMakeListsNrnMech.cmake

@@ -46,9 +46,9 @@ foreach(link_lib ${NRN_LINK_LIBS})
     set(link_flag "-l${link_lib}")
     set(description
         "Generating link flags from name '${link_lib}', beware that this can be fragile.")
-    # avoid library paths from special directory /nrnwheel which used to build wheels under docker
+    # avoid library paths from special directory /opt/nrnwheel which used to build wheels under docker
     # container
-  elseif("${dir_path}" MATCHES "^/nrnwheel")
+  elseif("${dir_path}" MATCHES "^/opt/nrnwheel")
     continue()
   elseif("${dir_path}" MATCHES "^(/lib|/lib64|/usr/lib|/usr/lib64)$")
     # NAME_WLE not avaialble with CMake version < 3.14

docs/install/python_wheels.md

@@ -98,9 +98,9 @@ The `neuronsimulator/neuron_wheel` provides out-of-the-box support for `mpich` a
 For `HPE-MPT MPI`, since it's not open source, you need to acquire the headers and mount them in the docker image:
 
 ```
-docker run -v $PWD/nrn:/root/nrn -w /root/nrn -v $PWD/mpt-headers/2.21/include:/nrnwheel/mpt/include -it neuronsimulator/neuron_wheel bash
+docker run -v $PWD/nrn:/root/nrn -w /root/nrn -v $PWD/mpt-headers/2.21/include:/opt/nrnwheel/mpt/include -it neuronsimulator/neuron_wheel bash
 ```
-where `$PWD/mpt-headers` is the path to the HPE-MPT MPI headers on the host machine that end up mounted at `/nrnwheel/mpt/include`.
+where `$PWD/mpt-headers` is the path to the HPE-MPT MPI headers on the host machine that end up mounted at `/opt/nrnwheel/mpt/include`.
 You can download the headers with:
 
 ```

packaging/python/Dockerfile

@@ -40,39 +40,39 @@ RUN rpmbuild --rebuild https://vault.centos.org/8-stream/AppStream/Source/SPacka
 RUN wget http://ftpmirror.gnu.org/ncurses/ncurses-6.2.tar.gz \
     && tar -xvzf ncurses-6.2.tar.gz \
     && cd ncurses-6.2  \
-    && ./configure --prefix=/nrnwheel/ncurses --without-shared CFLAGS="-fPIC" \
+    && ./configure --prefix=/opt/nrnwheel/ncurses --without-shared CFLAGS="-fPIC" \
     && make -j install
 
 RUN curl -L -o mpich-3.3.2.tar.gz http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz \
     && tar -xvzf mpich-3.3.2.tar.gz \
     && cd mpich-3.3.2 \
-    && ./configure --disable-fortran --prefix=/nrnwheel/mpich \
+    && ./configure --disable-fortran --prefix=/opt/nrnwheel/mpich \
     && make -j install
 
 RUN curl -L -o openmpi-4.0.3.tar.gz  https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz \
     && tar -xvzf openmpi-4.0.3.tar.gz \
     && cd openmpi-4.0.3 \
-    && ./configure --prefix=/nrnwheel/openmpi \
+    && ./configure --prefix=/opt/nrnwheel/openmpi \
     && make -j install
 
-ENV PATH /nrnwheel/openmpi/bin:$PATH
+ENV PATH /opt/nrnwheel/openmpi/bin:$PATH
 
 RUN curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/1.2.0.zip \
     && unzip MUSIC.zip \
     && mv MUSIC-* MUSIC \
     && cd MUSIC \
     && ./autogen.sh \
-    && ./configure --prefix=/nrnwheel/MUSIC --with-python-sys-prefix --disable-anysource \
+    && ./configure --prefix=/opt/nrnwheel/MUSIC --with-python-sys-prefix --disable-anysource \
     && make -j install
 
 RUN curl -L -o readline-7.0.tar.gz https://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz \
     && tar -xvzf readline-7.0.tar.gz \
     && cd readline-7.0  \
-    && ./configure --prefix=/nrnwheel/readline --disable-shared CFLAGS="-fPIC" \
+    && ./configure --prefix=/opt/nrnwheel/readline --disable-shared CFLAGS="-fPIC" \
     && make -j install
 
 # create readline with ncurses
-RUN cd /nrnwheel/readline/lib \
+RUN cd /opt/nrnwheel/readline/lib \
     && ar -x libreadline.a \
     && ar -x ../../ncurses/lib/libncurses.a \
     && ar cq libreadline.a *.o \

packaging/python/build_wheels.bash

@@ -104,7 +104,7 @@ build_wheel_linux() {
     # Workaround for https://github.com/pypa/manylinux/issues/1309
     git config --global --add safe.directory "*"
 
-    python setup.py build_ext --cmake-prefix="/nrnwheel/ncurses;/nrnwheel/readline;/nrnwheel/MUSIC" --cmake-defs="$CMAKE_DEFS" $setup_args bdist_wheel
+    python setup.py build_ext --cmake-prefix="/opt/nrnwheel/ncurses;/opt/nrnwheel/readline;/opt/nrnwheel/MUSIC" --cmake-defs="$CMAKE_DEFS" $setup_args bdist_wheel
 
     # For CI runs we skip wheelhouse repairs
     if [ "$SKIP_WHEELHOUSE_REPAIR" = true ] ; then
@@ -208,9 +208,9 @@ coreneuron=$3
 case "$1" in
 
   linux)
-    MPI_INCLUDE_HEADERS="/nrnwheel/openmpi/include;/nrnwheel/mpich/include"
+    MPI_INCLUDE_HEADERS="/opt/nrnwheel/openmpi/include;/opt/nrnwheel/mpich/include"
     # Check for MPT headers. On Azure, we extract them from a secure file and mount them in the docker image in:
-    MPT_INCLUDE_PATH="/nrnwheel/mpt/include"
+    MPT_INCLUDE_PATH="/opt/nrnwheel/mpt/include"
     if [ -d "$MPT_INCLUDE_PATH" ]; then
         MPI_INCLUDE_HEADERS="${MPI_INCLUDE_HEADERS};${MPT_INCLUDE_PATH}"
     fi

packaging/python/test_wheels.sh

@@ -113,8 +113,8 @@ run_mpi_test () {
   fi
 
   # test MUSIC if enabled
-  if [[ "$has_music" == "true" ]]  && [[ $mpi_name == *"OpenMPI"* || $mpi_name == *"MPICH"* ]]; then
-    export MUSIC_LIBDIR=/nrnwheel/MUSIC/lib
+  if [[ "$has_music" == "true" ]]  && [[ $mpi_name == *"OpenMPI"* || $mpi_name == *"MPICHz"* ]]; then
+    export MUSIC_LIBDIR=/opt/nrnwheel/MUSIC/lib
     $python_exe test/music_tests/runtests.py
   fi
 

test/music_tests/runtests.py

@@ -57,8 +57,8 @@ def run(cmd):
             name = musicpath + "/lib/libmusic." + suffix
             if exists(name):
                 break
-        os.environ["NRN_LIBMUSIC_PATH"] = name
-    print("NRN_LIBMUSIC_PATH={}".format(os.getenv("NRN_LIBMUSIC_PATH")))
+        my_env["NRN_LIBMUSIC_PATH"] = name
+    print("NRN_LIBMUSIC_PATH={}".format(my_env["NRN_LIBMUSIC_PATH"]))
 
 out2 = "numprocs=1\nRank 0: Event (0, 0.001175) detected at 0\nRank 0: Event (0, 0.013825) detected at 0\n"