Update Dane install to put sources in the workspace directory

Docs/source/install/hpc/dane.rst

@@ -24,18 +24,19 @@ If you are new to this system, **please see the following resources**:
 Preparation
 -----------
 
-Use the following commands to download the WarpX source code:
+Use the following commands to download the WarpX source code.
+Note that these commands and the shell scripts all assume the bash shell.
 
 .. code-block:: bash
 
-   git clone https://github.com/ECP-WarpX/WarpX.git $HOME/src/warpx
+   git clone https://github.com/ECP-WarpX/WarpX.git /usr/workspace/${USER}/dane/src/warpx
 
 We use system software modules, add environment hints and further dependencies via the file ``$HOME/dane_warpx.profile``.
 Create it now:
 
 .. code-block:: bash
 
-   cp $HOME/src/warpx/Tools/machines/dane-llnl/dane_warpx.profile.example $HOME/dane_warpx.profile
+   cp /usr/workspace/${USER}/dane/src/warpx/Tools/machines/dane-llnl/dane_warpx.profile.example $HOME/dane_warpx.profile
 
 .. dropdown:: Script Details
    :color: light
@@ -67,7 +68,7 @@ Finally, since Dane does not yet provide software modules for some of our depend
 
 .. code-block:: bash
 
-   bash $HOME/src/warpx/Tools/machines/dane-llnl/install_dependencies.sh
+   bash /usr/workspace/${USER}/dane/src/warpx/Tools/machines/dane-llnl/install_dependencies.sh
    source /usr/workspace/${USER}/dane/venvs/warpx-dane/bin/activate
 
 .. dropdown:: Script Details
@@ -88,13 +89,13 @@ Use the following :ref:`cmake commands <building-cmake>` to compile the applicat
 
 .. code-block:: bash
 
-   cd $HOME/src/warpx
+   cd /usr/workspace/${USER}/dane/src/warpx
    rm -rf build_dane
 
    cmake -S . -B build_dane -DWarpX_FFT=ON -DWarpX_QED_TABLE_GEN=ON -DWarpX_DIMS="1;2;RZ;3"
    cmake --build build_dane -j 6
 
-The WarpX application executables are now in ``$HOME/src/warpx/build_dane/bin/``.
+The WarpX application executables are now in ``/usr/workspace/${USER}/dane/src/warpx/build_dane/bin/``.
 Additionally, the following commands will install WarpX as a Python module:
 
 .. code-block:: bash
@@ -118,7 +119,7 @@ If you already installed WarpX in the past and want to update it, start by getti
 
 .. code-block:: bash
 
-   cd $HOME/src/warpx
+   cd /usr/workspace/${USER}/dane/src/warpx
 
    # read the output of this command - does it look ok?
    git status
@@ -137,7 +138,7 @@ And, if needed,
 - log out and into the system, activate the now updated environment profile as usual,
 - :ref:`execute the dependency install scripts <building-dane-preparation>`.
 
-As a last step, clean the build directory ``rm -rf $HOME/src/warpx/build_dane`` and rebuild WarpX.
+As a last step, clean the build directory ``rm -rf /usr/workspace/${USER}/dane/src/warpx/build_dane`` and rebuild WarpX.
 
 
 .. _running-cpp-dane:

Tools/machines/dane-llnl/dane_warpx.profile.example

@@ -16,15 +16,15 @@ module load boost/1.80.0
 module load hdf5-parallel/1.14.0
 
 SW_DIR="/usr/workspace/${USER}/dane"
-export CMAKE_PREFIX_PATH=${SW_DIR}/c-blosc-1.21.6:$CMAKE_PREFIX_PATH
-export CMAKE_PREFIX_PATH=${SW_DIR}/adios2-2.8.3:$CMAKE_PREFIX_PATH
-export PATH=${SW_DIR}/adios2-2.8.3/bin:${PATH}
+export CMAKE_PREFIX_PATH=${SW_DIR}/install/c-blosc-1.21.6:$CMAKE_PREFIX_PATH
+export CMAKE_PREFIX_PATH=${SW_DIR}/install/adios2-2.8.3:$CMAKE_PREFIX_PATH
+export PATH=${SW_DIR}/install/adios2-2.8.3/bin:${PATH}
 
 # optional: for PSATD in RZ geometry support
-export CMAKE_PREFIX_PATH=${SW_DIR}/blaspp-2024.10.26:$CMAKE_PREFIX_PATH
-export CMAKE_PREFIX_PATH=${SW_DIR}/lapackpp-2024.10.26:$CMAKE_PREFIX_PATH
-export LD_LIBRARY_PATH=${SW_DIR}/blaspp-2024.10.26/lib64:$LD_LIBRARY_PATH
-export LD_LIBRARY_PATH=${SW_DIR}/lapackpp-2024.10.26/lib64:$LD_LIBRARY_PATH
+export CMAKE_PREFIX_PATH=${SW_DIR}/install/blaspp-2024.10.26:$CMAKE_PREFIX_PATH
+export CMAKE_PREFIX_PATH=${SW_DIR}/install/lapackpp-2024.10.26:$CMAKE_PREFIX_PATH
+export LD_LIBRARY_PATH=${SW_DIR}/install/blaspp-2024.10.26/lib64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=${SW_DIR}/install/lapackpp-2024.10.26/lib64:$LD_LIBRARY_PATH
 
 # optional: for Python bindings
 module load python/3.12.2

Tools/machines/dane-llnl/install_dependencies.sh

@@ -18,11 +18,11 @@ set -eu -o pipefail
 if [ -z ${proj-} ]; then echo "WARNING: The 'proj' variable is not yet set in your dane_warpx.profile file! Please edit its line 2 to continue!"; exit 1; fi
 
 
-# Remove old dependencies #####################################################
+# The src directory should have already been created when cloning WarpX #######
 #
 SW_DIR="/usr/workspace/${USER}/dane"
-rm -rf ${SW_DIR}
-mkdir -p ${SW_DIR}
+rm -rf ${SW_DIR}/install
+mkdir -p ${SW_DIR}/install
 
 # remove common user mistakes in python, located in .local instead of a venv
 python3 -m pip uninstall -qq -y pywarpx
@@ -37,55 +37,55 @@ python3 -m pip uninstall -qqq -y mpi4py 2>/dev/null || true
 build_dir=$(mktemp -d)
 
 # c-blosc (I/O compression)
-if [ -d ${HOME}/src/c-blosc ]
+if [ -d ${SW_DIR}/src/c-blosc ]
 then
-  cd ${HOME}/src/c-blosc
+  cd ${SW_DIR}/src/c-blosc
   git fetch --prune
   git checkout v1.21.6
   cd -
 else
-  git clone -b v1.21.6 https://github.com/Blosc/c-blosc.git ${HOME}/src/c-blosc
+  git clone -b v1.21.6 https://github.com/Blosc/c-blosc.git ${SW_DIR}/src/c-blosc
 fi
-cmake -S ${HOME}/src/c-blosc -B ${build_dir}/c-blosc-dane-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=${SW_DIR}/c-blosc-1.21.6
+cmake -S ${SW_DIR}/src/c-blosc -B ${build_dir}/c-blosc-dane-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=${SW_DIR}/install/c-blosc-1.21.6
 cmake --build ${build_dir}/c-blosc-dane-build --target install --parallel 6
 
 # ADIOS2
-if [ -d ${HOME}/src/adios2 ]
+if [ -d ${SW_DIR}/src/adios2 ]
 then
-  cd ${HOME}/src/adios2
+  cd ${SW_DIR}/src/adios2
   git fetch --prune
   git checkout v2.8.3
   cd -
 else
-  git clone -b v2.8.3 https://github.com/ornladios/ADIOS2.git ${HOME}/src/adios2
+  git clone -b v2.8.3 https://github.com/ornladios/ADIOS2.git ${SW_DIR}/src/adios2
 fi
-cmake -S ${HOME}/src/adios2 -B ${build_dir}/adios2-dane-build -DBUILD_TESTING=OFF -DADIOS2_BUILD_EXAMPLES=OFF -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_SST=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=${SW_DIR}/adios2-2.8.3
+cmake -S ${SW_DIR}/src/adios2 -B ${build_dir}/adios2-dane-build -DBUILD_TESTING=OFF -DADIOS2_BUILD_EXAMPLES=OFF -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_SST=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=${SW_DIR}/install/adios2-2.8.3
 cmake --build ${build_dir}/adios2-dane-build --target install -j 6
 
 # BLAS++ (for PSATD+RZ)
-if [ -d ${HOME}/src/blaspp ]
+if [ -d ${SW_DIR}/src/blaspp ]
 then
-  cd ${HOME}/src/blaspp
+  cd ${SW_DIR}/src/blaspp
   git fetch --prune
   git checkout v2024.10.26
   cd -
 else
-  git clone -b v2024.10.26 https://github.com/icl-utk-edu/blaspp.git ${HOME}/src/blaspp
+  git clone -b v2024.10.26 https://github.com/icl-utk-edu/blaspp.git ${SW_DIR}/src/blaspp
 fi
-cmake -S ${HOME}/src/blaspp -B ${build_dir}/blaspp-dane-build -Duse_openmp=ON -Duse_cmake_find_blas=ON -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=${SW_DIR}/blaspp-2024.10.26
+cmake -S ${SW_DIR}/src/blaspp -B ${build_dir}/blaspp-dane-build -Duse_openmp=ON -Duse_cmake_find_blas=ON -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=${SW_DIR}/install/blaspp-2024.10.26
 cmake --build ${build_dir}/blaspp-dane-build --target install --parallel 6
 
 # LAPACK++ (for PSATD+RZ)
-if [ -d ${HOME}/src/lapackpp ]
+if [ -d ${SW_DIR}/src/lapackpp ]
 then
-  cd ${HOME}/src/lapackpp
+  cd ${SW_DIR}/src/lapackpp
   git fetch --prune
   git checkout v2024.10.26
   cd -
 else
-  git clone -b v2024.10.26 https://github.com/icl-utk-edu/lapackpp.git ${HOME}/src/lapackpp
+  git clone -b v2024.10.26 https://github.com/icl-utk-edu/lapackpp.git ${SW_DIR}/src/lapackpp
 fi
-CXXFLAGS="-DLAPACK_FORTRAN_ADD_" cmake -S ${HOME}/src/lapackpp -B ${build_dir}/lapackpp-dane-build -Duse_cmake_find_lapack=ON -DCMAKE_CXX_STANDARD=17 -Dbuild_tests=OFF -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON -DCMAKE_INSTALL_PREFIX=${SW_DIR}/lapackpp-2024.10.26
+CXXFLAGS="-DLAPACK_FORTRAN_ADD_" cmake -S ${SW_DIR}/src/lapackpp -B ${build_dir}/lapackpp-dane-build -Duse_cmake_find_lapack=ON -DCMAKE_CXX_STANDARD=17 -Dbuild_tests=OFF -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON -DCMAKE_INSTALL_PREFIX=${SW_DIR}/install/lapackpp-2024.10.26
 cmake --build ${build_dir}/lapackpp-dane-build --target install --parallel 6
 
 
@@ -111,7 +111,7 @@ python3 -m pip install --upgrade matplotlib
 python3 -m pip install --upgrade yt
 
 # install or update WarpX dependencies such as picmistandard
-python3 -m pip install --upgrade -r ${HOME}/src/warpx/requirements.txt
+python3 -m pip install --upgrade -r ${SW_DIR}/src/warpx/requirements.txt
 
 # ML dependencies
 python3 -m pip install --upgrade torch