Enable direct reading of UPF version >= 2 PP files (#980)

* Enable direct reading of UPF version >= 2 PP files

* update spack in cscs-ci

* use local spack recipe for cscs-ci

* Fix github CI

* increase timeout

* 4h -> 10h

---------

Co-authored-by: Simon Pintarelli <[email protected]>

Author: abussy

.github/workflows/build.yml

@@ -21,7 +21,7 @@ jobs:
           cd ${GITHUB_WORKSPACE}
           mkdir build
           cd build
-          spack --color always build-env $DEVSPEC -- cmake .. -DSIRIUS_USE_SCALAPACK=1 -DSIRIUS_USE_VDWXC=1 -DBUILD_TESTING=1 -DSIRIUS_CREATE_FORTRAN_BINDINGS=1 -DSIRIUS_CREATE_PYTHON_MODULE=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/sirius_install
+          spack --color always build-env $DEVSPEC -- cmake .. -DSIRIUS_USE_SCALAPACK=1 -DSIRIUS_USE_VDWXC=1 -DBUILD_TESTING=1 -DSIRIUS_CREATE_FORTRAN_BINDINGS=1 -DSIRIUS_CREATE_PYTHON_MODULE=1 -DSIRIUS_USE_PUGIXML=1 -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/sirius_install
       - name: Build SIRIUS
         run: |
           cd ${GITHUB_WORKSPACE}/build

CMakeLists.txt

@@ -32,6 +32,7 @@ option(SIRIUS_BUILD_APPS              "build apps" ON)
 option(SIRIUS_USE_OPENMP              "use OpenMP" ON)
 option(SIRIUS_USE_PROFILER            "measure execution of functions with timer" ON)
 option(SIRIUS_USE_MEMORY_POOL         "use memory pool" ON)
+option(SIRIUS_USE_PUGIXML             "enable reading of UPF v2 files with pugixml" OFF)
 option(SIRIUS_USE_POWER_COUNTER       "measure energy consumption with power counters" OFF)
 option(BUILD_TESTING                  "build test executables" OFF) # override default setting in CTest module
 option(SIRIUS_USE_VCSQNM              "use variable cell stabilized quasi Newton method" OFF)
@@ -135,6 +136,10 @@ include(cmake/hdf5_target.cmake)
 find_package(SpFFT 1.0.2 CONFIG REQUIRED)
 find_package(SPLA 1.4.0 CONFIG REQUIRED)
 
+if (SIRIUS_USE_PUGIXML)
+   find_package(pugixml REQUIRED)
+endif()
+
 # Check if SpFFT support single precision if required
 if(NOT SIRIUS_USE_FP32 STREQUAL "OFF")
   if(SPFFT_SINGLE_PRECISION)

ci/baseimage.cuda.Dockerfile

@@ -27,7 +27,11 @@ RUN wget https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cm
     tar zxvf cmake.tar.gz --strip-components=1 -C /usr
 
 # get latest version of spack
-RUN git clone -b v0.21.0 https://github.com/spack/spack.git
+RUN git clone -b v0.21.2 https://github.com/spack/spack.git
+
+# add local repo to spack
+COPY ./spack /opt/spack
+RUN spack repo add --scope system /opt/spack
 
 # set the location of packages built by spack
 RUN spack config add config:install_tree:root:/opt/local
@@ -71,46 +75,46 @@ RUN ldconfig
 
 # create environments for several configurations and install dependencies
 RUN spack env create -d /sirius-env-clang && \
-    spack -e /sirius-env-clang add "sirius@develop %clang build_type=RelWithDebInfo ~cuda ~fortran +tests ^openblas%gcc ^libxc%gcc ^mpich%gcc " && \
+    spack -e /sirius-env-clang add "sirius@develop %clang build_type=RelWithDebInfo ~cuda ~fortran +tests +pugixml ^openblas%gcc ^libxc%gcc ^mpich%gcc " && \
     spack -e /sirius-env-clang develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-clang install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-cuda && \
-    spack -e /sirius-env-cuda add "sirius@develop %gcc build_type=RelWithDebInfo +scalapack +tests +apps +cuda +magma +python ^netlib-scalapack ^mpich ^openblas threads=openmp" && \
+    spack -e /sirius-env-cuda add "sirius@develop %gcc build_type=RelWithDebInfo +scalapack +tests +pugixml +apps +cuda +magma +python ^netlib-scalapack ^mpich ^openblas threads=openmp" && \
     spack -e /sirius-env-cuda develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-cuda install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-cuda-mkl-mpich && \
-    spack -e /sirius-env-cuda-mkl-mpich add "sirius@develop %gcc build_type=RelWithDebInfo +tests +apps +cuda +scalapack +magma ^mpich ^intel-oneapi-mkl+cluster" && \
+    spack -e /sirius-env-cuda-mkl-mpich add "sirius@develop %gcc build_type=RelWithDebInfo +tests +pugixml +apps +cuda +scalapack +magma ^mpich ^intel-oneapi-mkl+cluster" && \
     spack -e /sirius-env-cuda-mkl-mpich develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-cuda-mkl-mpich install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-elpa && \
-    spack -e /sirius-env-elpa add "sirius@develop %gcc build_type=RelWithDebInfo +tests +apps +cuda +scalapack +elpa ^netlib-scalapack ^mpich ^openblas ^elpa+cuda" && \
+    spack -e /sirius-env-elpa add "sirius@develop %gcc build_type=RelWithDebInfo +tests +pugixml +apps +cuda +scalapack +elpa ^netlib-scalapack ^mpich ^openblas ^elpa+cuda" && \
     spack -e /sirius-env-elpa develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-elpa install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-fp32 && \
-    spack -e /sirius-env-fp32 add "sirius@develop %gcc build_type=RelWithDebInfo +tests +apps +cuda ^mpich ^openblas ^elpa+cuda ^spfft+single_precision+cuda" && \
+    spack -e /sirius-env-fp32 add "sirius@develop %gcc build_type=RelWithDebInfo +tests +pugixml +apps +cuda ^mpich ^openblas ^elpa+cuda ^spfft+single_precision+cuda" && \
     spack -e /sirius-env-fp32 develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-fp32 install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-nlcg && \
-    spack -e /sirius-env-nlcg add "sirius@develop %gcc build_type=RelWithDebInfo +fortran +tests +apps +cuda +nlcglib ^openblas ^mpich" && \
+    spack -e /sirius-env-nlcg add "sirius@develop %gcc build_type=RelWithDebInfo +fortran +tests +pugixml +apps +cuda +nlcglib ^openblas ^mpich" && \
     spack -e /sirius-env-nlcg develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-nlcg install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-openmpi && \
-    spack -e /sirius-env-openmpi add "sirius@develop %gcc +tests +apps +scalapack +fortran build_type=RelWithDebInfo ^netlib-scalapack ^openblas ^openmpi" && \
+    spack -e /sirius-env-openmpi add "sirius@develop %gcc +tests +pugixml +apps +scalapack +fortran build_type=RelWithDebInfo ^netlib-scalapack ^openblas ^openmpi" && \
     spack -e /sirius-env-openmpi develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-openmpi install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-cuda-sequential && \
-    spack -e /sirius-env-cuda-sequential add "sirius@develop %gcc +cuda +tests +apps +fortran build_type=RelWithDebInfo ^openblas ^openmpi" && \
+    spack -e /sirius-env-cuda-sequential add "sirius@develop %gcc +cuda +tests +pugixml +apps +fortran build_type=RelWithDebInfo ^openblas ^openmpi" && \
     spack -e /sirius-env-cuda-sequential develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-cuda-sequential install --only=dependencies --fail-fast
 
 RUN spack env create -d /sirius-env-vdwxc-cuda && \
-    spack -e /sirius-env-vdwxc-cuda add "sirius@develop %gcc build_type=RelWithDebInfo +fortran +tests +apps +vdwxc +cuda +nlcglib ^openblas ^mpich +cuda" && \
+    spack -e /sirius-env-vdwxc-cuda add "sirius@develop %gcc build_type=RelWithDebInfo +fortran +tests +pugixml +apps +vdwxc +cuda +nlcglib ^openblas ^mpich +cuda" && \
     spack -e /sirius-env-vdwxc-cuda develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-vdwxc-cuda install --only=dependencies --fail-fast

ci/baseimage.rocm.Dockerfile

@@ -23,7 +23,11 @@ RUN wget https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cm
     tar zxvf cmake.tar.gz --strip-components=1 -C /usr
 
 # get latest version of spack
-RUN git clone -b v0.21.0 https://github.com/spack/spack.git
+RUN git clone -b v0.21.2 https://github.com/spack/spack.git
+
+# add local repo to spack
+COPY ./spack /opt/spack
+RUN spack repo add --scope system /opt/spack
 
 # set the location of packages built by spack
 RUN spack config add config:install_tree:root:/opt/local
@@ -45,6 +49,6 @@ RUN spack install --fail-fast rocsolver%gcc
 RUN spack install --fail-fast hipfft%gcc
 
 RUN spack env create -d /sirius-env-rocm && \
-    spack -e /sirius-env-rocm add "sirius@develop %gcc build_type=Release +scalapack +fortran +tests +rocm ^openblas ^mpich ^spfft ^umpire+rocm~device_alloc" && \
+    spack -e /sirius-env-rocm add "sirius@develop %gcc build_type=Release +scalapack +fortran +tests +pugixml +rocm ^openblas ^mpich ^spfft ^umpire+rocm~device_alloc" && \
     spack -e /sirius-env-rocm develop -p /sirius-src sirius@develop && \
     spack -e /sirius-env-rocm install --only=dependencies --fail-fast

ci/cscs-daint.yml

@@ -9,7 +9,7 @@ stages:
 build base cuda image:
   extends: .container-builder-dynamic-name
   stage: baseimage
-  timeout: 2h
+  timeout: 10h
   variables:
     DOCKERFILE: ci/baseimage.cuda.Dockerfile
     WATCH_FILECHANGES: ci/baseimage.cuda.Dockerfile

spack/packages/sirius/package.py

@@ -108,6 +108,11 @@ class Sirius(CMakePackage, CudaPackage, ROCmPackage):
     )
     variant("nvtx", default=False, description="Use NVTX profiler")
 
+    with when("@7.6:"): 
+        variant("pugixml", default=False, description="Enable direct reading of UPF v2 pseudopotentials")
+        conflicts("+tests~pugixml")
+    depends_on("pugixml", when="+pugixml")
+
     depends_on("[email protected]:", type="build")
     depends_on("mpi")
     depends_on("gsl")
@@ -226,6 +231,7 @@ def cmake_args(self):
             self.define_from_variant(cm_label + "USE_PROFILER", "profiler"),
             self.define_from_variant(cm_label + "USE_NVTX", "nvtx"),
             self.define_from_variant(cm_label + "USE_WANNIER90", "wannier90"),
+            self.define_from_variant(cm_label + "USE_PUGIXML", "pugixml"),
             self.define_from_variant("BUILD_SHARED_LIBS", "shared"),
             self.define_from_variant("BUILD_TESTING", "tests"),
         ]

src/CMakeLists.txt

@@ -117,6 +117,7 @@ target_link_libraries(sirius_cxx PUBLIC ${GSL_LIBRARY}
   SpFFT::spfft
   SPLA::spla
   "${SIRIUS_LINALG_LIB}"
+  $<$<BOOL:${SIRIUS_USE_PUGIXML}>:pugixml::pugixml>
   $<$<BOOL:${SIRIUS_USE_MEMORY_POOL}>:umpire>
   $<$<BOOL:${SIRIUS_USE_NVTX}>:nvToolsExt>
   $<TARGET_NAME_IF_EXISTS:sirius::cudalibs>
@@ -141,6 +142,7 @@ target_compile_definitions(sirius_cxx PUBLIC
   $<$<BOOL:${SIRIUS_USE_MAGMA}>:SIRIUS_MAGMA>
   $<$<BOOL:${SIRIUS_USE_ROCM}>:SIRIUS_GPU SIRIUS_ROCM>
   $<$<BOOL:${SIRIUS_USE_VDWXC}>:SIRIUS_USE_VDWXC>
+  $<$<BOOL:${SIRIUS_USE_PUGIXML}>:SIRIUS_USE_PUGIXML>
   $<$<BOOL:${SIRIUS_USE_FP32_BOOL}>:SIRIUS_USE_FP32>
   $<$<BOOL:${SIRIUS_USE_VCSQNM}>:SIRIUS_VCSQNM>
   $<$<BOOL:${SIRIUS_HAVE_LIBVDW_WITH_MPI}>:SIRIUS_HAVE_VDWXC_MPI>