Merge branch 'develop' into fix-elpa

source/module_base/sph_bessel_recursive.h

@@ -7,7 +7,7 @@
 #define SPH_BESSEL_RECURSIVE_H
 
 #include <vector>
-#include"stddef.h"
+#include<cstddef>
 
 namespace ModuleBase
 {
@@ -32,7 +32,7 @@ class Sph_Bessel_Recursive::D1
 
 private:
 	std::vector<std::vector<double>> jlx;		// jlx[l][x]
-	double dx;
+	double dx = 0.0;
 	bool finish_set_dx = false;
 
 	void cal_jlx_0( const int l_size );
@@ -56,7 +56,7 @@ class Sph_Bessel_Recursive::D2
 
 private:
 	std::vector<std::vector<std::vector<double>>> jlx;		// jlx[l][x1][x2]
-	double dx;
+	double dx = 0.0;
 	bool finish_set_dx = false;
 
 	void cal_jlx_0( const int l_size, const size_t ix1_size, const size_t ix2_size );

toolchain/README.md

@@ -1,6 +1,6 @@
 # The ABACUS Toolchain
 
-Version 2024.2
+Version 2024.3
 
 ## Author
 
@@ -108,13 +108,13 @@ The needed dependencies version default:
 
 - `cmake` 3.30.0
 - `gcc` 13.2.0 (which will always NOT be installed, But use system)
-- `OpenMPI` 5.0.5
+- `OpenMPI` 4.1.6 (5.0.5 can be used but have some problem in OpenMP parallel computation in ELPA)
 - `MPICH` 4.2.2
-- `OpenBLAS` 0.3.27 (Intel toolchain need `get_vars.sh` tool from it)
-- `ScaLAPACK` 2.2.1
+- `OpenBLAS` 0.3.28 (Intel toolchain need `get_vars.sh` tool from it)
+- `ScaLAPACK` 2.2.1 (a developing version)
 - `FFTW` 3.3.10
 - `LibXC` 6.2.2
-- `ELPA` 2024.03.001
+- `ELPA` 2024.05.001
 - `CEREAL` 1.3.2
 - `RapidJSON` 1.1.0
 And Intel-oneAPI need user or server manager to manually install from Intel.

toolchain/build_abacus_gnu.sh

@@ -28,6 +28,7 @@ ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 FFTW3=$INSTALL_DIR/fftw-3.3.10
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
+RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
 # LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
@@ -47,7 +48,8 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
-        -DENABLE_RAPIDJSON=OFF \
+        -DENABLE_RAPIDJSON=ON \
+        -DRapdidJSON_DIR=$RAPIDJSON \
 #         -DENABLE_DEEPKS=1 \
 #         -DTorch_DIR=$LIBTORCH \
 #         -Dlibnpy_INCLUDE_DIR=$LIBNPY \

toolchain/build_abacus_intel-mpich.sh

@@ -26,6 +26,7 @@ PREFIX=$ABACUS_DIR
 ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
+RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
@@ -43,7 +44,8 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
-        -DENABLE_RAPIDJSON=OFF \
+        -DENABLE_RAPIDJSON=ON \
+        -DRapdidJSON_DIR=$RAPIDJSON \
 #       -DENABLE_DEEPKS=1 \
 #       -DTorch_DIR=$LIBTORCH \
 #       -Dlibnpy_INCLUDE_DIR=$LIBNPY \

toolchain/build_abacus_intel.sh

@@ -26,6 +26,7 @@ PREFIX=$ABACUS_DIR
 ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
+RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
@@ -44,7 +45,8 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
-        -DENABLE_RAPIDJSON=OFF \
+        -DENABLE_RAPIDJSON=ON \
+        -DRapdidJSON_DIR=$RAPIDJSON \
 #         -DENABLE_DEEPKS=1 \
 #         -DTorch_DIR=$LIBTORCH \
 #         -Dlibnpy_INCLUDE_DIR=$LIBNPY \

toolchain/scripts/VERSION

@@ -1,2 +1,2 @@
 # version file to force a rebuild of the entire toolchain
-VERSION="2024.2"
+VERSION="2024.3"

toolchain/scripts/get_openblas_arch.sh

@@ -8,8 +8,8 @@
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"
 
-openblas_ver="0.3.27" # Keep in sync with install_openblas.sh
-openblas_sha256="aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897"
+openblas_ver="0.3.28" # Keep in sync with install_openblas.sh
+openblas_sha256="f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1"
 openblas_pkg="OpenBLAS-${openblas_ver}.tar.gz"
 
 source "${SCRIPT_DIR}"/common_vars.sh

toolchain/scripts/stage0/install_cmake.sh

@@ -36,17 +36,18 @@ case "${with_cmake}" in
     pkg_install_dir="${INSTALLDIR}/cmake-${cmake_ver}"
     #pkg_install_dir="${HOME}/apps/cmake/${cmake_ver}"
     install_lock_file="$pkg_install_dir/install_successful"
+    cmake_pkg="cmake-${cmake_ver}-${cmake_arch}.sh"
     if verify_checksums "${install_lock_file}"; then
       echo "cmake-${cmake_ver} is already installed, skipping it."
     else
-      if [ -f cmake-${cmake_ver}-${cmake_arch}.sh ]; then
-        echo "cmake-${cmake_ver}-${cmake_arch}.sh is found"
+      if [ -f $cmake_pkg ]; then
+        echo "$cmake_pkg is found"
       else
-        download_pkg_from_ABACUS_org "${cmake_sha256}" "cmake-${cmake_ver}-${cmake_arch}.sh"
+        download_pkg_from_ABACUS_org "${cmake_sha256}" "$cmake_pkg"
       fi
       echo "Installing from scratch into ${pkg_install_dir}"
       mkdir -p ${pkg_install_dir}
-      /bin/sh cmake-${cmake_ver}-${cmake_arch}.sh --prefix=${pkg_install_dir} --skip-license > install.log 2>&1 || tail -n ${LOG_LINES} install.log
+      /bin/sh $cmake_pkg --prefix=${pkg_install_dir} --skip-license > install.log 2>&1 || tail -n ${LOG_LINES} install.log
       write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage0/$(basename ${SCRIPT_NAME})"
     fi
     ;;

toolchain/scripts/stage1/install_openmpi.sh

@@ -8,10 +8,10 @@
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-openmpi_ver="5.0.5"
-openmpi_sha256="6588d57c0a4bd299a24103f4e196051b29e8b55fbda49e11d5b3d32030a32776"
-# openmpi_ver="4.1.6"
-# openmpi_sha256="f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415"
+#openmpi_ver="5.0.5"
+#openmpi_sha256="6588d57c0a4bd299a24103f4e196051b29e8b55fbda49e11d5b3d32030a32776"
+openmpi_ver="4.1.6"
+openmpi_sha256="f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415"
 openmpi_pkg="openmpi-${openmpi_ver}.tar.bz2"
 
 source "${SCRIPT_DIR}"/common_vars.sh
@@ -64,6 +64,7 @@ case "${with_openmpi}" in
     # OpenMPI 5.0 only supports PMIx
     # PMI support is required for Slurm, but not for other schedulers
     # default not use
+    # for OpenMPI 4.1 with pmi slurm, we can open this setting manually
     #   if [ $(command -v srun) ]; then
     #     echo "Slurm installation found. OpenMPI will be configured with --with-pmi."
     #     EXTRA_CONFIGURE_FLAGS="--with-pmi"

toolchain/scripts/stage2/install_openblas.sh

@@ -8,8 +8,8 @@
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-openblas_ver="0.3.27" # Keep in sync with get_openblas_arch.sh
-openblas_sha256="aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897"
+openblas_ver="0.3.28" # Keep in sync with get_openblas_arch.sh
+openblas_sha256="f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1"
 openblas_pkg="OpenBLAS-${openblas_ver}.tar.gz"
 
 source "${SCRIPT_DIR}"/common_vars.sh

toolchain/scripts/stage3/install_elpa.sh

@@ -9,8 +9,8 @@
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
 # From https://elpa.mpcdf.mpg.de/software/tarball-archive/ELPA_TARBALL_ARCHIVE.html
-elpa_ver="2024.03.001"
-elpa_sha256="41c6cbf56d2dac26443faaba8a77307d261bf511682a64b96e24def77c813622"
+elpa_ver="2024.05.001"
+elpa_sha256="9caf41a3e600e2f6f4ce1931bd54185179dade9c171556d0c9b41bbc6940f2f6"
 
 
 source "${SCRIPT_DIR}"/common_vars.sh
@@ -59,13 +59,15 @@ case "$with_elpa" in
       echo "elpa-${elpa_ver} is already installed, skipping it."
     else
       require_env MATH_LIBS
-      if [ -f elpa-${elpa_ver}.tar.gz ]; then
-        echo "elpa-${elpa_ver}.tar.gz is found"
+      elpa_pkg="elpa-${elpa_ver}.tar.gz"
+      url=f"https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/${elpa_ver}/${elpa_pkg}"
+      if [ -f ${elpa_pkg} ]; then
+        echo "${elpa_pkg} is found"
       else
-        download_pkg_from_ABACUS_org "${elpa_sha256}" "elpa-${elpa_ver}.tar.gz"
+        download_pkg_from_url "${elpa_sha256}" "${elpa_pkg}" "${url}"
       fi
       [ -d elpa-${elpa_ver} ] && rm -rf elpa-${elpa_ver}
-      tar -xzf elpa-${elpa_ver}.tar.gz
+      tar -xzf ${elpa_pkg}
 
       # elpa expect FC to be an mpi fortran compiler that is happy
       # with long lines, and that a bunch of libs can be found

toolchain/scripts/stage4/install_rapidjson.sh

@@ -55,6 +55,8 @@ case "$with_rapidjson" in
         tar -xzf $filename
         mkdir -p "${pkg_install_dir}"
         cp -r $dirname/* "${pkg_install_dir}/"
+        # for CMake to find rapidjson
+        cp ${pkg_install_dir}/RapidJSONConfig.cmake.in ${pkg_install_dir}/RapidJSONConfig.cmake
         write_checksums "${install_lock_file}" "${SCRIPT_DIR}/stage4/$(basename ${SCRIPT_NAME})"
     fi
         ;;