Toolchain 202402 (#4945)

* basic toolchain update - remove ACML support - update dependence version - try to update scalapack for gcc-14 - tag libri 0.2.0 - enable rapidjson in build scripts (but not as default) * Update README.md * Version 2024.2 tag * Update install_elpa.sh * enable rapidjson as default in toolchain usage * fix #4601 for scalapack * modify export * reverse gcc default version to 13.2.0 * remove redundant option * update libtorch version and downloading * Update README.md * formatting * update database version * update v3 database link
abacusmodeling · Aug 12, 2024 · eaf27f8 · eaf27f8
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diff --git a/toolchain/README.md b/toolchain/README.md
@@ -1,5 +1,5 @@
 # The ABACUS Toolchain
-Version 2024.1
+Version 2024.2
 
 ## Author
 [QuantumMisaka](https://github.com/QuantumMisaka) 
@@ -19,7 +19,7 @@ and give setup files that you can use to compile ABACUS.
 ## Todo
 
 - [x] `gnu-openblas` toolchain support for `openmpi` and `mpich`.
-- [x] `intel-mkl-mpi` toolchain support using `icc` or `icx`. (`icx` version of ABACUS have some problem now, please be cautious)
+- [x] `intel-mkl-mpi` toolchain support using `icc`/`icpc`/`ifort` or `icx`/`icpx`/`ifort`. (`icx` as default, but will have problem for ELPA in AMD machine, one can specify `--with-intel-classic=yes` to use `icc`), 
 - [x] `intel-mkl-mpich` toolchain support.
 - [x] Automatic installation of [CEREAL](https://github.com/USCiLab/cereal) and [LIBNPY](https://github.com/llohse/libnpy) (by github.com)
 - [x] Support for [LibRI](https://github.com/abacusmodeling/LibRI) by submodule or automatic installation from github.com (but installed LibRI via `wget` seems to have some problem, please be cautious)
@@ -75,14 +75,14 @@ Notice: These packages will be downloaded by `wget` from `github.com`, which is
 
 Instead of github.com, we offer other package station, you can use it by:
 ```shell
-wget https://bohrium-api.dp.tech/ds-dl/abacus-deps-93wi-v2 -O abacus-deps-v2.zip
+wget https://bohrium-api.dp.tech/ds-dl/abacus-deps-93wi-v3 -O abacus-deps-v3.zip
 ```
 `unzip` it ,and you can do offline installation of these packages above after rename. The above station will be updated handly but one should notice that the version will always lower than github repo.
 
 If one want to install ABACUS by toolchain OFFLINE, 
 one can manually download all the packages from [cp2k-static/download](https://www.cp2k.org/static/downloads) or official website
 and put them in *build* directory by formatted name
-like *fftw-3.3.10.tar.gz*, or *openmpi-4.1.5.tar.gz*, 
+like *fftw-3.3.10.tar.gz*, or *openmpi-5.0.3.tar.gz*, 
 then run this toolchain. 
 All package will be detected and installed automatically. 
 Also, one can install parts of packages OFFLINE and parts of packages ONLINE
@@ -96,22 +96,22 @@ just by using this toolchain
 ```
 
 The needed dependencies version default:
-- `cmake` 3.28.1
+- `cmake` 3.30.0
 - `gcc` 13.2.0 (which will always NOT be installed, But use system)
-- `OpenMPI` 5.0.0
+- `OpenMPI` 5.0.3
 - `MPICH` 4.1.2
-- `OpenBLAS` 0.3.25 (Intel toolchain need `get_vars.sh` tool from it)
+- `OpenBLAS` 0.3.27 (Intel toolchain need `get_vars.sh` tool from it)
 - `ScaLAPACK` 2.2.1
 - `FFTW` 3.3.10
 - `LibXC` 6.2.2
-- `ELPA` 2023.05.001
+- `ELPA` 2024.03.001
 - `CEREAL` 1.3.2
 - `RapidJSON` 1.1.0
 And Intel-oneAPI need user or server manager to manually install from Intel.
 [Intel-oneAPI](https://www.intel.cn/content/www/cn/zh/developer/tools/oneapi/toolkits.html)
 
 Dependencies below are optional， which is NOT installed by default:
-- `LibTorch` 2.0.1
+- `LibTorch` 2.1.2
 - `Libnpy` 1.0.1
 - `LibRI` 0.1.1
 - `LibComm` 0.1.0

diff --git a/toolchain/build_abacus_gnu.sh b/toolchain/build_abacus_gnu.sh
@@ -22,15 +22,15 @@ BUILD_DIR=build_abacus_gnu
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-LAPACK=$INSTALL_DIR/openblas-0.3.25/lib
+LAPACK=$INSTALL_DIR/openblas-0.3.27/lib
 SCALAPACK=$INSTALL_DIR/scalapack-2.2.1/lib
-ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 FFTW3=$INSTALL_DIR/fftw-3.3.10
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
-# LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
+# LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # DEEPMD=$HOME/apps/anaconda3/envs/deepmd
 
@@ -47,6 +47,7 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
+        -DENABLE_RAPIDJSON=ON \
 #         -DENABLE_DEEPKS=1 \
 #         -DTorch_DIR=$LIBTORCH \
 #         -Dlibnpy_INCLUDE_DIR=$LIBNPY \
@@ -55,7 +56,7 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 #         -DLIBCOMM_DIR=$LIBCOMM \
 # 	      -DDeePMD_DIR=$DEEPMD \
 # 	      -DTensorFlow_DIR=$DEEPMD \
-#         -DENABLE_RAPIDJSON=ON \
+
 
 # # add mkl env for libtorch to link
 # if one want to install libtorch, mkl should be load in build process

diff --git a/toolchain/build_abacus_intel-mpich.sh b/toolchain/build_abacus_intel-mpich.sh
@@ -23,10 +23,10 @@ BUILD_DIR=build_abacus_intel-mpich
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
-# LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
+# LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
@@ -43,15 +43,16 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
-        # -DENABLE_DEEPKS=1 \
-        # -DTorch_DIR=$LIBTORCH \
-        # -Dlibnpy_INCLUDE_DIR=$LIBNPY \
-        # -DENABLE_LIBRI=ON \
-        # -DLIBRI_DIR=$LIBRI \
-        # -DLIBCOMM_DIR=$LIBCOMM \
-	    # -DDeePMD_DIR=$DEEPMD \
-	    # -DTensorFlow_DIR=$DEEPMD \
-#         -DENABLE_RAPIDJSON=ON \
+        -DENABLE_RAPIDJSON=ON \
+#       -DENABLE_DEEPKS=1 \
+#       -DTorch_DIR=$LIBTORCH \
+#       -Dlibnpy_INCLUDE_DIR=$LIBNPY \
+#       -DENABLE_LIBRI=ON \
+#       -DLIBRI_DIR=$LIBRI \
+#       -DLIBCOMM_DIR=$LIBCOMM \
+#       -DDeePMD_DIR=$DEEPMD \
+#       -DTensorFlow_DIR=$DEEPMD \
+
 
 # if one want's to include deepmd, your gcc version should be >= 11.3.0
 

diff --git a/toolchain/build_abacus_intel.sh b/toolchain/build_abacus_intel.sh
@@ -23,10 +23,10 @@ BUILD_DIR=build_abacus_intel
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2024.03.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
-# LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
+# LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.1
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
@@ -44,6 +44,7 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
         -DUSE_ELPA=ON \
+        -DENABLE_RAPIDJSON=ON \
 #         -DENABLE_DEEPKS=1 \
 #         -DTorch_DIR=$LIBTORCH \
 #         -Dlibnpy_INCLUDE_DIR=$LIBNPY \
@@ -52,7 +53,7 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 #         -DLIBCOMM_DIR=$LIBCOMM \
 # 	      -DDeePMD_DIR=$DEEPMD \
 # 	      -DTensorFlow_DIR=$DEEPMD \
-#         -DENABLE_RAPIDJSON=ON \
+
 
 cmake --build $BUILD_DIR -j `nproc` 
 cmake --install $BUILD_DIR 2>/dev/null

diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
@@ -171,8 +171,6 @@ The --with-PKG options follow the rules:
                           Default = install
   --with-fftw             FFTW3, library for fast fourier transform
                           Default = install
-  --with-acml             AMD core maths library, which provides LAPACK and BLAS
-                          Default = system
   --with-mkl              Intel Math Kernel Library, which provides LAPACK, and BLAS.
                           If MKL's FFTW3 interface is suitable (no FFTW-MPI support),
                           it replaces the FFTW library. If the ScaLAPACK component is

diff --git a/toolchain/scripts/VERSION b/toolchain/scripts/VERSION
@@ -1,2 +1,2 @@
 # version file to force a rebuild of the entire toolchain
-VERSION="2024.1"
+VERSION="2024.2"
diff --git a/toolchain/scripts/get_openblas_arch.sh b/toolchain/scripts/get_openblas_arch.sh
@@ -3,13 +3,13 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0219
+# Last Update in 2024-0811
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")" && pwd -P)"
 
-openblas_ver="0.3.25" # Keep in sync with install_openblas.sh
-openblas_sha256="4c25cb30c4bb23eddca05d7d0a85997b8db6144f5464ba7f8c09ce91e2f35543"
+openblas_ver="0.3.27" # Keep in sync with install_openblas.sh
+openblas_sha256="aa2d68b1564fe2b13bc292672608e9cdeeeb6dc34995512e65c3b10f4599e897"
 openblas_pkg="OpenBLAS-${openblas_ver}.tar.gz"
 
 source "${SCRIPT_DIR}"/common_vars.sh

diff --git a/toolchain/scripts/stage0/install_cmake.sh b/toolchain/scripts/stage0/install_cmake.sh
@@ -3,7 +3,7 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0219
+# Last Update in 2024-0811
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
@@ -21,13 +21,13 @@ cd "${BUILDDIR}"
 case "${with_cmake}" in
   __INSTALL__)
     echo "==================== Installing CMake ===================="
-    cmake_ver="3.28.1"
+    cmake_ver="3.30.0"
     if [ "${OPENBLAS_ARCH}" = "arm64" ]; then
       cmake_arch="linux-aarch64"
-      cmake_sha256="4ecba78ef9499a973d012a83feab5f888e86fc5388e9a768037ab4f7232cab16"
+      cmake_sha256="daa89552fd9102fb70399b31b5605c4f61125023bbbed947757a7b53ce36c4d0"
     elif [ "${OPENBLAS_ARCH}" = "x86_64" ]; then
       cmake_arch="linux-x86_64"
-      cmake_sha256="ada6a46be9da5f8cbeb00b9523ffe45ee6b36172eb81aaa5bdc6a2a8231b677c"
+      cmake_sha256="1a5969fe81fea6e5220d053d9d3e3754cbc85be07d2d428bebdcfe87137971a9"
     else
       report_error ${LINENO} \
         "cmake installation for ARCH=${ARCH} is not supported. You can try to use the system installation using the flag --with-cmake=system instead."
@@ -67,7 +67,7 @@ if [ "${with_cmake}" != "__DONTUSE__" ]; then
   if [ "${with_cmake}" != "__SYSTEM__" ]; then
     cat << EOF > "${BUILDDIR}/setup_cmake"
 prepend_path PATH "${pkg_install_dir}/bin"
-export PATH="${pkg_install_dir}/bin:":\${PATH}
+export PATH="${pkg_install_dir}/bin":\${PATH}
 EOF
     cat "${BUILDDIR}/setup_cmake" >> $SETUPFILE
   fi

diff --git a/toolchain/scripts/stage0/install_gcc.sh b/toolchain/scripts/stage0/install_gcc.sh
@@ -3,13 +3,16 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2023-1111
+# Last Update in 2024-0811
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
-
+# gcc 13 is good
 gcc_ver="13.2.0"
 gcc_sha256="8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078"
+# use gcc 14 with caution
+#gcc_ver="14.1.0"
+#gcc_sha256="a0be066c02775002a0fa65ad3c65fb56a8bfd923d072a26ed148c0439ecdb68f"
 
 source "${SCRIPT_DIR}"/common_vars.sh
 source "${SCRIPT_DIR}"/tool_kit.sh
@@ -61,7 +64,7 @@ case "${with_gcc}" in
       # TODO: Unfortunately, we can not simply use --disable-shared, because
       # it would break OpenBLAS build and probably others too.
       COMMON_FLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g"
-      CFLAGS="${COMMON_FLAGS} -std=gnu99"
+      CFLAGS="${COMMON_FLAGS}"
       CXXFLAGS="${CFLAGS}"
       FCFLAGS="${COMMON_FLAGS} -fbacktrace"
       ${GCCROOT}/configure --prefix="${pkg_install_dir}" \

diff --git a/toolchain/scripts/stage0/install_intel.sh b/toolchain/scripts/stage0/install_intel.sh
@@ -3,7 +3,7 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2023-0901
+# Last Update in 2024-0811
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0}
 SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
@@ -56,10 +56,10 @@ case "${with_intel}" in
       check_command ${pkg_install_dir}/bin/icpc "intel" && CXX="${pkg_install_dir}/bin/icpc" || exit 1
       check_command ${pkg_install_dir}/bin/ifort "intel" && FC="${pkg_install_dir}/bin/ifort" || exit 1
     else
-    # abacus do not need icx, the key is mkl
       check_command ${pkg_install_dir}/bin/icx "intel" && CC="${pkg_install_dir}/bin/icx" || exit 1
       check_command ${pkg_install_dir}/bin/icpx "intel" && CXX="${pkg_install_dir}/bin/icpx" || exit 1
       check_command ${pkg_install_dir}/bin/ifort "intel" && FC="${pkg_install_dir}/bin/ifort" || exit 1
+      # is ifx needed ?
     fi
     F90="${FC}"
     F77="${FC}"

diff --git a/toolchain/scripts/stage1/install_openmpi.sh b/toolchain/scripts/stage1/install_openmpi.sh
@@ -3,13 +3,13 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0219
+# Last Update in 2024-0811
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-openmpi_ver="5.0.0"
-openmpi_sha256="9d845ca94bc1aeb445f83d98d238cd08f6ec7ad0f73b0f79ec1668dbfdacd613"
+openmpi_ver="5.0.3"
+openmpi_sha256="990582f206b3ab32e938aa31bbf07c639368e4405dca196fabe7f0f76eeda90b"
 openmpi_pkg="openmpi-${openmpi_ver}.tar.bz2"
 
 source "${SCRIPT_DIR}"/common_vars.sh

diff --git a/toolchain/scripts/stage2/install_acml.sh b/toolchain/scripts/stage2/install_acml.sh
diff --git a/toolchain/scripts/stage2/install_mathlibs.sh b/toolchain/scripts/stage2/install_mathlibs.sh
@@ -3,7 +3,7 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2023-0901
+# Last Update in 2024-0810
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
@@ -25,10 +25,6 @@ case "$MATH_MODE" in
     "${SCRIPTDIR}"/stage2/install_mkl.sh "${with_mkl}"
     load "${BUILDDIR}/setup_mkl"
     ;;
-  acml)
-    "${SCRIPTDIR}"/stage2/install_acml.sh "${with_acml}"
-    load "${BUILDDIR}/setup_acml"
-    ;;
   openblas)
     "${SCRIPTDIR}"/stage2/install_openblas.sh "${with_openblas}"
     load "${BUILDDIR}/setup_openblas"