From d8d23a83ac3675968d6459c92355b0aea0ce6b89 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 10:56:04 +0800
Subject: [PATCH 01/21] update cmake

---
 toolchain/scripts/stage0/install_amd.sh   | 90 +++++++++++++++++++++++
 toolchain/scripts/stage0/install_cmake.sh |  8 +-
 toolchain/scripts/stage0/install_gcc.sh   |  2 +-
 3 files changed, 95 insertions(+), 5 deletions(-)
 create mode 100755 toolchain/scripts/stage0/install_amd.sh

diff --git a/toolchain/scripts/stage0/install_amd.sh b/toolchain/scripts/stage0/install_amd.sh
new file mode 100755
index 0000000000..84fa7d9cd3
--- /dev/null
+++ b/toolchain/scripts/stage0/install_amd.sh
@@ -0,0 +1,90 @@
+#!/bin/bash -e
+
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
+[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0}
+SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
+
+source "${SCRIPT_DIR}"/common_vars.sh
+source "${SCRIPT_DIR}"/tool_kit.sh
+source "${SCRIPT_DIR}"/signal_trap.sh
+source "${INSTALLDIR}"/toolchain.conf
+source "${INSTALLDIR}"/toolchain.env
+
+[ -f "${BUILDDIR}/setup_amd" ] && rm "${BUILDDIR}/setup_amd"
+
+AMD_CFLAGS=""
+AMD_LDFLAGS=""
+AMD_LIBS=""
+mkdir -p "${BUILDDIR}"
+cd "${BUILDDIR}"
+
+case "${with_amd}" in
+  __INSTALL__)
+    echo "==================== Installing the AMD compiler ======================"
+    echo "__INSTALL__ is not supported; please install the AMD compiler manually"
+    exit 1
+    ;;
+  __SYSTEM__)
+    echo "==================== Finding AMD compiler from system paths ===================="
+    check_command clang "amd" && CC="$(realpath $(command -v clang))" || exit 1
+    check_command clang++ "amd" && CXX="$(realpath $(command -v clang++))" || exit 1
+    check_command flang "amd" && FC="$(realpath $(command -v flang))" || exit 1
+    F90="${FC}"
+    F77="${FC}"
+    ;;
+  __DONTUSE__)
+    # Nothing to do
+    ;;
+  *)
+    echo "==================== Linking AMD compiler to user paths ===================="
+    pkg_install_dir="${with_amd}"
+    check_dir "${pkg_install_dir}/bin"
+    check_dir "${pkg_install_dir}/lib"
+    check_dir "${pkg_install_dir}/include"
+    check_command ${pkg_install_dir}/bin/clang "amd" && CC="${pkg_install_dir}/bin/clang" || exit 1
+    check_command ${pkg_install_dir}/bin/clang++ "amd" && CXX="${pkg_install_dir}/bin/clang++" || exit 1
+    check_command ${pkg_install_dir}/bin/flang "amd" && FC="${pkg_install_dir}/bin/flang" || exit 1
+    F90="${FC}"
+    F77="${FC}"
+    AMD_CFLAGS="-I'${pkg_install_dir}/include'"
+    AMD_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
+    ;;
+esac
+if [ "${with_amd}" != "__DONTUSE__" ]; then
+  echo "CC  is ${CC}"
+  [ $(realpath $(command -v clang) | grep -e aocc-compiler) ] || echo "Check the AMD C compiler path"
+  echo "CXX is ${CXX}"
+  [ $(realpath $(command -v clang++) | grep -e aocc-compiler) ] || echo "Check the AMD C++ compiler path"
+  echo "FC  is ${FC}"
+  [ $(realpath $(command -v flang) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
+  cat << EOF > "${BUILDDIR}/setup_amd"
+export CC="${CC}"
+export CXX="${CXX}"
+export FC="${FC}"
+export F90="${F90}"
+export F77="${F77}"
+EOF
+  if [ "${with_amd}" != "__SYSTEM__" ]; then
+    cat << EOF >> "${BUILDDIR}/setup_amd"
+prepend_path PATH "${pkg_install_dir}/bin"
+prepend_path LD_LIBRARY_PATH "${pkg_install_dir}/lib"
+prepend_path LD_RUN_PATH "${pkg_install_dir}/lib"
+prepend_path LIBRARY_PATH "${pkg_install_dir}/lib"
+prepend_path CPATH "${pkg_install_dir}/include"
+EOF
+  fi
+  cat << EOF >> "${BUILDDIR}/setup_amd"
+export AMD_CFLAGS="${AMD_CFLAGS}"
+export AMD_LDFLAGS="${AMD_LDFLAGS}"
+export AMD_LIBS="${AMD_LIBS}"
+EOF
+  cat "${BUILDDIR}/setup_amd" >> ${SETUPFILE}
+fi
+
+load "${BUILDDIR}/setup_amd"
+write_toolchain_env "${INSTALLDIR}"
+
+cd "${ROOTDIR}"
+report_timing "amd"
diff --git a/toolchain/scripts/stage0/install_cmake.sh b/toolchain/scripts/stage0/install_cmake.sh
index b16c9719b2..c0c16fc4a0 100755
--- 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 2024-0811
+# Last Update in 2025-0308
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${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="3.30.0"
+    cmake_ver="3.31.2"
     if [ "${OPENBLAS_ARCH}" = "arm64" ]; then
       cmake_arch="linux-aarch64"
-      cmake_sha256="daa89552fd9102fb70399b31b5605c4f61125023bbbed947757a7b53ce36c4d0"
+      cmake_sha256="85cc81f782cd8b5ac346e570ad5cfba3bdbe5aa01f27f7ce6266c4cef93342550"
     elif [ "${OPENBLAS_ARCH}" = "x86_64" ]; then
       cmake_arch="linux-x86_64"
-      cmake_sha256="1a5969fe81fea6e5220d053d9d3e3754cbc85be07d2d428bebdcfe87137971a9"
+      cmake_sha256="b81cf3f4892683133f330cd7c016c28049b5725617db24ca8763360883545d34"
     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."
diff --git a/toolchain/scripts/stage0/install_gcc.sh b/toolchain/scripts/stage0/install_gcc.sh
index 7ea611acdb..dc8bb9e1d4 100755
--- a/toolchain/scripts/stage0/install_gcc.sh
+++ b/toolchain/scripts/stage0/install_gcc.sh
@@ -10,7 +10,7 @@ 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
+# use gcc 14 with caution, do not compatible with GPU-ABACUS
 #gcc_ver="14.2.0"
 #gcc_sha256="7d376d445f93126dc545e2c0086d0f647c3094aae081cdb78f42ce2bc25e7293"
 

From 81149e50be3871d97cc5613486636471519a1848 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 11:02:14 +0800
Subject: [PATCH 02/21] add aocc support

---
 toolchain/install_abacus_toolchain.sh | 21 +++++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
index 68836133ed..854d6738f6 100755
--- a/toolchain/install_abacus_toolchain.sh
+++ b/toolchain/install_abacus_toolchain.sh
@@ -156,6 +156,8 @@ The --with-PKG options follow the rules:
                           Default = no
   --with-ifx              Use the new Intel Fortran compiler ifx instead of ifort to compile dependence of ABACUS, along with mpiifx (if --with-intel-classic=no)
                           Default = yes
+  --with-amd              Use the AMD compiler to build CP2K.
+                          Default = system
   --with-cmake            Cmake utilities
                           Default = install
   --with-openmpi          OpenMPI, important if you want a parallel version of ABACUS.
@@ -233,7 +235,7 @@ EOF
 # PACKAGE LIST: register all new dependent tools and libs here. Order
 # is important, the first in the list gets installed first
 # ------------------------------------------------------------------------
-tool_list="gcc intel cmake"
+tool_list="gcc intel amd cmake"
 mpi_list="mpich openmpi intelmpi"
 math_list="mkl openblas"
 lib_list="fftw libxc scalapack elpa cereal rapidjson libtorch libnpy libri libcomm"
@@ -288,6 +290,7 @@ if (command -v mpiexec > /dev/null 2>&1); then
   elif (mpiexec --version 2>&1 | grep -s -q "Intel"); then
     echo "MPI is detected and it appears to be Intel MPI"
     with_gcc="__DONTUSE__"
+    with_amd="__DONTUSE__"
     with_intel="__SYSTEM__"
     with_intelmpi="__SYSTEM__"
     export MPI_MODE="intelmpi"
@@ -336,6 +339,7 @@ if [ "${CRAY_LD_LIBRARY_PATH}" ]; then
   export MPI_MODE="mpich"
   # set default value for some installers appropriate for CLE
   with_gcc="__DONTUSE__"
+  with_amd="__DONTUSE__"
   with_intel="__DONTUSE__"
   with_fftw="__SYSTEM__"
   with_scalapack="__DONTUSE__"
@@ -373,7 +377,9 @@ while [ $# -ge 1 ]; do
     --install-all)
       # set all package to the default installation status
       for ii in ${package_list}; do
-        if [ "${ii}" != "intel" ] && [ "${ii}" != "intelmpi" ]; then
+        if [ "${ii}" != "intel" ] && 
+          [ "${ii}" != "intelmpi" ] &&
+          [ "${ii}" != "amd" ]; then
           eval with_${ii}="__INSTALL__"
         fi
       done
@@ -508,6 +514,9 @@ while [ $# -ge 1 ]; do
         export MPI_MODE=intelmpi
       fi
       ;;
+    --with-amd*)
+      with_amd=$(read_with "${1}" "__SYSTEM__")
+      ;;
     --with-intel-classic*)
       intel_classic=$(read_with "${1}" "no") # default new intel compiler
       ;;
@@ -593,6 +602,14 @@ if [ "${with_intel}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; th
   echo "You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped."
   with_gcc="__SYSTEM__"
 fi
+if [ "${with_amd}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; then
+  echo "You have chosen to use the AMD compiler, therefore the installation of the GNU compiler will be skipped."
+  with_gcc="__SYSTEM__"
+fi
+if [ "${with_amd}" != "__DONTUSE__" ] && [ "${with_intel}" != "__DONTUSE__" ]; then
+  report_error "You have chosen to use the AMD and the Intel compiler. Select only one compiler."
+  exit 1
+fi
 # MPI library conflicts
 if [ "${MPI_MODE}" = "no" ]; then
   if [ "${with_scalapack}" != "__DONTUSE__" ]; then

From 864ff28df528d5a523c0a8c2c13b15a28c0e0b5e Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 11:35:19 +0800
Subject: [PATCH 03/21] update mpich

---
 toolchain/scripts/stage1/install_mpich.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/toolchain/scripts/stage1/install_mpich.sh b/toolchain/scripts/stage1/install_mpich.sh
index dd89fa8e1f..cd561519fb 100755
--- a/toolchain/scripts/stage1/install_mpich.sh
+++ b/toolchain/scripts/stage1/install_mpich.sh
@@ -3,7 +3,7 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0912
+# Last Update in 2025-0308
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
@@ -12,8 +12,8 @@ SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 # mpich_sha256="17406ea90a6ed4ecd5be39c9ddcbfac9343e6ab4f77ac4e8c5ebe4a3e3b6c501"
 # mpich_ver="4.1.2"
 # mpich_sha256="3492e98adab62b597ef0d292fb2459b6123bc80070a8aa0a30be6962075a12f0"
-mpich_ver="4.2.2"
-mpich_sha256="883f5bb3aeabf627cb8492ca02a03b191d09836bbe0f599d8508351179781d41"
+mpich_ver="4.3.0"
+mpich_sha256="5e04132984ad83cab9cc53f76072d2b5ef5a6d24b0a9ff9047a8ff96121bcc63"
 mpich_pkg="mpich-${mpich_ver}.tar.gz"
 
 source "${SCRIPT_DIR}"/common_vars.sh

From a235308d77f205f1dd53568c773b4949674cc550 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 11:35:38 +0800
Subject: [PATCH 04/21] update VERSION

---
 toolchain/scripts/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/toolchain/scripts/VERSION b/toolchain/scripts/VERSION
index bce1d6fc01..d50de5efde 100644
--- a/toolchain/scripts/VERSION
+++ b/toolchain/scripts/VERSION
@@ -1,2 +1,2 @@
 # version file to force a rebuild of the entire toolchain
-VERSION="2024.3"
+VERSION="2025.1"
\ No newline at end of file

From 2e202ed588023a963db778459e66fd4e45db84f1 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 11:58:33 +0800
Subject: [PATCH 05/21] update openmpi, allow user to switch version easily

---
 toolchain/install_abacus_toolchain.sh       |  4 ++++
 toolchain/scripts/stage1/install_openmpi.sh | 14 +++++++++-----
 toolchain/toolchain_gnu.sh                  |  4 +++-
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
index 854d6738f6..6430a3f32d 100755
--- a/toolchain/install_abacus_toolchain.sh
+++ b/toolchain/install_abacus_toolchain.sh
@@ -320,6 +320,7 @@ export intel_classic="no"
 # zhaoqing by 2023.08
 export intelmpi_classic="no"
 export with_ifx="yes"
+export openmpi_4th="no"
 export GPUVER="no"
 export MPICH_DEVICE="ch4"
 export TARGET_CPU="native"
@@ -508,6 +509,9 @@ while [ $# -ge 1 ]; do
         export MPI_MODE=openmpi
       fi
       ;;
+    --with-openmpi-4th)
+      openmpi_4th=$(read_with "${1}" "no") # default new openmpi
+      ;;
     --with-intelmpi*)
       with_intelmpi=$(read_with "${1}" "__SYSTEM__")
       if [ "${with_intelmpi}" != "__DONTUSE__" ]; then
diff --git a/toolchain/scripts/stage1/install_openmpi.sh b/toolchain/scripts/stage1/install_openmpi.sh
index 99adfc5bd9..4f1bb6989b 100755
--- a/toolchain/scripts/stage1/install_openmpi.sh
+++ b/toolchain/scripts/stage1/install_openmpi.sh
@@ -3,15 +3,19 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0912
+# Last Update in 2025-0308
+# Change default version to openmpi 5
+# allow user to choose openmpi 4 in used scripts
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${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"
+if [ "${openmpi_4th}" = "yes" ]; then
+    openmpi_ver="4.1.6"
+    openmpi_sha256="f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415"
+else
+    openmpi_ver="5.0.6"
+    openmpi_sha256="bd4183fcbc43477c254799b429df1a6e576c042e74a2d2f8b37d537b2ff98157"
 openmpi_pkg="openmpi-${openmpi_ver}.tar.bz2"
 
 source "${SCRIPT_DIR}"/common_vars.sh
diff --git a/toolchain/toolchain_gnu.sh b/toolchain/toolchain_gnu.sh
index 26e4b71c55..e6de0a9ea0 100755
--- a/toolchain/toolchain_gnu.sh
+++ b/toolchain/toolchain_gnu.sh
@@ -26,4 +26,6 @@
 --with-libnpy=no \
 --with-libri=no \
 --with-libcomm=no \
-| tee compile.log
\ No newline at end of file
+--with-openmpi-4th=no \
+| tee compile.log
+# if you want to use openmpi-version4: set --with-openmpi-4th=yes
\ No newline at end of file

From 8a1f4ac8fa90fc688b9c91be4351f70990d2fe1f Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 12:15:41 +0800
Subject: [PATCH 06/21] update elpa

---
 toolchain/scripts/stage3/install_elpa.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/toolchain/scripts/stage3/install_elpa.sh b/toolchain/scripts/stage3/install_elpa.sh
index c077097f36..89da411eeb 100755
--- a/toolchain/scripts/stage3/install_elpa.sh
+++ b/toolchain/scripts/stage3/install_elpa.sh
@@ -3,14 +3,16 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2024-0811
+# Last Update in 2025-0308
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
 # From https://elpa.mpcdf.mpg.de/software/tarball-archive/ELPA_TARBALL_ARCHIVE.html
-elpa_ver="2024.05.001"
-elpa_sha256="9caf41a3e600e2f6f4ce1931bd54185179dade9c171556d0c9b41bbc6940f2f6"
+# elpa_ver="2024.05.001"
+# elpa_sha256="9caf41a3e600e2f6f4ce1931bd54185179dade9c171556d0c9b41bbc6940f2f6"
+elpa_ver="2025.01.001"
+elpa_sha256="3ef0c6aed9a3e05db6efafe6e14d66eb88b2a1354d61e765b7cde0d3d5f3951e"
 
 
 source "${SCRIPT_DIR}"/common_vars.sh

From 2519fc27225294e0e2a865f9ae7af57d229af171 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 12:55:00 +0800
Subject: [PATCH 07/21] create aocl script

---
 toolchain/scripts/stage2/install_aocl.sh | 27 ++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 toolchain/scripts/stage2/install_aocl.sh

diff --git a/toolchain/scripts/stage2/install_aocl.sh b/toolchain/scripts/stage2/install_aocl.sh
new file mode 100644
index 0000000000..e151371064
--- /dev/null
+++ b/toolchain/scripts/stage2/install_aocl.sh
@@ -0,0 +1,27 @@
+#!/bin/bash -e
+
+# TODO: Review and if possible fix shellcheck errors.
+# shellcheck disable=all
+
+# Last Update in 2025-0308
+
+[ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
+SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
+
+source "${SCRIPT_DIR}"/common_vars.sh
+source "${SCRIPT_DIR}"/tool_kit.sh
+source "${SCRIPT_DIR}"/signal_trap.sh
+source "${INSTALLDIR}"/toolchain.conf
+source "${INSTALLDIR}"/toolchain.env
+
+[ -f "${BUILDDIR}/setup_mkl" ] && rm "${BUILDDIR}/setup_mkl"
+
+MKL_CFLAGS=""
+MKL_LDFLAGS=""
+MKL_LIBS=""
+MKL_FFTW="yes"
+
+! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
+cd "${BUILDDIR}"
+
+# Not Completed
\ No newline at end of file

From f1e16c6db3d345b25a4079018ca7eea932b715a2 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 17:39:35 +0800
Subject: [PATCH 08/21] aocc install setup

---
 toolchain/install_abacus_toolchain.sh        | 11 ++++++-----
 toolchain/scripts/stage0/install_stage0.sh   |  1 +
 toolchain/scripts/stage0/setup_buildtools.sh |  7 +++++--
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
index 6430a3f32d..37ad8181c2 100755
--- a/toolchain/install_abacus_toolchain.sh
+++ b/toolchain/install_abacus_toolchain.sh
@@ -59,10 +59,11 @@ USAGE:
 
 $(basename $SCRIPT_NAME) [options]
 
-Or a more RECOMMENDED way is to use it by pre-setting workflow scripts:
+A MORE RECOMMENDED way is to use it by pre-setting workflow scripts:
 > gcc-openmpi-openblas environments: toolchain_gnu.sh
 > intel-mkl-mpi environments: toolchain_intel.sh
 > intel-mpich environments: toolchain_intel_mpich.sh
+> AMD environments: toolchain_amd.sh [in development]
 
 OPTIONS:
 
@@ -148,9 +149,9 @@ The --with-PKG options follow the rules:
   --with-PKG              The option keyword alone will be equivalent to
                           --with-PKG=install
 
-  --with-gcc              The GCC compiler to use to compile ABACUS.
+  --with-gcc              Use the GNU compiler to use to build ABACUS.
                           Default = system
-  --with-intel            Use the Intel compiler to compile ABACUS.
+  --with-intel            Use the Intel compiler to build ABACUS.
                           Default = system
   --with-intel-classic    Use the classic Intel compiler (icc, icpc, ifort) to compile ABACUS.
                           Default = no
@@ -603,7 +604,7 @@ export ENABLE_CRAY="${enable_cray}"
 # ------------------------------------------------------------------------
 # Compiler conflicts
 if [ "${with_intel}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; then
-  echo "You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped."
+  echo "You have chosen to use the Intel compiler, therefore the installation of the GNU compiler will be skipped."
   with_gcc="__SYSTEM__"
 fi
 if [ "${with_amd}" != "__DONTUSE__" ] && [ "${with_gcc}" = "__INSTALL__" ]; then
@@ -627,7 +628,7 @@ if [ "${MPI_MODE}" = "no" ]; then
 else
   # if gcc is installed, then mpi needs to be installed too
   if [ "${with_gcc}" = "__INSTALL__" ]; then
-    echo "You have chosen to install the GCC compiler, therefore MPI libraries have to be installed too"
+    echo "You have chosen to install the GNU compiler, therefore MPI libraries have to be installed too"
     case ${MPI_MODE} in
       mpich)
         with_mpich="__INSTALL__"
diff --git a/toolchain/scripts/stage0/install_stage0.sh b/toolchain/scripts/stage0/install_stage0.sh
index a398fdc0fa..7c2eb2568c 100755
--- a/toolchain/scripts/stage0/install_stage0.sh
+++ b/toolchain/scripts/stage0/install_stage0.sh
@@ -5,6 +5,7 @@
 
 ./scripts/stage0/install_gcc.sh
 ./scripts/stage0/install_intel.sh
+./scripts/stage0/install_amd.sh
 ./scripts/stage0/setup_buildtools.sh
 ./scripts/stage0/install_cmake.sh
 
diff --git a/toolchain/scripts/stage0/setup_buildtools.sh b/toolchain/scripts/stage0/setup_buildtools.sh
index 5172574a22..b5e27d178d 100755
--- a/toolchain/scripts/stage0/setup_buildtools.sh
+++ b/toolchain/scripts/stage0/setup_buildtools.sh
@@ -33,6 +33,9 @@ if [ "${with_intel}" != "__DONTUSE__" ]; then
     CFLAGS="${CFLAGS} -march=${TARGET_CPU} -mtune=${TARGET_CPU}"
   fi
   FFLAGS="${CFLAGS}"
+elif [ "${with_amd}" != "__DONTUSE__" ]; then
+  CFLAGS="-O2 -fPIC -fopenmp -g -mtune=${TARGET_CPU}"
+  FFLAGS="${CFLAGS}"
 else
   CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g"
   if [ "${TARGET_CPU}" = "generic" ]; then
@@ -47,7 +50,7 @@ F77FLAGS="${FFLAGS}"
 F90FLAGS="${FFLAGS}"
 FCFLAGS="${FFLAGS}"
 
-if [ "${with_intel}" == "__DONTUSE__" ]; then
+if [ "${with_intel}" == "__DONTUSE__" ] && [ "${with_amd}" == "__DONTUSE__" ]; then
   export CFLAGS="$(allowed_gcc_flags ${CFLAGS})"
   export FFLAGS="$(allowed_gfortran_flags ${FFLAGS})"
   export F77FLAGS="$(allowed_gfortran_flags ${F77FLAGS})"
@@ -55,7 +58,7 @@ if [ "${with_intel}" == "__DONTUSE__" ]; then
   export FCFLAGS="$(allowed_gfortran_flags ${FCFLAGS})"
   export CXXFLAGS="$(allowed_gxx_flags ${CXXFLAGS})"
 else
-  # TODO Check functions for allowed Intel compiler flags
+  # TODO Check functions for allowed Intel or AMD compiler flags
   export CFLAGS
   export FFLAGS
   export F77FLAGS

From 4c260bbd6c7f07fdc470efd3d200e9e7bc16b6e8 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 18:15:00 +0800
Subject: [PATCH 09/21] bug fix and update readme

---
 toolchain/README.md                         | 70 +++++++++++++--------
 toolchain/scripts/stage1/install_openmpi.sh |  1 +
 2 files changed, 44 insertions(+), 27 deletions(-)

diff --git a/toolchain/README.md b/toolchain/README.md
index 1336e67573..e4ea124a12 100644
--- a/toolchain/README.md
+++ b/toolchain/README.md
@@ -1,6 +1,6 @@
 # The ABACUS Toolchain
 
-Version 2024.3
+Version 2025.1
 
 ## Author
 
@@ -27,12 +27,12 @@ and give setup files that you can use to compile ABACUS.
 - [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)
 - [x] A mirror station by Bohrium database, which can download CEREAL, LibNPY, LibRI and LibComm by `wget` in China Internet. 
 - [x] Support for GPU compilation, users can add `-DUSE_CUDA=1` in builder scripts.
+- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC`
 - [ ] Change the downloading url from cp2k mirror to other mirror or directly downloading from official website. (doing)
 - [ ] A better README and Detail markdown file.
 - [ ] Automatic installation of [DEEPMD](https://github.com/deepmodeling/deepmd-kit).
 - [ ] Better compliation method for ABACUS-DEEPMD and ABACUS-DEEPKS.
 - [ ] Modulefile generation scripts.
-- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC`
 
 
 ## Usage Online & Offline
@@ -109,15 +109,15 @@ just by using this toolchain
 
 The needed dependencies version default:
 
-- `cmake` 3.30.0
+- `cmake` 3.31.2
 - `gcc` 13.2.0 (which will always NOT be installed, But use system)
-- `OpenMPI` 4.1.6 (5.0.5 can be used but have some problem in OpenMP parallel computation in ELPA)
-- `MPICH` 4.2.2
+- `OpenMPI` 5.0.6 (Version 5 OpenMPI is good but will have compability problem, user can manually downarade to Version 4 in toolchain scripts)
+- `MPICH` 4.3.2
 - `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` 2024.05.001
+- `ELPA` 2025.01.001
 - `CEREAL` 1.3.2
 - `RapidJSON` 1.1.0
 And Intel-oneAPI need user or server manager to manually install from Intel.
@@ -180,11 +180,47 @@ or you can also do it in a more completely way:
 
 ## Common Problems and Solutions
 
-### LibRI and LibComm for EXX
+### Intel-oneAPI problem
+
+#### ELPA problem via Intel-oneAPI toolchain in AMD server
+
+The default compiler for Intel-oneAPI is `icpx` and `icx`, which will cause problem when compling ELPA in AMD server. (Which is a problem and needed to have more check-out)
+
+The best way is to change `icpx` to `icpc`, `icx` to `icc`. user can manually change it in *toolchain_intel.sh* via `--with-intel-classic=yes`
+
+Notice: `icc` and `icpc` from Intel Classic Compiler of Intel-oneAPI is not supported for 2024.0 and newer version. And Intel-OneAPI 2023.2.0 can be found in QE website. You need to download Base-toolkit for MKL and HPC-toolkit for MPi and compiler for Intel-OneAPI 2023.2.0, while in Intel-OneAPI 2024.x, only the HPC-toolkit is needed.
+
+You can get Intel-OneAPI in [QE-managed website](https://pranabdas.github.io/espresso/setup/hpc/#installing-intel-oneapi-libraries), and use this code to get Intel oneAPI Base Toolkit and HPC Toolkit:
+```shell
+wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/992857b9-624c-45de-9701-f6445d845359/l_BaseKit_p_2023.2.0.49397_offline.sh
+wget https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0722521a-34b5-4c41-af3f-d5d14e88248d/l_HPCKit_p_2023.2.0.49440_offline.sh
+```
+
+Related discussion here [#4976](https://github.com/deepmodeling/abacus-develop/issues/4976)
+
+#### link problem in early 2023 version oneAPI
+
+Sometimes Intel-oneAPI have problem to link `mpirun`, 
+which will always show in 2023.2.0 version of MPI in Intel-oneAPI. 
+Try `source /path/to/setvars.sh` or install another version of IntelMPI may help.
+
+which is fixed in 2024.0.0 version of Intel-oneAPI, 
+And will not occur in Intel-MPI before 2021.10.0 (Intel-oneAPI before 2023.2.0)
+
+More problem and possible solution can be accessed via [#2928](https://github.com/deepmodeling/abacus-develop/issues/2928)
+
+
+### OpenMPI problem
+
+#### in EXX and LibRI
 
 - GCC toolchain with OpenMPI cannot compile LibComm v0.1.1 due to the different MPI variable type from MPICH and IntelMPI, see discussion here [#5033](https://github.com/deepmodeling/abacus-develop/issues/5033), you can switch to GCC-MPICH or Intel toolchain
 - It is recommended to use Intel toolchain if one wants to include EXX feature in ABACUS, which can have much better performance and can use more than 16 threads in OpenMP parallelization to accelerate the EXX process.
 
+#### OpenMPI-v5 
+
+OpenMPI in version 5 has huge update, lead to compatibility problem. If one wants to use the OpenMPI in version 4 (4.1.6), one can specify `--with-openmpi-4th=yes` in *toolchain_gnu.sh*
+
 ### GPU version of ABACUS
 
 For GPU version of ABACUS (do not GPU version installer of ELPA, which is still doing work), add following options in build*.sh:
@@ -242,26 +278,6 @@ When you encounter problem like `GLIBCXX_3.4.29 not found`, it is sure that your
 
 After my test, you need `gcc`>11.3.1 to enable deepmd feature in ABACUS.
 
-### Intel-oneAPI problem
-
-#### ELPA problem via Intel-oneAPI toolchain in AMD server
-
-The default compiler for Intel-oneAPI is `icpx` and `icx`, which will cause problem when compling ELPA in AMD server. (Which is a problem and needed to have more check-out)
-
-The best way is to change `icpx` to `icpc`, `icx` to `icc`. user can manually change it in toolchain*.sh via `--with-intel-classic=yes`
-
-Notice: `icc` and `icpc` from Intel Classic Compiler of Intel-oneAPI is not supported for 2024.0 and newer version. And Intel-OneAPI 2023.2.0 can be found in website. See discussion here [#4976](https://github.com/deepmodeling/abacus-develop/issues/4976)
-
-#### link problem in early 2023 version oneAPI
-
-Sometimes Intel-oneAPI have problem to link `mpirun`, 
-which will always show in 2023.2.0 version of MPI in Intel-oneAPI. 
-Try `source /path/to/setvars.sh` or install another version of IntelMPI may help.
-
-which is fixed in 2024.0.0 version of Intel-oneAPI, 
-And will not occur in Intel-MPI before 2021.10.0 (Intel-oneAPI before 2023.2.0)
-
-More problem and possible solution can be accessed via [#2928](https://github.com/deepmodeling/abacus-develop/issues/2928)
 
 ## Advanced Installation Usage
 
diff --git a/toolchain/scripts/stage1/install_openmpi.sh b/toolchain/scripts/stage1/install_openmpi.sh
index 4f1bb6989b..fa19fa2552 100755
--- a/toolchain/scripts/stage1/install_openmpi.sh
+++ b/toolchain/scripts/stage1/install_openmpi.sh
@@ -16,6 +16,7 @@ if [ "${openmpi_4th}" = "yes" ]; then
 else
     openmpi_ver="5.0.6"
     openmpi_sha256="bd4183fcbc43477c254799b429df1a6e576c042e74a2d2f8b37d537b2ff98157"
+fi
 openmpi_pkg="openmpi-${openmpi_ver}.tar.bz2"
 
 source "${SCRIPT_DIR}"/common_vars.sh

From 05b0095113155dd1f7c966ffdfb415229523369f Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sat, 8 Mar 2025 19:58:40 +0800
Subject: [PATCH 10/21] fix openmpi switch

---
 toolchain/install_abacus_toolchain.sh | 8 ++++----
 toolchain/toolchain_gnu.sh            | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
index 37ad8181c2..0ee26dd395 100755
--- a/toolchain/install_abacus_toolchain.sh
+++ b/toolchain/install_abacus_toolchain.sh
@@ -504,15 +504,15 @@ while [ $# -ge 1 ]; do
         export MPI_MODE=mpich
       fi
       ;;
+    --with-4th-openmpi*)
+      openmpi_4th=$(read_with "${1}" "no") # default new openmpi
+      ;;
     --with-openmpi*)
       with_openmpi=$(read_with "${1}")
       if [ "${with_openmpi}" != "__DONTUSE__" ]; then
         export MPI_MODE=openmpi
       fi
       ;;
-    --with-openmpi-4th)
-      openmpi_4th=$(read_with "${1}" "no") # default new openmpi
-      ;;
     --with-intelmpi*)
       with_intelmpi=$(read_with "${1}" "__SYSTEM__")
       if [ "${with_intelmpi}" != "__DONTUSE__" ]; then
@@ -528,7 +528,7 @@ while [ $# -ge 1 ]; do
     --with-intel-mpi-clas*)
       intelmpi_classic=$(read_with "${1}" "no") # default new intel mpi compiler
       ;;
-    --with-intel*)
+    --with-intel*)  # must be read after items above
       with_intel=$(read_with "${1}" "__SYSTEM__")
       ;;
     --with-ifx*)
diff --git a/toolchain/toolchain_gnu.sh b/toolchain/toolchain_gnu.sh
index e6de0a9ea0..68f559128e 100755
--- a/toolchain/toolchain_gnu.sh
+++ b/toolchain/toolchain_gnu.sh
@@ -26,6 +26,6 @@
 --with-libnpy=no \
 --with-libri=no \
 --with-libcomm=no \
---with-openmpi-4th=no \
+--with-4th-openmpi=no \
 | tee compile.log
-# if you want to use openmpi-version4: set --with-openmpi-4th=yes
\ No newline at end of file
+# if you want to use openmpi-version4: set --with-4th-openmpi=yes
\ No newline at end of file

From b46c7260abfcf55f77c66df486631d69c204d516 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 00:06:21 +0800
Subject: [PATCH 11/21] modification

---
 toolchain/scripts/stage0/install_amd.sh     | 13 ++++++++++---
 toolchain/scripts/stage1/install_openmpi.sh |  6 ++----
 toolchain/scripts/stage2/install_aocl.sh    |  3 ++-
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/toolchain/scripts/stage0/install_amd.sh b/toolchain/scripts/stage0/install_amd.sh
index 84fa7d9cd3..822c001b51 100755
--- a/toolchain/scripts/stage0/install_amd.sh
+++ b/toolchain/scripts/stage0/install_amd.sh
@@ -3,6 +3,9 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
+# Last Update in 2025-0308
+# NOTICE: flang cannot be used when compiling ELPA
+
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=${0}
 SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
 
@@ -30,7 +33,9 @@ case "${with_amd}" in
     echo "==================== Finding AMD compiler from system paths ===================="
     check_command clang "amd" && CC="$(realpath $(command -v clang))" || exit 1
     check_command clang++ "amd" && CXX="$(realpath $(command -v clang++))" || exit 1
-    check_command flang "amd" && FC="$(realpath $(command -v flang))" || exit 1
+    check_command gfortran "gcc" && FC="gfortran" || exit 1
+    add_lib_from_paths GCC_LDFLAGS "libgfortran.*" ${LIB_PATHS}
+    #check_command flang "amd" && FC="$(realpath $(command -v flang))" || exit 1
     F90="${FC}"
     F77="${FC}"
     ;;
@@ -45,7 +50,8 @@ case "${with_amd}" in
     check_dir "${pkg_install_dir}/include"
     check_command ${pkg_install_dir}/bin/clang "amd" && CC="${pkg_install_dir}/bin/clang" || exit 1
     check_command ${pkg_install_dir}/bin/clang++ "amd" && CXX="${pkg_install_dir}/bin/clang++" || exit 1
-    check_command ${pkg_install_dir}/bin/flang "amd" && FC="${pkg_install_dir}/bin/flang" || exit 1
+    check_command gfortran "gcc" && FC="$(command -v gfortran)" || exit 1
+    #check_command ${pkg_install_dir}/bin/flang "amd" && FC="${pkg_install_dir}/bin/flang" || exit 1
     F90="${FC}"
     F77="${FC}"
     AMD_CFLAGS="-I'${pkg_install_dir}/include'"
@@ -58,7 +64,8 @@ if [ "${with_amd}" != "__DONTUSE__" ]; then
   echo "CXX is ${CXX}"
   [ $(realpath $(command -v clang++) | grep -e aocc-compiler) ] || echo "Check the AMD C++ compiler path"
   echo "FC  is ${FC}"
-  [ $(realpath $(command -v flang) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
+  #[ $(realpath $(command -v flang) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
+  [ $(realpath $(command -v gfortran) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
   cat << EOF > "${BUILDDIR}/setup_amd"
 export CC="${CC}"
 export CXX="${CXX}"
diff --git a/toolchain/scripts/stage1/install_openmpi.sh b/toolchain/scripts/stage1/install_openmpi.sh
index fa19fa2552..6f95239975 100755
--- a/toolchain/scripts/stage1/install_openmpi.sh
+++ b/toolchain/scripts/stage1/install_openmpi.sh
@@ -106,10 +106,8 @@ case "${with_openmpi}" in
     check_command mpifort "openmpi" && MPIFC="$(command -v mpifort)" || exit 1
     MPIFORT="${MPIFC}"
     MPIF77="${MPIFC}"
-    # Fortran code in ABACUS is built via the mpifort wrapper, but we may need additional
-    # libraries and linker flags for C/C++-based MPI codepaths, pull them in at this point.
-    OPENMPI_CFLAGS="$(mpicxx --showme:compile)"
-    OPENMPI_LDFLAGS="$(mpicxx --showme:link)"
+    # OPENMPI_CFLAGS="$(mpicxx --showme:compile)"
+    # OPENMPI_LDFLAGS="$(mpicxx --showme:link)"
     ;;
   __DONTUSE__)
     # Nothing to do
diff --git a/toolchain/scripts/stage2/install_aocl.sh b/toolchain/scripts/stage2/install_aocl.sh
index e151371064..bd36ff9541 100644
--- a/toolchain/scripts/stage2/install_aocl.sh
+++ b/toolchain/scripts/stage2/install_aocl.sh
@@ -24,4 +24,5 @@ MKL_FFTW="yes"
 ! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
 cd "${BUILDDIR}"
 
-# Not Completed
\ No newline at end of file
+# Not Completed
+# Only need to deal with LAPACK in AOCL, ScaLAPACK and FFTW can use other scripts
\ No newline at end of file

From e57e2ccf248b838d5f913082dcc1882c3cb9fdc0 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 21:20:22 +0800
Subject: [PATCH 12/21] add openmpi configure option

---
 toolchain/scripts/stage1/install_openmpi.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/toolchain/scripts/stage1/install_openmpi.sh b/toolchain/scripts/stage1/install_openmpi.sh
index 6f95239975..ab65a89553 100755
--- a/toolchain/scripts/stage1/install_openmpi.sh
+++ b/toolchain/scripts/stage1/install_openmpi.sh
@@ -79,6 +79,7 @@ case "${with_openmpi}" in
       ./configure CFLAGS="${CFLAGS}" \
         --prefix=${pkg_install_dir} \
         --libdir="${pkg_install_dir}/lib" \
+        --with-libevent=internal \
         ${EXTRA_CONFIGURE_FLAGS} \
         > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
       make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
@@ -106,8 +107,9 @@ case "${with_openmpi}" in
     check_command mpifort "openmpi" && MPIFC="$(command -v mpifort)" || exit 1
     MPIFORT="${MPIFC}"
     MPIF77="${MPIFC}"
-    # OPENMPI_CFLAGS="$(mpicxx --showme:compile)"
-    # OPENMPI_LDFLAGS="$(mpicxx --showme:link)"
+    # libraries and linker flags for C/C++-based MPI codepaths, pull them in at this point.
+    OPENMPI_CFLAGS="$(mpicxx --showme:compile)"
+    OPENMPI_LDFLAGS="$(mpicxx --showme:link)"
     ;;
   __DONTUSE__)
     # Nothing to do

From 2de91a1ab7c72b244f8eee5fcc8c0f501a1c17bb Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 22:38:57 +0800
Subject: [PATCH 13/21] update elpa setting (gpu setting for 2070s)

---
 toolchain/scripts/stage3/install_elpa.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/toolchain/scripts/stage3/install_elpa.sh b/toolchain/scripts/stage3/install_elpa.sh
index 89da411eeb..7698530bbb 100755
--- a/toolchain/scripts/stage3/install_elpa.sh
+++ b/toolchain/scripts/stage3/install_elpa.sh
@@ -112,19 +112,19 @@ case "$with_elpa" in
           --disable-c-tests \
           --disable-cpp-tests \
           ${config_flags} \
-          --enable-nvidia-gpu=$([ "$TARGET" = "nvidia" ] && echo "yes" || echo "no") \
+          --enable-nvidia-gpu-kernels=$([ "$TARGET" = "nvidia" ] && echo "yes" || echo "no") \
           --with-cuda-path=${CUDA_PATH:-${CUDA_HOME:-/CUDA_HOME-notset}} \
-          --with-NVIDIA-GPU-compute-capability=$([ "$TARGET" = "nvidia" ] && echo "sm_$ARCH_NUM" || echo "sm_35") \
+          --with-NVIDIA-GPU-compute-capability=$([ "$TARGET" = "nvidia" ] && echo "sm_$ARCH_NUM" || echo "sm_75") \
           CUDA_CFLAGS="-std=c++14 -allow-unsupported-compiler" \
           OMPI_MCA_plm_rsh_agent=/bin/false \
           FC=${MPIFC} \
           CC=${MPICC} \
           CXX=${MPICXX} \
           CPP="cpp -E" \
-          FCFLAGS="${FCFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} -ffree-line-length-none ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
+          FCFLAGS="${FCFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
           CFLAGS="${CFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
           CXXFLAGS="${CXXFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
-          LDFLAGS="-Wl,--allow-multiple-definition -Wl,--enable-new-dtags ${MATH_LDFLAGS} ${SCALAPACK_LDFLAGS} ${cray_ldflags}" \
+          LDFLAGS="-Wl,--allow-multiple-definition -Wl,--enable-new-dtags ${MATH_LDFLAGS} ${SCALAPACK_LDFLAGS} ${cray_ldflags} -lstdc++" \
           LIBS="${SCALAPACK_LIBS} $(resolve_string "${MATH_LIBS}" "MPI")" \
           > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
         make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log

From 2302a27d8117098c985d79bc7de2a9ce5d56d8a2 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 23:26:39 +0800
Subject: [PATCH 14/21] update libxc version and download

---
 toolchain/scripts/stage3/install_libxc.sh | 33 ++++++++++++++++-------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/toolchain/scripts/stage3/install_libxc.sh b/toolchain/scripts/stage3/install_libxc.sh
index 40cc371d41..04c96b7aad 100755
--- a/toolchain/scripts/stage3/install_libxc.sh
+++ b/toolchain/scripts/stage3/install_libxc.sh
@@ -3,13 +3,15 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2023-0901
+# Last Update in 2025-0309
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "$SCRIPT_NAME")/.." && pwd -P)"
 
-libxc_ver="6.2.2"
-libxc_sha256="a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045"
+# libxc_ver="6.2.2"
+# libxc_sha256="a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045"
+libxc_ver="7.0.0"
+libxc_sha256="e9ae69f8966d8de6b7585abd9fab588794ada1fab8f689337959a35abbf9527d"
 source "${SCRIPT_DIR}"/common_vars.sh
 source "${SCRIPT_DIR}"/tool_kit.sh
 source "${SCRIPT_DIR}"/signal_trap.sh
@@ -30,22 +32,33 @@ case "$with_libxc" in
     pkg_install_dir="${INSTALLDIR}/libxc-${libxc_ver}"
     #pkg_install_dir="${HOME}/lib/libxc/${libxc_ver}-gcc8"
     install_lock_file="$pkg_install_dir/install_successful"
+    libxc_pkg="libxc-${libxc_ver}.tar.bz2"
     if verify_checksums "${install_lock_file}"; then
       echo "libxc-${libxc_ver} is already installed, skipping it."
     else
-      if [ -f libxc-${libxc_ver}.tar.gz ]; then
-        echo "libxc-${libxc_ver}.tar.gz is found"
+      if [ -f ${libxc_pkg} ]; then
+        echo "${libxc_pkg} is found"
       else
-        download_pkg_from_ABACUS_org "${libxc_sha256}" "libxc-${libxc_ver}.tar.gz"
+        #download_pkg_from_ABACUS_org "${libxc_sha256}" "${libxc_pkg}"
+        libxc_url="https://gitlab.com/libxc/libxc/-/archive/${libxc_ver}/${libxc_pkg}"
+        download_pkg_from_url  "${libxc_sha256}" "${libxc_pkg}" "${libxc_url}"
       fi
       echo "Installing from scratch into ${pkg_install_dir}"
       [ -d libxc-${libxc_ver} ] && rm -rf libxc-${libxc_ver}
-      tar -xzf libxc-${libxc_ver}.tar.gz
+      tar -xjf ${libxc_pkg}
       cd libxc-${libxc_ver}
       # using cmake method to install libxc is neccessary for abacus
-      mkdir build && cd build
-      cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${pkg_install_dir} \
-        -DBUILD_SHARED_LIBS=YES -DCMAKE_INSTALL_LIBDIR=lib -DENABLE_FORTRAN=ON -DENABLE_PYTHON=OFF -DBUILD_TESTING=NO .. \
+      mkdir build 
+      cd build
+      cmake \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=${pkg_install_dir} \
+        -DBUILD_SHARED_LIBS=YES \
+        -DCMAKE_INSTALL_LIBDIR=lib \
+        -DCMAKE_VERBOSE_MAKEFILE=ON \
+        -DENABLE_FORTRAN=ON \
+        -DENABLE_PYTHON=OFF \
+        -DBUILD_TESTING=OFF .. \
         > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
       make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
       make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log

From a7b87cfcb644337bae1354bb4d1de2ce07751fc2 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 23:34:27 +0800
Subject: [PATCH 15/21] minor update

---
 .gitignore                            | 1 -
 toolchain/build_abacus_gnu.sh         | 6 +++---
 toolchain/build_abacus_intel-mpich.sh | 6 +++---
 toolchain/build_abacus_intel.sh       | 6 +++---
 4 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3ce0cf6879..9afd1b1944 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,7 +17,6 @@ STRU_READIN_ADJUST.cif
 build
 dist
 .idea
-toolchain.tar.gz
 time.json
 *.pyc
 __pycache__
diff --git a/toolchain/build_abacus_gnu.sh b/toolchain/build_abacus_gnu.sh
index e6a9798fd0..5020b1ec33 100755
--- a/toolchain/build_abacus_gnu.sh
+++ b/toolchain/build_abacus_gnu.sh
@@ -5,7 +5,7 @@
 #SBATCH -o install.log
 #SBATCH -e install.err
 # install ABACUS with libxc and deepks
-# JamesMisaka in 2023.08.31
+# JamesMisaka in 2025.03.09
 
 # Build ABACUS by gnu-toolchain
 
@@ -24,10 +24,10 @@ rm -rf $BUILD_DIR
 PREFIX=$ABACUS_DIR
 LAPACK=$INSTALL_DIR/openblas-0.3.28/lib
 SCALAPACK=$INSTALL_DIR/scalapack-2.2.1/lib
-ELPA=$INSTALL_DIR/elpa-2024.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2025.01.001/cpu
 FFTW3=$INSTALL_DIR/fftw-3.3.10
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
-LIBXC=$INSTALL_DIR/libxc-6.2.2
+LIBXC=$INSTALL_DIR/libxc-7.0.0
 RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
diff --git a/toolchain/build_abacus_intel-mpich.sh b/toolchain/build_abacus_intel-mpich.sh
index 6ed443668e..47221825c6 100755
--- a/toolchain/build_abacus_intel-mpich.sh
+++ b/toolchain/build_abacus_intel-mpich.sh
@@ -5,7 +5,7 @@
 #SBATCH -o install.log
 #SBATCH -e install.err
 # build and install ABACUS with libxc, also can with deepks and deepmd
-# JamesMisaka in 2023.08.31
+# JamesMisaka in 2025.03.09
 
 # Build ABACUS by intel-toolchain with mpich
 
@@ -23,9 +23,9 @@ BUILD_DIR=build_abacus_intel-mpich
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2024.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2025.01.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
-LIBXC=$INSTALL_DIR/libxc-6.2.2
+LIBXC=$INSTALL_DIR/libx-7.0.0
 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
diff --git a/toolchain/build_abacus_intel.sh b/toolchain/build_abacus_intel.sh
index 064c9c8bf8..77071cecd8 100755
--- a/toolchain/build_abacus_intel.sh
+++ b/toolchain/build_abacus_intel.sh
@@ -5,7 +5,7 @@
 #SBATCH -o install.log
 #SBATCH -e install.err
 # install ABACUS with libxc and deepks
-# JamesMisaka in 2023.08.22
+# JamesMisaka in 2025.03.09
 
 # Build ABACUS by intel-toolchain
 
@@ -23,9 +23,9 @@ BUILD_DIR=build_abacus_intel
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2024.05.001/cpu
+ELPA=$INSTALL_DIR/elpa-2025.01.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
-LIBXC=$INSTALL_DIR/libxc-6.2.2
+LIBXC=$INSTALL_DIR/libxc-7.0.0
 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

From e1a83036a45fffcc20ab83a7e0a3fe99d7bddf2e Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 23:38:36 +0800
Subject: [PATCH 16/21] update README

---
 toolchain/README.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/toolchain/README.md b/toolchain/README.md
index e4ea124a12..d5982c83b0 100644
--- a/toolchain/README.md
+++ b/toolchain/README.md
@@ -27,8 +27,9 @@ and give setup files that you can use to compile ABACUS.
 - [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)
 - [x] A mirror station by Bohrium database, which can download CEREAL, LibNPY, LibRI and LibComm by `wget` in China Internet. 
 - [x] Support for GPU compilation, users can add `-DUSE_CUDA=1` in builder scripts.
-- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC`
+- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC` (doing)
 - [ ] Change the downloading url from cp2k mirror to other mirror or directly downloading from official website. (doing)
+- [ ] Support a JSON or YAML configuration file for toolchain, which can be easily modified by users.
 - [ ] A better README and Detail markdown file.
 - [ ] Automatic installation of [DEEPMD](https://github.com/deepmodeling/deepmd-kit).
 - [ ] Better compliation method for ABACUS-DEEPMD and ABACUS-DEEPKS.
@@ -94,7 +95,7 @@ The above station will be updated handly but one should notice that the version
 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-5.0.5.tar.bz2*, 
+like *fftw-3.3.10.tar.gz*, or *openmpi-5.0.6.tar.bz2*, 
 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
@@ -116,7 +117,7 @@ The needed dependencies version default:
 - `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
+- `LibXC` 7.0.0
 - `ELPA` 2025.01.001
 - `CEREAL` 1.3.2
 - `RapidJSON` 1.1.0
@@ -130,7 +131,7 @@ Dependencies below are optional， which is NOT installed by default:
 - `LibRI` 0.2.0
 - `LibComm` 0.1.1
 
-Users can install them by using `--with-*=install` in toolchain*.sh, which is `no` in default.
+Users can install them by using `--with-*=install` in toolchain*.sh, which is `no` in default. Also, user can specify the absolute path of the package by `--with-*=path/to/package` in toolchain*.sh to allow toolchain to use the package.
 > Notice: LibRI, LibComm and Libnpy is on actively development, you should check-out the package version when using this toolchain. Also, LibRI and LibComm can be installed by github submodule, that is also work for libnpy, which is more recommended.
 
 Users can easily compile and install dependencies of ABACUS

From 3adb9e7edfcac4773b2a8c39c33fa97f07fd4664 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 23:55:52 +0800
Subject: [PATCH 17/21] minor update

---
 toolchain/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/toolchain/README.md b/toolchain/README.md
index d5982c83b0..461aecd227 100644
--- a/toolchain/README.md
+++ b/toolchain/README.md
@@ -113,7 +113,7 @@ The needed dependencies version default:
 - `cmake` 3.31.2
 - `gcc` 13.2.0 (which will always NOT be installed, But use system)
 - `OpenMPI` 5.0.6 (Version 5 OpenMPI is good but will have compability problem, user can manually downarade to Version 4 in toolchain scripts)
-- `MPICH` 4.3.2
+- `MPICH` 4.3.0
 - `OpenBLAS` 0.3.28 (Intel toolchain need `get_vars.sh` tool from it)
 - `ScaLAPACK` 2.2.1 (a developing version)
 - `FFTW` 3.3.10

From 0bda24fcee4024f35204616d57227306d91a161c Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Sun, 9 Mar 2025 23:59:44 +0800
Subject: [PATCH 18/21] minor checkout

---
 toolchain/build_abacus_gnu.sh         | 4 +---
 toolchain/build_abacus_intel-mpich.sh | 3 +--
 toolchain/build_abacus_intel.sh       | 3 +--
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/toolchain/build_abacus_gnu.sh b/toolchain/build_abacus_gnu.sh
index 5020b1ec33..41f86ff41c 100755
--- a/toolchain/build_abacus_gnu.sh
+++ b/toolchain/build_abacus_gnu.sh
@@ -33,7 +33,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
 # LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=g++ \
@@ -57,8 +57,6 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 #         -DLIBRI_DIR=$LIBRI \
 #         -DLIBCOMM_DIR=$LIBCOMM \
 # 	      -DDeePMD_DIR=$DEEPMD \
-# 	      -DTensorFlow_DIR=$DEEPMD \
-
 
 # # 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
index 47221825c6..07f1a8f5f4 100755
--- a/toolchain/build_abacus_intel-mpich.sh
+++ b/toolchain/build_abacus_intel-mpich.sh
@@ -31,7 +31,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=icpx \
@@ -53,7 +53,6 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 #       -DLIBRI_DIR=$LIBRI \
 #       -DLIBCOMM_DIR=$LIBCOMM \
 #       -DDeePMD_DIR=$DEEPMD \
-#       -DTensorFlow_DIR=$DEEPMD \
 
 
 # if one want's to include deepmd, your system gcc version should be >= 11.3.0 for glibc requirements
diff --git a/toolchain/build_abacus_intel.sh b/toolchain/build_abacus_intel.sh
index 77071cecd8..e37bb2f666 100755
--- a/toolchain/build_abacus_intel.sh
+++ b/toolchain/build_abacus_intel.sh
@@ -31,7 +31,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
 
 # if use deepks and deepmd
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
@@ -54,7 +54,6 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 #         -DLIBRI_DIR=$LIBRI \
 #         -DLIBCOMM_DIR=$LIBCOMM \
 # 	      -DDeePMD_DIR=$DEEPMD \
-# 	      -DTensorFlow_DIR=$DEEPMD \
 
 
 cmake --build $BUILD_DIR -j `nproc` 

From b17cc349f9f901c7fca8b7c61a6513163fbd75b3 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Mon, 10 Mar 2025 10:50:09 +0800
Subject: [PATCH 19/21] deepmd-v3 add-in test note

---
 toolchain/build_abacus_gnu.sh         | 2 +-
 toolchain/build_abacus_intel-mpich.sh | 2 +-
 toolchain/build_abacus_intel.sh       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/toolchain/build_abacus_gnu.sh b/toolchain/build_abacus_gnu.sh
index 41f86ff41c..03129233a5 100755
--- a/toolchain/build_abacus_gnu.sh
+++ b/toolchain/build_abacus_gnu.sh
@@ -33,7 +33,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
 # LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # v3.0 might have problem
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=g++ \
diff --git a/toolchain/build_abacus_intel-mpich.sh b/toolchain/build_abacus_intel-mpich.sh
index 07f1a8f5f4..6479a7eb2a 100755
--- a/toolchain/build_abacus_intel-mpich.sh
+++ b/toolchain/build_abacus_intel-mpich.sh
@@ -31,7 +31,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # v3.0 might have problem
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=icpx \
diff --git a/toolchain/build_abacus_intel.sh b/toolchain/build_abacus_intel.sh
index e37bb2f666..f780f51f0c 100755
--- a/toolchain/build_abacus_intel.sh
+++ b/toolchain/build_abacus_intel.sh
@@ -31,7 +31,7 @@ RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
 # LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
-# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # can be v3.0
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # v3.0 might have problem
 
 # if use deepks and deepmd
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \

From 2ac981d9d416229e89464d69bbd0b93289e79b63 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Mon, 10 Mar 2025 21:36:54 +0800
Subject: [PATCH 20/21] AMD-AOCC-AOCL update and minor fixed

---
 toolchain/README.md                          | 39 +++++++++-
 toolchain/build_abacus_gnu-aocl.sh           | 82 ++++++++++++++++++++
 toolchain/build_abacus_gnu.sh                |  1 -
 toolchain/build_abacus_intel-mpich.sh        |  3 +-
 toolchain/build_abacus_intel.sh              |  3 +-
 toolchain/install_abacus_toolchain.sh        | 42 ++++++++--
 toolchain/scripts/stage0/install_amd.sh      | 23 ++++--
 toolchain/scripts/stage0/setup_buildtools.sh | 13 +---
 toolchain/scripts/stage2/install_aocl.sh     | 80 +++++++++++++++++--
 toolchain/scripts/stage2/install_mathlibs.sh |  4 +
 toolchain/scripts/stage3/install_elpa.sh     | 32 ++++++++
 toolchain/toolchain_amd.sh                   | 37 +++++++++
 toolchain/toolchain_gnu.sh                   |  7 +-
 toolchain/toolchain_intel-mpich.sh           |  6 +-
 toolchain/toolchain_intel.sh                 |  6 +-
 15 files changed, 330 insertions(+), 48 deletions(-)
 create mode 100755 toolchain/build_abacus_gnu-aocl.sh
 create mode 100755 toolchain/toolchain_amd.sh

diff --git a/toolchain/README.md b/toolchain/README.md
index 461aecd227..7c35a15d4a 100644
--- a/toolchain/README.md
+++ b/toolchain/README.md
@@ -27,7 +27,7 @@ and give setup files that you can use to compile ABACUS.
 - [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)
 - [x] A mirror station by Bohrium database, which can download CEREAL, LibNPY, LibRI and LibComm by `wget` in China Internet. 
 - [x] Support for GPU compilation, users can add `-DUSE_CUDA=1` in builder scripts.
-- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC` (doing)
+- [x] Support for AMD compiler and math lib  `AOCL` and `AOCC` (not fully complete due to flang and AOCC-ABACUS compliation error)
 - [ ] Change the downloading url from cp2k mirror to other mirror or directly downloading from official website. (doing)
 - [ ] Support a JSON or YAML configuration file for toolchain, which can be easily modified by users.
 - [ ] A better README and Detail markdown file.
@@ -50,6 +50,8 @@ There are also well-modified script to run *install_abacus_toolchain.sh* for `gn
 > ./toolchain_gnu.sh
 # for intel-mkl
 > ./toolchain_intel.sh
+# for amd aocc-aocl
+> ./toolchain_amd.sh
 # for intel-mkl-mpich
 > ./toolchain_intel-mpich.sh
 ```
@@ -121,8 +123,12 @@ The needed dependencies version default:
 - `ELPA` 2025.01.001
 - `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)
+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)
+- AMD AOCC-AOCL need user or server manager to manually install from AMD.
+- - [AOCC](https://www.amd.com/zh-cn/developer/aocc.html)
+- - [AOCL](https://www.amd.com/zh-cn/developer/aocl.html)
 
 Dependencies below are optional， which is NOT installed by default:
 
@@ -152,6 +158,8 @@ If compliation is successful, a message will be shown like this:
 >     ./build_abacus_gnu.sh
 > To build ABACUS by intel-toolchain, just use:
 >     ./build_abacus_intel.sh
+> To build ABACUS by amd-toolchain in gcc-aocl, just use:
+>     ./build_abacus_amd.sh
 > or you can modify the builder scripts to suit your needs.
 ```
 
@@ -183,6 +191,14 @@ or you can also do it in a more completely way:
 
 ### Intel-oneAPI problem
 
+#### OneAPI 2025.0 problem
+
+Generally, OneAPI 2025.0 can be useful to compile basic function of ABACUS, but one will encounter compatible problem related to something. Here is the treatment
+- related to rapidjson: 
+- - Not to use rapidjson in your toolchain
+- - or use the master branch of [RapidJSON](https://github.com/Tencent/rapidjson)
+- related to LibRI: not to use LibRI or downgrade your OneAPI.
+
 #### ELPA problem via Intel-oneAPI toolchain in AMD server
 
 The default compiler for Intel-oneAPI is `icpx` and `icx`, which will cause problem when compling ELPA in AMD server. (Which is a problem and needed to have more check-out)
@@ -210,12 +226,27 @@ And will not occur in Intel-MPI before 2021.10.0 (Intel-oneAPI before 2023.2.0)
 
 More problem and possible solution can be accessed via [#2928](https://github.com/deepmodeling/abacus-develop/issues/2928)
 
+### AMD AOCC-AOCL problem
+
+You cannot use AOCC to complie abacus now, see [#5982](https://github.com/deepmodeling/abacus-develop/issues/5982) .
+
+However, use AOCC-AOCL to compile dependencies is permitted and usually get boosting in ABACUS effciency. But you need to get rid of `flang` while compling ELPA. Toolchain itself help you make this `flang` shade in default, and you can manully use `flang` by setting `--with-flang=yes` in `toolchain_amd.sh` to have a try. 
+
+Notice: ABACUS via GCC-AOCL in AOCC-AOCL toolchain have no application with DeePKS, DeePMD and LibRI. 
 
 ### OpenMPI problem
 
 #### in EXX and LibRI
 
-- GCC toolchain with OpenMPI cannot compile LibComm v0.1.1 due to the different MPI variable type from MPICH and IntelMPI, see discussion here [#5033](https://github.com/deepmodeling/abacus-develop/issues/5033), you can switch to GCC-MPICH or Intel toolchain
+- GCC toolchain with OpenMPI cannot compile LibComm v0.1.1 due to the different MPI variable type from MPICH and IntelMPI, see discussion here [#5033](https://github.com/deepmodeling/abacus-develop/issues/5033), you can try use a newest branch of LibComm by 
+```
+git clone https://gitee.com/abacus_dft/LibComm -b MPI_Type_Contiguous_Pool
+``` 
+or pull the newest master branch of LibComm
+```
+git clone https://github.com/abacusmodeling/LibComm
+```
+. yet another is switching to GCC-MPICH or Intel toolchain
 - It is recommended to use Intel toolchain if one wants to include EXX feature in ABACUS, which can have much better performance and can use more than 16 threads in OpenMP parallelization to accelerate the EXX process.
 
 #### OpenMPI-v5 
diff --git a/toolchain/build_abacus_gnu-aocl.sh b/toolchain/build_abacus_gnu-aocl.sh
new file mode 100755
index 0000000000..3ab0ce97fd
--- /dev/null
+++ b/toolchain/build_abacus_gnu-aocl.sh
@@ -0,0 +1,82 @@
+#!/bin/bash
+#SBATCH -J build
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o install.log
+#SBATCH -e install.err
+# JamesMisaka in 2025.03.09
+
+# Build ABACUS by amd-openmpi toolchain
+
+# module load openmpi aocc aocl
+
+ABACUS_DIR=..
+TOOL=$(pwd)
+INSTALL_DIR=$TOOL/install
+source $INSTALL_DIR/setup
+cd $ABACUS_DIR
+ABACUS_DIR=$(pwd)
+#AOCLhome=/opt/aocl  # user can specify this parameter
+
+BUILD_DIR=build_abacus_gnu
+rm -rf $BUILD_DIR
+
+PREFIX=$ABACUS_DIR
+ELPA=$INSTALL_DIR/elpa-2025.01.001/cpu
+CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
+LIBXC=$INSTALL_DIR/libxc-7.0.0
+RAPIDJSON=$INSTALL_DIR/rapidjson-1.1.0/
+# LAPACK=$AOCLhome/lib
+# SCALAPACK=$AOCLhome/lib
+# FFTW3=$AOCLhome
+# LIBRI=$INSTALL_DIR/LibRI-0.2.1.0
+# LIBCOMM=$INSTALL_DIR/LibComm-0.1.1
+# LIBTORCH=$INSTALL_DIR/libtorch-2.1.2/share/cmake/Torch
+# LIBNPY=$INSTALL_DIR/libnpy-1.0.1/include
+# DEEPMD=$HOME/apps/anaconda3/envs/deepmd # v3.0 might have problem
+
+# if clang++ have problem, switch back to g++
+
+cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
+        -DCMAKE_CXX_COMPILER=clang++ \
+        -DMPI_CXX_COMPILER=mpicxx \
+        -DELPA_DIR=$ELPA \
+        -DCEREAL_INCLUDE_DIR=$CEREAL \
+        -DLibxc_DIR=$LIBXC \
+        -DENABLE_LCAO=ON \
+        -DENABLE_LIBXC=ON \
+        -DUSE_OPENMP=ON \
+        -DUSE_ELPA=ON \
+        -DENABLE_RAPIDJSON=ON \
+        -DRapidJSON_DIR=$RAPIDJSON \
+#         -DLAPACK_DIR=$LAPACK \
+#         -DSCALAPACK_DIR=$SCALAPACK \
+#         -DFFTW3_DIR=$FFTW3 \
+#         -DENABLE_DEEPKS=1 \
+#         -DTorch_DIR=$LIBTORCH \
+#         -Dlibnpy_INCLUDE_DIR=$LIBNPY \
+#         -DENABLE_LIBRI=ON \
+#         -DLIBRI_DIR=$LIBRI \
+#         -DLIBCOMM_DIR=$LIBCOMM \
+# 	      -DDeePMD_DIR=$DEEPMD \
+
+# if one want's to include deepmd, your system gcc version should be >= 11.3.0 for glibc requirements
+
+cmake --build $BUILD_DIR -j `nproc` 
+cmake --install $BUILD_DIR 2>/dev/null
+
+# generate abacus_env.sh
+cat << EOF > "${TOOL}/abacus_env.sh"
+#!/bin/bash
+source $INSTALL_DIR/setup
+export PATH="${PREFIX}/bin":\${PATH}
+EOF
+
+# generate information
+cat << EOF
+========================== usage =========================
+Done!
+To use the installed ABACUS version
+You need to source ${TOOL}/abacus_env.sh first !
+"""
+EOF
\ No newline at end of file
diff --git a/toolchain/build_abacus_gnu.sh b/toolchain/build_abacus_gnu.sh
index 03129233a5..27328c7eec 100755
--- a/toolchain/build_abacus_gnu.sh
+++ b/toolchain/build_abacus_gnu.sh
@@ -4,7 +4,6 @@
 #SBATCH -n 16
 #SBATCH -o install.log
 #SBATCH -e install.err
-# install ABACUS with libxc and deepks
 # JamesMisaka in 2025.03.09
 
 # Build ABACUS by gnu-toolchain
diff --git a/toolchain/build_abacus_intel-mpich.sh b/toolchain/build_abacus_intel-mpich.sh
index 6479a7eb2a..59e93967ae 100755
--- a/toolchain/build_abacus_intel-mpich.sh
+++ b/toolchain/build_abacus_intel-mpich.sh
@@ -4,13 +4,12 @@
 #SBATCH -n 16
 #SBATCH -o install.log
 #SBATCH -e install.err
-# build and install ABACUS with libxc, also can with deepks and deepmd
 # JamesMisaka in 2025.03.09
 
 # Build ABACUS by intel-toolchain with mpich
 
 # module load mkl compiler
-# source path/to/vars.sh
+# source path/to/setvars.sh
 
 ABACUS_DIR=..
 TOOL=$(pwd)
diff --git a/toolchain/build_abacus_intel.sh b/toolchain/build_abacus_intel.sh
index f780f51f0c..a2ef7dd8b0 100755
--- a/toolchain/build_abacus_intel.sh
+++ b/toolchain/build_abacus_intel.sh
@@ -4,13 +4,12 @@
 #SBATCH -n 16
 #SBATCH -o install.log
 #SBATCH -e install.err
-# install ABACUS with libxc and deepks
 # JamesMisaka in 2025.03.09
 
 # Build ABACUS by intel-toolchain
 
 # module load mkl compiler mpi
-# source path/to/vars.sh
+# source path/to/setvars.sh
 
 ABACUS_DIR=..
 TOOL=$(pwd)
diff --git a/toolchain/install_abacus_toolchain.sh b/toolchain/install_abacus_toolchain.sh
index 0ee26dd395..2ed465f646 100755
--- a/toolchain/install_abacus_toolchain.sh
+++ b/toolchain/install_abacus_toolchain.sh
@@ -159,6 +159,8 @@ The --with-PKG options follow the rules:
                           Default = yes
   --with-amd              Use the AMD compiler to build CP2K.
                           Default = system
+  --with-flang            Use flang in AMD compiler, which may lead to problem and efficiency loss in ELPA
+                          Default = no
   --with-cmake            Cmake utilities
                           Default = install
   --with-openmpi          OpenMPI, important if you want a parallel version of ABACUS.
@@ -183,6 +185,10 @@ The --with-PKG options follow the rules:
                           it replaces the FFTW library. If the ScaLAPACK component is
                           found, it replaces the one specified by --with-scalapack.
                           Default = system
+  --with-aocl             AMD Optimizing CPU Libraries, which provides LAPACK, BLAS, FFTW, ScaLAPACK
+                          the ScaLAPACK and FFTW can directly use which in AOCL by setting --with-scalapack=system and --with-fftw=system if AOCL in system environment.
+                          related scripts are in development to incorporate scalapack and fftw once for all.
+                          Default = system
   --with-openblas         OpenBLAS is a free high performance LAPACK and BLAS library,
                           the successor to GotoBLAS.
                           Default = install
@@ -238,7 +244,7 @@ EOF
 # ------------------------------------------------------------------------
 tool_list="gcc intel amd cmake"
 mpi_list="mpich openmpi intelmpi"
-math_list="mkl openblas"
+math_list="mkl aocl openblas"
 lib_list="fftw libxc scalapack elpa cereal rapidjson libtorch libnpy libri libcomm"
 package_list="${tool_list} ${mpi_list} ${math_list} ${lib_list}"
 # ------------------------------------------------------------------------
@@ -266,6 +272,9 @@ with_scalapack="__INSTALL__"
 if [ "${MKLROOT}" ]; then
   export MATH_MODE="mkl"
   with_mkl="__SYSTEM__"
+elif [ "${AOCLhome}" ]; then
+  export MATH_MODE="aocl"
+  with_aocl="__SYSTEM__"
 else
   export MATH_MODE="openblas"
 fi
@@ -292,6 +301,7 @@ if (command -v mpiexec > /dev/null 2>&1); then
     echo "MPI is detected and it appears to be Intel MPI"
     with_gcc="__DONTUSE__"
     with_amd="__DONTUSE__"
+    with_aocl="__DONTUSE__"
     with_intel="__SYSTEM__"
     with_intelmpi="__SYSTEM__"
     export MPI_MODE="intelmpi"
@@ -318,10 +328,11 @@ export intel_classic="no"
 # and will lead to problem in force calculation
 # but icx is recommended by intel compiler
 # option: --with-intel-classic can change it to yes/no
-# zhaoqing by 2023.08
+# JamesMisaka by 2023.08
 export intelmpi_classic="no"
-export with_ifx="yes"
-export openmpi_4th="no"
+export with_ifx="yes" # whether ifx is used in oneapi
+export with_flang="no" # whether flang is used in aocc
+export openmpi_4th="no" # whether openmpi downgrade
 export GPUVER="no"
 export MPICH_DEVICE="ch4"
 export TARGET_CPU="native"
@@ -342,6 +353,7 @@ if [ "${CRAY_LD_LIBRARY_PATH}" ]; then
   # set default value for some installers appropriate for CLE
   with_gcc="__DONTUSE__"
   with_amd="__DONTUSE__"
+  with_aocl="__DONTUSE__"
   with_intel="__DONTUSE__"
   with_fftw="__SYSTEM__"
   with_scalapack="__DONTUSE__"
@@ -416,6 +428,12 @@ while [ $# -ge 1 ]; do
         cray)
           export MATH_MODE="cray"
           ;;
+        aocl)
+          export MATH_MODE="aocl"
+          with_aocl="__SYSTEM__"
+          with_fftw="__SYSTEM__"
+          with_scalapack="__SYSTEM__"
+          ;;
         mkl)
           export MATH_MODE="mkl"
           ;;
@@ -424,7 +442,7 @@ while [ $# -ge 1 ]; do
           ;;
         *)
           report_error ${LINENO} \
-            "--math-mode currently only supports mkl, and openblas as options"
+            "--math-mode currently only supports mkl, aocl, openblas and cray as options"
           ;;
       esac
       ;;
@@ -519,9 +537,6 @@ while [ $# -ge 1 ]; do
         export MPI_MODE=intelmpi
       fi
       ;;
-    --with-amd*)
-      with_amd=$(read_with "${1}" "__SYSTEM__")
-      ;;
     --with-intel-classic*)
       intel_classic=$(read_with "${1}" "no") # default new intel compiler
       ;;
@@ -534,6 +549,15 @@ while [ $# -ge 1 ]; do
     --with-ifx*)
       with_ifx=$(read_with "${1}" "yes") # default yes
       ;;
+    --with-amd*)
+      with_amd=$(read_with "${1}" "__SYSTEM__")
+      ;;
+    --with-flang*)
+      with_flang=$(read_with "${1}" "no")
+      ;;
+    --with-aocl*)
+      with_aocl=$(read_with "${1}" "__SYSTEM__")
+      ;;
     --with-libxc*)
       with_libxc=$(read_with "${1}")
       ;;
@@ -864,6 +888,8 @@ To build ABACUS by gnu-toolchain, just use:
     ./build_abacus_gnu.sh
 To build ABACUS by intel-toolchain, just use:
     ./build_abacus_intel.sh
+To build ABACUS by amd-toolchain in gcc-aocl, just use:
+    ./build_abacus_gnu-aocl.sh
 or you can modify the builder scripts to suit your needs.
 """
 EOF
diff --git a/toolchain/scripts/stage0/install_amd.sh b/toolchain/scripts/stage0/install_amd.sh
index 822c001b51..c79aca5381 100755
--- a/toolchain/scripts/stage0/install_amd.sh
+++ b/toolchain/scripts/stage0/install_amd.sh
@@ -33,9 +33,12 @@ case "${with_amd}" in
     echo "==================== Finding AMD compiler from system paths ===================="
     check_command clang "amd" && CC="$(realpath $(command -v clang))" || exit 1
     check_command clang++ "amd" && CXX="$(realpath $(command -v clang++))" || exit 1
-    check_command gfortran "gcc" && FC="gfortran" || exit 1
-    add_lib_from_paths GCC_LDFLAGS "libgfortran.*" ${LIB_PATHS}
-    #check_command flang "amd" && FC="$(realpath $(command -v flang))" || exit 1
+    if [ "${with_flang}" = "yes" ]; then
+        check_command flang "amd" && FC="$(realpath $(command -v flang))" || exit 1
+    else
+        check_command gfortran "gcc" && FC="gfortran" || exit 1
+        add_lib_from_paths GCC_LDFLAGS "libgfortran.*" ${LIB_PATHS}
+    fi
     F90="${FC}"
     F77="${FC}"
     ;;
@@ -50,8 +53,11 @@ case "${with_amd}" in
     check_dir "${pkg_install_dir}/include"
     check_command ${pkg_install_dir}/bin/clang "amd" && CC="${pkg_install_dir}/bin/clang" || exit 1
     check_command ${pkg_install_dir}/bin/clang++ "amd" && CXX="${pkg_install_dir}/bin/clang++" || exit 1
-    check_command gfortran "gcc" && FC="$(command -v gfortran)" || exit 1
-    #check_command ${pkg_install_dir}/bin/flang "amd" && FC="${pkg_install_dir}/bin/flang" || exit 1
+    if [ "${with_flang}" = "yes" ]; then
+        check_command ${pkg_install_dir}/bin/flang "amd" && FC="${pkg_install_dir}/bin/flang" || exit 1
+    else
+        check_command gfortran "gcc" && FC="$(command -v gfortran)" || exit 1
+    fi
     F90="${FC}"
     F77="${FC}"
     AMD_CFLAGS="-I'${pkg_install_dir}/include'"
@@ -64,8 +70,11 @@ if [ "${with_amd}" != "__DONTUSE__" ]; then
   echo "CXX is ${CXX}"
   [ $(realpath $(command -v clang++) | grep -e aocc-compiler) ] || echo "Check the AMD C++ compiler path"
   echo "FC  is ${FC}"
-  #[ $(realpath $(command -v flang) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
-  [ $(realpath $(command -v gfortran) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
+  if [ "${with_flang}" = "yes" ]; then
+    [ $(realpath $(command -v flang) | grep -e aocc-compiler) ] || echo "Check the AMD Fortran compiler path"
+  else
+    [ $(realpath $(command -v gfortran) | grep -e aocc-compiler) ] || echo "Check the GNU Fortran compiler path"
+  fi
   cat << EOF > "${BUILDDIR}/setup_amd"
 export CC="${CC}"
 export CXX="${CXX}"
diff --git a/toolchain/scripts/stage0/setup_buildtools.sh b/toolchain/scripts/stage0/setup_buildtools.sh
index b5e27d178d..924282ed41 100755
--- a/toolchain/scripts/stage0/setup_buildtools.sh
+++ b/toolchain/scripts/stage0/setup_buildtools.sh
@@ -3,7 +3,7 @@
 # TODO: Review and if possible fix shellcheck errors.
 # shellcheck disable=all
 
-# Last Update in 2023-0901
+# Last Update in 2025-0310
 
 [ "${BASH_SOURCE[0]}" ] && SCRIPT_NAME="${BASH_SOURCE[0]}" || SCRIPT_NAME=$0
 SCRIPT_DIR="$(cd "$(dirname "${SCRIPT_NAME}")/.." && pwd -P)"
@@ -27,22 +27,15 @@ if [ "${with_intel}" != "__DONTUSE__" ]; then
   CFLAGS="-O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback"
   if [ "${TARGET_CPU}" = "native" ]; then
     CFLAGS="${CFLAGS} -xHost"
-  elif [ "${TARGET_CPU}" = "generic" ]; then
-    CFLAGS="${CFLAGS} -mtune=${TARGET_CPU}"
   else
-    CFLAGS="${CFLAGS} -march=${TARGET_CPU} -mtune=${TARGET_CPU}"
+    CFLAGS="${CFLAGS} -mtune=${TARGET_CPU}"
   fi
   FFLAGS="${CFLAGS}"
 elif [ "${with_amd}" != "__DONTUSE__" ]; then
   CFLAGS="-O2 -fPIC -fopenmp -g -mtune=${TARGET_CPU}"
   FFLAGS="${CFLAGS}"
 else
-  CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g"
-  if [ "${TARGET_CPU}" = "generic" ]; then
-    CFLAGS="${CFLAGS} -mtune=generic ${TSANFLAGS}"
-  else
-    CFLAGS="${CFLAGS} -march=${TARGET_CPU} -mtune=${TARGET_CPU} ${TSANFLAGS}"
-  fi
+  CFLAGS="-O2 -fPIC -fno-omit-frame-pointer -fopenmp -g -mtune=${TARGET_CPU} ${TSANFLAGS}"
   FFLAGS="${CFLAGS} -fbacktrace"
 fi
 CXXFLAGS="${CFLAGS}"
diff --git a/toolchain/scripts/stage2/install_aocl.sh b/toolchain/scripts/stage2/install_aocl.sh
index bd36ff9541..b6c61a6c52 100644
--- a/toolchain/scripts/stage2/install_aocl.sh
+++ b/toolchain/scripts/stage2/install_aocl.sh
@@ -14,15 +14,79 @@ source "${SCRIPT_DIR}"/signal_trap.sh
 source "${INSTALLDIR}"/toolchain.conf
 source "${INSTALLDIR}"/toolchain.env
 
-[ -f "${BUILDDIR}/setup_mkl" ] && rm "${BUILDDIR}/setup_mkl"
-
-MKL_CFLAGS=""
-MKL_LDFLAGS=""
-MKL_LIBS=""
-MKL_FFTW="yes"
+[ -f "${BUILDDIR}/setup_aocl" ] && rm "${BUILDDIR}/setup_aocl"
 
+AOCL_CFLAGS=""
+AOCL_LDFLAGS=""
+AOCL_LIBS=""
+AOCL_ROOT=""
 ! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}"
 cd "${BUILDDIR}"
 
-# Not Completed
-# Only need to deal with LAPACK in AOCL, ScaLAPACK and FFTW can use other scripts
\ No newline at end of file
+case "${with_aocl}" in
+  __INSTALL__)
+    echo "==================== Installing AOCL ===================="
+    report_error ${LINENO} "To install AOCL, please contact your system administrator."
+    exit 1
+    ;;
+  __SYSTEM__)
+    echo "==================== Finding AOCL from system paths ===================="
+    check_lib -lblis "AOCL"
+    check_lib -lframe "AOCL"
+    AOCL_LIBS="-lblis -lflame"
+    add_include_from_paths AOCL_CFLAGS "blis.h" $INCLUDE_PATHS
+    add_lib_from_paths AOCL_LDFLAGS "libblis.*" $LIB_PATHS
+    add_include_from_paths AOCL_CFLAGS "lapack.h" $INCLUDE_PATHS
+    add_lib_from_paths AOCL_LDFLAGS "libflame.*" $LIB_PATHS
+    ;;
+  __DONTUSE__) ;;
+
+  *)
+    echo "==================== Linking AOCL to user paths ===================="
+    pkg_install_dir="$with_openblas"
+    check_dir "${pkg_install_dir}/include"
+    check_dir "${pkg_install_dir}/lib"
+    AOCL_CFLAGS="-I'${pkg_install_dir}/include'"
+    AOCL_LDFLAGS="-L'${pkg_install_dir}/lib' -Wl,-rpath,'${pkg_install_dir}/lib'"
+    AOCL_LIBS="-lblis -lflame"
+    ;;
+esac
+if [ "$with_openblas" != "__DONTUSE__" ]; then
+  if [ "$with_openblas" != "__SYSTEM__" ]; then
+    cat << EOF > "${BUILDDIR}/setup_aocl"
+prepend_path LD_LIBRARY_PATH "$pkg_install_dir/lib"
+prepend_path LD_RUN_PATH "$pkg_install_dir/lib"
+prepend_path LIBRARY_PATH "$pkg_install_dir/lib"
+prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
+prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
+prepend_path CPATH "$pkg_install_dir/include"
+export LD_LIBRARY_PATH="$pkg_install_dir/lib:"\${LD_LIBRARY_PATH}
+export LD_RUN_PATH="$pkg_install_dir/lib:"\${LD_RUN_PATH}
+export LIBRARY_PATH="$pkg_install_dir/lib:"\${LIBRARY_PATH}
+export CPATH="$pkg_install_dir/include:"\${CPATH}
+export PKG_CONFIG_PATH="$pkg_install_dir/lib/pkgconfig:"\${PKG_CONFIG_PATH}
+export CMAKE_PREFIX_PATH="$pkg_install_dir:"\${CMAKE_PREFIX_PATH}
+export AOCL_ROOT=${pkg_install_dir}
+EOF
+    cat "${BUILDDIR}/setup_aocl" >> $SETUPFILE
+  fi
+  cat << EOF >> "${BUILDDIR}/setup_aocl"
+export AOCL_ROOT="${pkg_install_dir}"
+export AOCL_CFLAGS="${AOCL_CFLAGS}"
+export AOCL_LDFLAGS="${AOCL_LDFLAGS}"
+export AOCL_LIBS="${AOCL_LIBS}"
+export MATH_CFLAGS="\${MATH_CFLAGS} ${AOCL_CFLAGS}"
+export MATH_LDFLAGS="\${MATH_LDFLAGS} ${AOCL_LDFLAGS}"
+export MATH_LIBS="\${MATH_LIBS} ${AOCL_LIBS}"
+export PKG_CONFIG_PATH="${pkg_install_dir}/lib/pkgconfig"
+export CMAKE_PREFIX_PATH="${pkg_install_dir}"
+prepend_path PKG_CONFIG_PATH "$pkg_install_dir/lib/pkgconfig"
+prepend_path CMAKE_PREFIX_PATH "$pkg_install_dir"
+EOF
+fi
+
+load "${BUILDDIR}/setup_aocl"
+write_toolchain_env "${INSTALLDIR}"
+
+cd "${ROOTDIR}"
+report_timing "aocl"
\ No newline at end of file
diff --git a/toolchain/scripts/stage2/install_mathlibs.sh b/toolchain/scripts/stage2/install_mathlibs.sh
index ed78957882..3ad3aef336 100755
--- a/toolchain/scripts/stage2/install_mathlibs.sh
+++ b/toolchain/scripts/stage2/install_mathlibs.sh
@@ -25,6 +25,10 @@ case "$MATH_MODE" in
     "${SCRIPTDIR}"/stage2/install_mkl.sh "${with_mkl}"
     load "${BUILDDIR}/setup_mkl"
     ;;
+  aocl)
+    "${SCRIPTDIR}"/stage2/install_aocl.sh "${with_aocl}"
+    load "${BUILDDIR}/setup_aocl"
+    ;;
   openblas)
     "${SCRIPTDIR}"/stage2/install_openblas.sh "${with_openblas}"
     load "${BUILDDIR}/setup_openblas"
diff --git a/toolchain/scripts/stage3/install_elpa.sh b/toolchain/scripts/stage3/install_elpa.sh
index 7698530bbb..01e7980810 100755
--- a/toolchain/scripts/stage3/install_elpa.sh
+++ b/toolchain/scripts/stage3/install_elpa.sh
@@ -104,6 +104,37 @@ case "$with_elpa" in
 
         mkdir -p "build_${TARGET}"
         cd "build_${TARGET}"
+        if [ "${with_amd}" != "__DONTUSE__" ]; then
+        echo "AMD compiler detected, enable special option operation"
+        ../configure --prefix="${pkg_install_dir}/${TARGET}/" \
+          --libdir="${pkg_install_dir}/${TARGET}/lib" \
+          --enable-openmp=${enable_openmp} \
+          --enable-shared=yes \
+          --enable-static=yes \
+          --disable-c-tests \
+          --disable-cpp-tests \
+          ${config_flags} \
+          --enable-nvidia-gpu-kernels=$([ "$TARGET" = "nvidia" ] && echo "yes" || echo "no") \
+          --with-cuda-path=${CUDA_PATH:-${CUDA_HOME:-/CUDA_HOME-notset}} \
+          --with-NVIDIA-GPU-compute-capability=$([ "$TARGET" = "nvidia" ] && echo "sm_$ARCH_NUM" || echo "sm_75") \
+          CUDA_CFLAGS="-std=c++14 -allow-unsupported-compiler" \
+          OMPI_MCA_plm_rsh_agent=/bin/false \
+          FC=${MPIFC} \
+          CC=${MPICC} \
+          CXX=${MPICXX} \
+          CPP="cpp -E" \
+          FCFLAGS="${FCFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
+          CFLAGS="${CFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
+          CXXFLAGS="${CXXFLAGS} ${MATH_CFLAGS} ${SCALAPACK_CFLAGS} ${AVX_flag} ${FMA_flag} ${SSE4_flag} ${AVX512_flags} -fno-lto" \
+          LDFLAGS="${MATH_LDFLAGS} ${SCALAPACK_LDFLAGS} ${cray_ldflags} -lstdc++" \
+          LIBS="${SCALAPACK_LIBS} $(resolve_string "${MATH_LIBS}" "MPI")" \
+          > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
+          # remove unsupported compile option in libtool
+          sed -i ./libtool \
+          -e 's/\\$wl-soname //g' \
+          -e 's/\\$wl--whole-archive\\$convenience \\$wl--no-whole-archive//g' \
+          -e 's/\\$wl\\$soname //g'
+        else
         ../configure --prefix="${pkg_install_dir}/${TARGET}/" \
           --libdir="${pkg_install_dir}/${TARGET}/lib" \
           --enable-openmp=${enable_openmp} \
@@ -127,6 +158,7 @@ case "$with_elpa" in
           LDFLAGS="-Wl,--allow-multiple-definition -Wl,--enable-new-dtags ${MATH_LDFLAGS} ${SCALAPACK_LDFLAGS} ${cray_ldflags} -lstdc++" \
           LIBS="${SCALAPACK_LIBS} $(resolve_string "${MATH_LIBS}" "MPI")" \
           > configure.log 2>&1 || tail -n ${LOG_LINES} configure.log
+        fi
         make -j $(get_nprocs) > make.log 2>&1 || tail -n ${LOG_LINES} make.log
         make install > install.log 2>&1 || tail -n ${LOG_LINES} install.log
         cd ..
diff --git a/toolchain/toolchain_amd.sh b/toolchain/toolchain_amd.sh
new file mode 100755
index 0000000000..b8055176c6
--- /dev/null
+++ b/toolchain/toolchain_amd.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+#SBATCH -J install
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o compile.log
+#SBATCH -e compile.err
+
+# JamesMisaka in 2023-09-16
+# install abacus dependency by gnu-toolchain
+# one can use mpich or openmpi.
+# openmpi will be faster, but not compatible in some cases.
+# libtorch and libnpy are for deepks support, which can be =no
+# if you want to run EXX calculation, you should set --with-libri=install
+# mpich (and intel toolchain) is recommended for EXX support
+
+./install_abacus_toolchain.sh \
+--with-amd=system \
+--math-mode=aocl \
+--with-intel=no \
+--with-gcc=no \
+--with-openmpi=install \
+--with-cmake=install \
+--with-scalapack=system \
+--with-libxc=install \
+--with-fftw=system \
+--with-elpa=install \
+--with-cereal=install \
+--with-rapidjson=install \
+--with-libtorch=no \
+--with-libnpy=no \
+--with-libri=no \
+--with-libcomm=no \
+--with-4th-openmpi=no \
+--with-flang=no \
+| tee compile.log
+# if you want to use openmpi-version4: set --with-4th-openmpi=yes
+# flang is not recommended to use in this stage
\ No newline at end of file
diff --git a/toolchain/toolchain_gnu.sh b/toolchain/toolchain_gnu.sh
index 68f559128e..bf5be6a129 100755
--- a/toolchain/toolchain_gnu.sh
+++ b/toolchain/toolchain_gnu.sh
@@ -13,8 +13,11 @@
 # if you want to run EXX calculation, you should set --with-libri=install
 # mpich (and intel toolchain) is recommended for EXX support
 
-./install_abacus_toolchain.sh --with-openmpi=install \
---with-intel=no --with-gcc=system \
+./install_abacus_toolchain.sh \
+--with-gcc=system \
+--with-intel=no \
+--with-openblas=install \
+--with-openmpi=install \
 --with-cmake=install \
 --with-scalapack=install \
 --with-libxc=install \
diff --git a/toolchain/toolchain_intel-mpich.sh b/toolchain/toolchain_intel-mpich.sh
index 059ef541dd..1f50679f1a 100755
--- a/toolchain/toolchain_intel-mpich.sh
+++ b/toolchain/toolchain_intel-mpich.sh
@@ -13,8 +13,10 @@
 # module load mkl compiler
 
 ./install_abacus_toolchain.sh \
---with-intel=system --math-mode=mkl \
---with-gcc=no --with-mpich=install \
+--with-intel=system \
+--math-mode=mkl \
+--with-gcc=no \
+--with-mpich=install \
 --with-cmake=install \
 --with-scalapack=no \
 --with-libxc=install \
diff --git a/toolchain/toolchain_intel.sh b/toolchain/toolchain_intel.sh
index e5298c570d..d12afc919d 100755
--- a/toolchain/toolchain_intel.sh
+++ b/toolchain/toolchain_intel.sh
@@ -14,8 +14,10 @@
 # module load mkl mpi compiler
 
 ./install_abacus_toolchain.sh \
---with-intel=system --math-mode=mkl \
---with-gcc=no --with-intelmpi=system \
+--with-intel=system \
+--math-mode=mkl \
+--with-gcc=no \
+--with-intelmpi=system \
 --with-cmake=install \
 --with-scalapack=no \
 --with-libxc=install \

From 20c4c8d850f369383c939df4f8717733e9e516c7 Mon Sep 17 00:00:00 2001
From: JamesMisaka <ff6757442@gmail.com>
Date: Mon, 10 Mar 2025 22:26:53 +0800
Subject: [PATCH 21/21] fix bug in aocl.sh

---
 toolchain/scripts/stage2/install_aocl.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 toolchain/scripts/stage2/install_aocl.sh

diff --git a/toolchain/scripts/stage2/install_aocl.sh b/toolchain/scripts/stage2/install_aocl.sh
old mode 100644
new mode 100755
index b6c61a6c52..51bcc8c4dd
--- a/toolchain/scripts/stage2/install_aocl.sh
+++ b/toolchain/scripts/stage2/install_aocl.sh
@@ -32,7 +32,7 @@ case "${with_aocl}" in
   __SYSTEM__)
     echo "==================== Finding AOCL from system paths ===================="
     check_lib -lblis "AOCL"
-    check_lib -lframe "AOCL"
+    check_lib -lflame "AOCL"
     AOCL_LIBS="-lblis -lflame"
     add_include_from_paths AOCL_CFLAGS "blis.h" $INCLUDE_PATHS
     add_lib_from_paths AOCL_LDFLAGS "libblis.*" $LIB_PATHS
@@ -89,4 +89,4 @@ load "${BUILDDIR}/setup_aocl"
 write_toolchain_env "${INSTALLDIR}"
 
 cd "${ROOTDIR}"
-report_timing "aocl"
\ No newline at end of file
+report_timing "aocl"