Toolchain 202501

.gitignore

@@ -17,7 +17,6 @@ STRU_READIN_ADJUST.cif
 build
 dist
 .idea
-toolchain.tar.gz
 time.json
 *.pyc
 __pycache__

toolchain/README.md

@@ -1,6 +1,6 @@
 # The ABACUS Toolchain
 
-Version 2024.3
+Version 2025.1
 
 ## Author
 
@@ -27,12 +27,13 @@ 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.
+- [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.
 - [ ] 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
@@ -49,6 +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
 ```
@@ -94,7 +97,7 @@ 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
@@ -109,19 +112,23 @@ 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` 4.3.0
 - `OpenBLAS` 0.3.28 (Intel toolchain need `get_vars.sh` tool from it)
 - `ScaLAPACK` 2.2.1 (a developing version)
 - `FFTW` 3.3.10
-- `LibXC` 6.2.2
-- `ELPA` 2024.05.001
+- `LibXC` 7.0.0
+- `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:
 
@@ -130,7 +137,7 @@ 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
@@ -151,6 +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.
 ```
 
@@ -180,11 +189,70 @@ or you can also do it in a more completely way:
 
 ## Common Problems and Solutions
 
-### LibRI and LibComm for EXX
+### 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)
+
+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)
+
+### 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. 
 
-- 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
+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 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 
+
+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 +310,6 @@ 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
 

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

toolchain/build_abacus_gnu.sh

@@ -4,8 +4,7 @@
 #SBATCH -n 16
 #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
 
@@ -24,16 +23,16 @@ 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=$INSTALL_DIR/LibComm-0.1.1
 # LIBTORCH=$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 # v3.0 might have problem
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=g++ \
@@ -57,8 +56,6 @@ 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

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 2023.08.31
+# 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)
@@ -23,15 +22,15 @@ 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=$INSTALL_DIR/libnpy-1.0.1/include
 # LIBRI=$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 # v3.0 might have problem
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DCMAKE_CXX_COMPILER=icpx \
@@ -53,7 +52,6 @@ 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