Merge branch 'develop' into hotfix

docs/advanced/input_files/input-main.md

@@ -438,7 +438,7 @@ These variables are used to control general system parameters.
 - **Description**: Control how to deal with error in symmetry analysis due to inaccurate lattice parameters or atom positions in STRU file, especially useful when *[calculation](#calculation)==cell-relax*
   - False: quit with an error message
   - True: automatically set symmetry to 0 and continue running without symmetry analysis
-- **Default**: False
+- **Default**: True
 
 ### kpar
 

source/module_io/input.cpp

@@ -211,7 +211,7 @@ void Input::Default(void)
     init_vel = false;
     ref_cell_factor = 1.0;
     symmetry_prec = 1.0e-6; // LiuXh add 2021-08-12, accuracy for symmetry
-    symmetry_autoclose = false; // whether to close symmetry automatically when error occurs in symmetry analysis
+    symmetry_autoclose = true; // whether to close symmetry automatically when error occurs in symmetry analysis
     cal_force = 0;
     force_thr = 1.0e-3;
     force_thr_ev2 = 0;

source/module_io/test/input_test.cpp

@@ -89,7 +89,7 @@ TEST_F(InputTest, Default)
         EXPECT_FALSE(INPUT.init_vel);
         EXPECT_DOUBLE_EQ(INPUT.ref_cell_factor,1.0);
         EXPECT_DOUBLE_EQ(INPUT.symmetry_prec, 1.0e-6);
-        EXPECT_FALSE(INPUT.symmetry_autoclose);
+        EXPECT_TRUE(INPUT.symmetry_autoclose);
         EXPECT_EQ(INPUT.cal_force, 0);
         EXPECT_DOUBLE_EQ(INPUT.force_thr,1.0e-3);
         EXPECT_DOUBLE_EQ(INPUT.force_thr_ev2,0);
@@ -445,8 +445,8 @@ TEST_F(InputTest, Read)
         EXPECT_TRUE(INPUT.search_pbc);
         EXPECT_EQ(INPUT.symmetry,"1");
         EXPECT_FALSE(INPUT.init_vel);
-        EXPECT_DOUBLE_EQ(INPUT.symmetry_prec, 1.0e-5);
-        EXPECT_FALSE(INPUT.symmetry_autoclose);
+        EXPECT_DOUBLE_EQ(INPUT.symmetry_prec, 1.0e-6);
+        EXPECT_TRUE(INPUT.symmetry_autoclose);
         EXPECT_EQ(INPUT.cal_force, 0);
         EXPECT_NEAR(INPUT.force_thr,1.0e-3,1.0e-7);
         EXPECT_DOUBLE_EQ(INPUT.force_thr_ev2,0);

source/module_io/test/input_test_para.cpp

@@ -95,7 +95,7 @@ TEST_F(InputParaTest,Bcast)
         EXPECT_EQ(INPUT.symmetry,"default");
         EXPECT_FALSE(INPUT.init_vel);
         EXPECT_DOUBLE_EQ(INPUT.symmetry_prec, 1.0e-6);
-        EXPECT_FALSE(INPUT.symmetry_autoclose);
+        EXPECT_TRUE(INPUT.symmetry_autoclose);
         EXPECT_EQ(INPUT.cal_force, 0);
         EXPECT_DOUBLE_EQ(INPUT.force_thr,1.0e-3);
         EXPECT_DOUBLE_EQ(INPUT.force_thr_ev2,0);

source/module_io/test/support/INPUT

@@ -22,7 +22,7 @@ nbands_sto                     256 #number of stochastic bands
 nbands_istate                  5 #number of bands around Fermi level for get_pchg calulation
 symmetry                       1 #the control of symmetry
 init_vel                       False #read velocity from STRU or not
-symmetry_prec                  1e-05 #accuracy for symmetry
+symmetry_prec                  1e-06 #accuracy for symmetry
 nelec                          0 #input number of electrons
 out_mul                        0 # mulliken  charge or not
 noncolin                       0 #using non-collinear-spin

source/module_io/test/write_input_test.cpp

@@ -72,7 +72,7 @@ TEST_F(write_input, General1)
     EXPECT_THAT(output, testing::HasSubstr("init_vel                       0 #read velocity from STRU or not"));
     EXPECT_THAT(output, testing::HasSubstr("symmetry_prec                  1e-05 #accuracy for symmetry"));
     EXPECT_THAT(output,
-                testing::HasSubstr("symmetry_autoclose             0 #whether to close symmetry automatically when "
+                testing::HasSubstr("symmetry_autoclose             1 #whether to close symmetry automatically when "
                                    "error occurs in symmetry analysis"));
     EXPECT_THAT(output, testing::HasSubstr("nelec                          0 #input number of electrons"));
     EXPECT_THAT(output, testing::HasSubstr("out_mul                        0 # mulliken  charge or not"));

toolchain/README.md

@@ -1,5 +1,5 @@
 # The ABACUS Toolchain
-Version 2023.4
+Version 2023.5
 
 ## Author
 [QuantumMisaka](https://github.com/QuantumMisaka) 
@@ -31,14 +31,16 @@ and give setup files that you can use to compile ABACUS.
 - [ ] Better compliation method for ABACUS-DEEPMD and ABACUS-DEEPKS.
 - [ ] A better `setup` and toolchain code structure.
 - [ ] Modulefile generation scripts.
-- [ ] Support for `acml` toolchain (scripts are partly in toolchain now) or other AMD compiler and math lib like `AOCL` and `AOCC`
+- [ ] Support for AMD compiler and math lib like `AOCL` and `AOCC`
 
 
 ## Usage Online & Offline
 Main script is `install_abacus_toolchain.sh`, 
 which will use scripts in `scripts` directory 
 to compile install dependencies of ABACUS.
 
+You can just `./install_abacus_toolchain.sh -h` to get more help message.
+
 **Notice: You SHOULD `source` or `module load` related environments before use toolchain method for installation, espacially for `gcc` or `intel-oneAPI` !!!! for example, `module load mkl mpi icc compiler`**
 
 **Notice: You SHOULD keep your environments systematic, for example, you CANNOT load `intel-OneAPI` environments while use gcc toolchain !!!**
@@ -51,7 +53,7 @@ to compile install dependencies of ABACUS.
 
 All packages will be downloaded from [cp2k-static/download](https://www.cp2k.org/static/downloads). by  `wget` , and will be detailedly compiled and installed in `install` directory by toolchain scripts, despite of:
 - `CEREAL` which will be downloaded from [CEREAL](https://github.com/USCiLab/cereal)  
-- `LibNPY` which will be downloaded from [LIBNPY](https://github.com/llohse/libnpy)
+- `Libnpy` which will be downloaded from [LIBNPY](https://github.com/llohse/libnpy)
 - `LibRI` which will be downloaded from [LibRI](https://github.com/abacusmodeling/LibRI)
 - `LibCOMM` which will be downloaded from [LibComm](https://github.com/abacusmodeling/LibComm)
 Notice: These packages will be downloaded by `wget` from `github.com`, which is hard to be done in Chinese Internet. You may need to use offline installation method. 
@@ -78,7 +80,28 @@ just by using this toolchain
 > cp ***.tar.gz build/
 ```
 
-Notice: for `CEREAL`, `LibNPY`, `LibRI` and `LibCOMM`, 
+The needed dependencies version default:
+- `cmake` 3.27.6
+- `gcc` 13.2.0 (which will always NOT be installed, But use system)
+- `OpenMPI` 4.1.5
+- `MPICH` 4.1.2
+- `OpenBLAS` 0.3.24 (Intel toolchain need `get_vars.sh` tool from it)
+- `ScaLAPACK` 2.2.1
+- `FFTW` 3.3.10
+- `LibXC` 6.2.2
+- `ELPA` 2023.05.001
+- `CEREAL` 1.3.2
+And Intel-oneAPI need user or server manager to manually install from Intel.
+[Intel-oneAPI](https://www.intel.cn/content/www/cn/zh/developer/tools/oneapi/toolkits.html)
+
+Dependencies below are optional， which is NOT installed by default:
+- `LibTorch` 2.0.1
+- `Libnpy` 0.1.0
+- `LibRI` 0.1.0
+- `LibComm` 0.1.0
+Users can install them by using `--with-*=install` in toolchain*.sh, which is `no` in default.
+
+Notice: for `CEREAL`, `Libnpy`, `LibRI` and `LibComm`, 
 you need to download them from github.com, 
 rename it as formatted, and put them in `build` directory at the same time
 e.g.:
@@ -118,7 +141,7 @@ If compliation is successful, a message will be shown like this:
 >     ./build_abacus_intel.sh
 > or you can modify the builder scripts to suit your needs.
 ```
-You can run build_abacus_gnu.sh or build_abacus_intel.sh to build ABACUS 
+You can run `build_abacus_gnu.sh` or `build_abacus_intel.sh` to build ABACUS 
 by gnu-toolchain or intel-toolchain respectively, the builder scripts will
 automatically locate the environment and compile ABACUS.
 You can manually change the builder scripts to suit your needs.
@@ -139,13 +162,20 @@ or you can also do it in a more completely way:
 > rm -rf install build/*/* build/OpenBLAS*/ build/setup_*
 ```
 
-Users can get help messages by simply:
+## Common Problem and Solution
+### GPU version of ABACUS
+add following options in build*.sh:
 ```shell
-> ./install_abacus_toolchain.sh -h # or --help
+cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
+        -DCMAKE_CXX_COMPILER=icpx \
+        -DMPI_CXX_COMPILER=mpiicpc \
+        ......
+        -DUSE_CUDA=1 \
+        -DCMAKE_CUDA_COMPILER=${path to cuda toolkit}/bin/nvcc \
+        ......
 ```
 
-
-## Common Problem and Solution
+### shell problem
 If you encounter problem like:
 ```shell
 /bin/bash^M: bad interpreter: No such file or directory
@@ -157,6 +187,36 @@ or   `permission denied` problem, you can simply run:
 And also, you can fix `permission denied` problem via `chmod +x`
 if `pre_set.sh` have no execution permission.
 
+### libtorch and deepks problem
+If deepks feature have problem, you can manually change libtorch version
+from 2.0.1 to 1.12.0 in `toolchain/scripts/stage4/install_libtorch.sh`.
+Also, you can install ABACUS without deepks by removing all the deepks and related options.
+
+NOTICE: if you want deepks feature, your intel-mkl environment should be accessible in building process. you can check it in `build_abacus_gnu.sh`
+
+### deepmd feature problem
+When you encounter problem like `GLIBCXX_3.4.29 not found`, it is sure that your `gcc` version is lower than the requirement of `libdeepmd`.
+
+After my test, you need `gcc`>11.3.1 to enable deepmd feature in ABACUS.
+
+### 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.
+
+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`
+
+
+### LibRI and LibComm problem
+(There is some problem sometimes when compling with LibRI and LibComm, detailed information is needed)
+
+
+### Intel-oneAPI problem
+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.
+
+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.sh

@@ -18,13 +18,13 @@ source $INSTALL_DIR/setup
 cd $ABACUS_DIR
 ABACUS_DIR=$(pwd)
 
-BUILD_DIR=build_abacus
+BUILD_DIR=build_abacus_gnu
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-LAPACK=$INSTALL_DIR/openblas-0.3.23/lib
+LAPACK=$INSTALL_DIR/openblas-0.3.24/lib
 SCALAPACK=$INSTALL_DIR/scalapalack-2.2.1/lib
-ELPA=$INSTALL_DIR/elpa-2021.11.002/cpu
+ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
 FFTW3=$INSTALL_DIR/fftw-3.3.10
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
@@ -46,7 +46,6 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LCAO=ON \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
-        -DENABLE_ASAN=OFF \
         -DUSE_ELPA=ON \
 #         -DENABLE_DEEPKS=1 \
 #         -DTorch_DIR=$LIBTORCH \
@@ -58,12 +57,14 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
 # 	      -DTensorFlow_DIR=$DEEPMD \
 
 # # add mkl env for libtorch to link
-# # gnu-toolchain will lack of -lmkl when load libtorch
-# # need to fix -- zhaoqing in 2023-09-02
+# if one want to install libtorch, mkl should be load in build process
+# for -lmkl when load libtorch
 # module load mkl
 
+# if one want's to include deepmd, your gcc version should be >= 11.3.0
+
 cmake --build $BUILD_DIR -j `nproc` 
-cmake --install $BUILD_DIR 
+cmake --install $BUILD_DIR 2>/dev/null
 
 # generate abacus_env.sh
 cat << EOF > "${TOOL}/abacus_env.sh"

toolchain/build_abacus_intel-mpich.sh

@@ -4,7 +4,7 @@
 #SBATCH -n 16
 #SBATCH -o install.log
 #SBATCH -e install.err
-# install ABACUS with libxc and deepks
+# build and install ABACUS with libxc, also can with deepks and deepmd
 # JamesMisaka in 2023.08.31
 
 # Build ABACUS by intel-toolchain with mpich
@@ -19,21 +19,21 @@ source $INSTALL_DIR/setup
 cd $ABACUS_DIR
 ABACUS_DIR=$(pwd)
 
-BUILD_DIR=build_abacus
+BUILD_DIR=build_abacus_intel-mpich
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2021.11.002/cpu
+ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
-LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
-LIBNPY=$INSTALL_DIR/libnpy-0.1.0/include
+# LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
+# LIBNPY=$INSTALL_DIR/libnpy-0.1.0/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
 # DEEPMD=$HOME/apps/anaconda3/envs/deepmd
 
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
-        -DCMAKE_CXX_COMPILER=icpc \
+        -DCMAKE_CXX_COMPILER=icpx \
         -DMPI_CXX_COMPILER=mpicxx \
         -DMKLROOT=$MKLROOT \
         -DELPA_DIR=$ELPA \
@@ -42,19 +42,20 @@ cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
         -DENABLE_LCAO=ON \
         -DENABLE_LIBXC=ON \
         -DUSE_OPENMP=ON \
-        -DENABLE_ASAN=OFF \
         -DUSE_ELPA=ON \
-        -DENABLE_DEEPKS=1 \
-        -DTorch_DIR=$LIBTORCH \
-        -Dlibnpy_INCLUDE_DIR=$LIBNPY \
+        # -DENABLE_DEEPKS=1 \
+        # -DTorch_DIR=$LIBTORCH \
+        # -Dlibnpy_INCLUDE_DIR=$LIBNPY \
         # -DENABLE_LIBRI=ON \
         # -DLIBRI_DIR=$LIBRI \
         # -DLIBCOMM_DIR=$LIBCOMM \
 	    # -DDeePMD_DIR=$DEEPMD \
 	    # -DTensorFlow_DIR=$DEEPMD \
 
+# if one want's to include deepmd, your gcc version should be >= 11.3.0
+
 cmake --build $BUILD_DIR -j `nproc` 
-cmake --install $BUILD_DIR 
+cmake --install $BUILD_DIR 2>/dev/null
 
 # generate abacus_env.sh
 cat << EOF > "${TOOL}/abacus_env.sh"

toolchain/build_abacus_intel.sh

@@ -19,44 +19,44 @@ source $INSTALL_DIR/setup
 cd $ABACUS_DIR
 ABACUS_DIR=$(pwd)
 
-BUILD_DIR=build_abacus
+BUILD_DIR=build_abacus_intel
 rm -rf $BUILD_DIR
 
 PREFIX=$ABACUS_DIR
-ELPA=$INSTALL_DIR/elpa-2021.11.002/cpu
+ELPA=$INSTALL_DIR/elpa-2023.05.001/cpu
 CEREAL=$INSTALL_DIR/cereal-1.3.2/include/cereal
 LIBXC=$INSTALL_DIR/libxc-6.2.2
-LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
-LIBNPY=$INSTALL_DIR/libnpy-0.1.0/include
+# LIBTORCH=$INSTALL_DIR/libtorch-2.0.1/share/cmake/Torch
+# LIBNPY=$INSTALL_DIR/libnpy-0.1.0/include
 # LIBRI=$INSTALL_DIR/LibRI-0.1.0
 # LIBCOMM=$INSTALL_DIR/LibComm-0.1.0
 # DEEPMD=$HOME/apps/anaconda3/envs/deepmd
 
 # if use deepks and deepmd
 cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$PREFIX \
-        -DCMAKE_CXX_COMPILER=icpc \
+        -DCMAKE_CXX_COMPILER=icpx \
         -DMPI_CXX_COMPILER=mpiicpc \
         -DMKLROOT=$MKLROOT \
         -DELPA_DIR=$ELPA \
         -DCEREAL_INCLUDE_DIR=$CEREAL \
         -DLibxc_DIR=$LIBXC \
         -DENABLE_LCAO=ON \
         -DENABLE_LIBXC=ON \
-        -DENABLE_LIBRI=OFF \
         -DUSE_OPENMP=ON \
-        -DENABLE_ASAN=OFF \
         -DUSE_ELPA=ON \
-        -DENABLE_DEEPKS=1 \
-        -DTorch_DIR=$LIBTORCH \
-        -Dlibnpy_INCLUDE_DIR=$LIBNPY \
+#         -DENABLE_DEEPKS=1 \
+#         -DTorch_DIR=$LIBTORCH \
+#         -Dlibnpy_INCLUDE_DIR=$LIBNPY \
 #         -DENABLE_LIBRI=ON \
 #         -DLIBRI_DIR=$LIBRI \
 #         -DLIBCOMM_DIR=$LIBCOMM \
 # 	      -DDeePMD_DIR=$DEEPMD \
 # 	      -DTensorFlow_DIR=$DEEPMD \
 
 cmake --build $BUILD_DIR -j `nproc` 
-cmake --install $BUILD_DIR 
+cmake --install $BUILD_DIR 2>/dev/null
+
+# if one want's to include deepmd, your gcc version should be >= 11.3.0
 
 # generate abacus_env.sh
 cat << EOF > "${TOOL}/abacus_env.sh"

toolchain/install_abacus_toolchain.sh

@@ -118,7 +118,7 @@ The --enable-FEATURE options follow the rules:
   --enable-FEATURE=no     Disable this particular feature
   --enable-FEATURE        The option keyword alone is equivalent to
                           --enable-FEATURE=yes
-
+  ===== NOTICE: THESE FEATURE AER NOT INCLUDED IN ABACUS =====
   --enable-cuda           Turn on GPU (CUDA) support (can be combined
                           with --enable-opencl).
                           Default = no
@@ -302,9 +302,9 @@ enable_tsan="__FALSE__"
 enable_opencl="__FALSE__"
 enable_cuda="__FALSE__"
 enable_hip="__FALSE__"
-export intel_classic="yes" 
+export intel_classic="no" 
 # no, then icc->icx, icpc->icpx, 
-# which cannot compile elpa-2021 and fftw.3.3.10 in some place
+# which cannot compile elpa in AMD server
 # due to some so-called cross-compile problem
 # and will lead to problem in force calculation
 # but icx is recommended by intel compiler

toolchain/scripts/VERSION

@@ -1,2 +1,2 @@
 # version file to force a rebuild of the entire toolchain
-VERSION="2023.4"
+VERSION="2023.5"