DFTB+_Build

作者

手册编译

1. 环境的准备

1.1 Fortran编译器

[qihuanye@QHY ~]$ gfortran --version
GNU Fortran (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

GFortran当前版本为11.5.0，而要求GFortran >= 13，下载并配置GFortran 13到启动文件

sudo dnf install -y gcc-toolset-13-gcc-gfortran
echo 'source /opt/rh/gcc-toolset-13/enable' >> ~/.bashrc
source ~/.bashrc

再次检查版本

[qihuanye@QHY ~]$ gfortran --version
GNU Fortran (GCC) 13.3.1 20240611 (Red Hat 13.3.1-2)
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

完成

1.2 MPI框架

检查发现无openmpi，安装openmpi并添加到环境变量：

[qihuanye@QHY ~]$ sudo dnf install -y openmpi openmpi-devel
[qihuanye@QHY ~]$ echo 'export PATH=/usr/lib64/openmpi/bin:$PATH' >> ~/.bashrc
[qihuanye@QHY ~]$ source ~/.bashrc
[qihuanye@QHY ~]$ mpirun --version
mpirun (Open MPI) 4.1.1

Report bugs to http://www.open-mpi.org/community/help/

完成

1.3 CMake

[qihuanye@QHY ~]$ cmake --version
cmake version 3.26.5

CMake suite maintained and supported by Kitware (kitware.com/cmake).

完成

1.4 BLAS & LAPACK

检查发现无两个库，安装并检查：

[qihuanye@QHY ~]$ sudo dnf install -y openblas openblas-devel lapack lapack-devel
[qihuanye@QHY ~]$ pkg-config --exists blas && echo "y" || echo "n"
y
[qihuanye@QHY ~]$ pkg-config --exists lapack && echo "y" || echo "n"
y

1.5 ScaLAPACK

无ScaLAPACK库，安装：

[qihuanye@QHY ~]$ sudo dnf install -y scalapack scalapack-devel
Last metadata expiration check: 0:45:41 ago on Sun 14 Dec 2025 05:20:13 PM CST.
No match for argument: scalapack
No match for argument: scalapack-devel
Error: Unable to find a match: scalapack scalapack-devel

产生以上错误，搜索scalapack库：

[qihuanye@QHY ~]$ dnf search scalapack
Last metadata expiration check: 0:49:19 ago on Sun 14 Dec 2025 05:19:25 PM CST.
========================================== Name & Summary Matched: scalapack ===========================================
scalapack-common.x86_64 : Common files for scalapack
scalapack-openmpi.x86_64 : ScaLAPACK libraries compiled against openmpi
scalapack-openmpi-devel.x86_64 : Development libraries for ScaLAPACK (openmpi)
scalapack-openmpi-static.x86_64 : Static libraries for ScaLAPACK (openmpi)

找到正确的scalapack库，安装并配置：

[qihuanye@QHY ~]$ sudo dnf install -y scalapack-openmpi scalapack-openmpi-devel
[qihuanye@QHY ~]$ find /usr -name "*scalapack*" 2>/dev/null | grep -E ".(so|a)$"
/usr/lib64/openmpi/lib/libscalapack.so
[qihuanye@QHY ~]$ echo 'export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
[qihuanye@QHY ~]$ source ~/.bashrc
[qihuanye@QHY ~]$ pkg-config --exists scalapack && echo "y" || echo "n"
n

按理说我应该正确配置了，但为什么仍旧无法查询到正确的库？查询发现ScaLAPACK的OpenMPI版本通常不提供pkg-config支持
完成

1.6 ELSI库

搜索发现没有，先安装ELSI的依赖：

sudo dnf install -y gcc-gfortran gcc-c++ make cmake git

我准备从源码开始构建：

[qihuanye@QHY ~]$ mkdir -p ~/build && cd ~/build
[qihuanye@QHY build]$ git clone https://gitlab.com/elsi_project/elsi_interface.git elsi
[qihuanye@QHY build]$ cd elsi
[qihuanye@QHY elsi]$ git checkout v2.12.0
[qihuanye@QHY elsi]$ vim my_toolchain.cmake

在创建的工具链文件中写入：

set(CMAKE_Fortran_COMPILER "/usr/lib64/openmpi/bin/mpif90" CACHE STRING "MPI Fortran compiler")
set(CMAKE_C_COMPILER "/usr/lib64/openmpi/bin/mpicc" CACHE STRING "MPI C compiler")
set(CMAKE_Fortran_FLAGS "-O3 -ffree-line-length-none -fallow-argument-mismatch" CACHE STRING "Fortran flags")
set(CMAKE_C_FLAGS "-O3 -std=c99" CACHE STRING "C flags")
set(LIB_PATHS "/usr/lib64/openmpi/lib" CACHE STRING "External library paths")
set(LIBS "scalapack openblas lapack" CACHE STRING "External libraries")
set(CMAKE_INSTALL_PREFIX "/usr/local" CACHE STRING "Installation path")

编译：

[qihuanye@QHY build]$ cmake -DCMAKE_TOOLCHAIN_FILE=../my_toolchain.cmake 
        -DENABLE_PEXSI=OFF 
        -DENABLE_SIPS=OFF 
        -DENABLE_NTPOLY=OFF 
        -DENABLE_BSEPACK=OFF 
        -DENABLE_TEST=OFF 
        ..
[qihuanye@QHY build]$ make -j$(nproc)

安装：

[qihuanye@QHY build]$ sudo make install

完成

2. 下载DFTB+ 24.1


[qihuanye@QHY build]$ cd ~
[qihuanye@QHY ~]$ mkdir -p dftbplus-build && cd dftbplus-build
[qihuanye@QHY dftbplus-build]$ wget https://github.com/dftbplus/dftbplus/releases/download/24.1/dftbplus-24.1.tar.xz
[qihuanye@QHY dftbplus-build]$ tar -xf dftbplus-24.1.tar.xz
[qihuanye@QHY dftbplus-build]$ cd dftbplus-24.1

3. 配置编译DFTB+

3.1 配置环境变量

[qihuanye@QHY dftbplus-24.1]$ echo 'export FC=mpif90' >> ~/.bashrc
[qihuanye@QHY dftbplus-24.1]$ echo 'export CC=mpicc' >> ~/.bashrc
[qihuanye@QHY dftbplus-24.1]$ echo 'export CMAKE_PREFIX_PATH="/usr/local:/usr/lib64/openmpi:$CMAKE_PREFIX_PATH"' >> ~/.bashrc
[qihuanye@QHY dftbplus-24.1]$ source ~/.bashrc

检查环境变量

[qihuanye@QHY dftbplus-24.1]$ echo $CC && echo $FC
mpicc
mpif90

完成

3.2 构建配置


[qihuanye@QHY dftbplus-24.1]$ mkdir build && cd build
[qihuanye@QHY build]$ cmake .. 
    -DCMAKE_INSTALL_PREFIX=/usr/local 
    -DWITH_MPI=ON 
    -DWITH_ELSI=ON 
    -DWITH_OMP=ON 
    -DWITH_ARPACK=OFF 
    -DWITH_GPU=OFF 
    -DWITH_TRANSPORT=OFF 
    -DWITH_SOCKETS=OFF 
    -DSCALAPACK_LIBRARY=scalapack
#编译
[qihuanye@QHY build]$ make -j$(nproc)

4. 测试DFTB+

4.1 下载参数文件并测试：

[qihuanye@QHY dftbplus-24.1]$ ./utils/get_opt_externals slakos
[qihuanye@QHY dftbplus-24.1]$ cd build
[qihuanye@QHY build]$ ctest -j$(nproc)

得到如下结果：

99% tests passed, 2 tests failed out of 229

Total Test time (real) = 169.71 sec

The following tests FAILED:
        115 - dftb+_solvation/gbsa_param1 (Failed)
        116 - dftb+_solvation/gbsa_param3 (Failed)
Errors while running CTest
Output from these tests are in: /home/qihuanye/dftbplus-build/dftbplus-24.1/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

关于GBSA隐式溶剂化模型的参数测试失败，查看日志：

Status: FAIL

    Start 116: dftb+_solvation/gbsa_param3
2/2 Test #116: dftb+_solvation/gbsa_param3 ......***Failed    1.40 sec
cp: cannot stat 'solvation/gbsa_param3/param_gbsa_dmso.txt': No such file or directory
solvation/gbsa_param3:  Test script returned non-zero exit code: deleting file 'autotest.tag'
 TODO.

失败的原因是缺少溶剂化模型的参数文件，但暂且与DFTB+核心功能无关，不影响正常使用，故而先忽略

4.2 安装DFTB+到系统

[qihuanye@QHY build]$ which dftb+
/usr/local/bin/dftb+
[qihuanye@QHY build]$ dftb+ --version
|===============================================================================
|
|  DFTB+ release 24.1
|
|  Copyright (C) 2006 - 2024  DFTB+ developers group
|
|===============================================================================
|
|  When publishing results obtained with DFTB+, please cite the following
|  reference:
|
|  * DFTB+, a software package for efficient approximate density functional
|    theory based atomistic simulations, J. Chem. Phys. 152, 124101 (2020).
|    [doi: 10.1063/1.5143190]
|
|  You should also cite additional publications crediting the parametrization
|  data you use. Please consult the documentation of the SK-files for the
|  references.
|
|===============================================================================

ERROR!
-> No input file 'dftb_in.hsd' not found.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

DFTB+已成功安装并可以运行，错误信息是正常的，因为确实没有输入文件dftb_in.hsd

4.3 sic测试

[qihuanye@QHY build]$ cd ~
[qihuanye@QHY ~]$ mkdir -p dftbplus-test && cd dftbplus-test
[qihuanye@QHY dftbplus-test]$ wget https://hpcadvisorycouncil.atlassian.net/wiki/download/attachments/3759866661/SiC.0064.tar.xz
[qihuanye@QHY dftbplus-test]$ wget https://hpcadvisorycouncil.atlassian.net/wiki/download/attachments/3759866661/pbc-0-3.tar.xz
[qihuanye@QHY dftbplus-test]$ tar -xf SiC.0064.tar.xz
[qihuanye@QHY dftbplus-test]$ tar -xf pbc-0-3.tar.xz
[qihuanye@QHY dftbplus-test]$ mkdir -p ~/opt/slakos
[qihuanye@QHY dftbplus-test]$ mv pbc-0-3/* ~/opt/slakos/
[qihuanye@QHY SiC.0064]$ DFTBPLUS_PARAM_DIR=~/opt/slakos dftb+
|===============================================================================
|
|  DFTB+ release 24.1
|
|  Copyright (C) 2006 - 2024  DFTB+ developers group
|
|===============================================================================
|
|  When publishing results obtained with DFTB+, please cite the following
|  reference:
|
|  * DFTB+, a software package for efficient approximate density functional
|    theory based atomistic simulations, J. Chem. Phys. 152, 124101 (2020).
|    [doi: 10.1063/1.5143190]
|
|  You should also cite additional publications crediting the parametrization
|  data you use. Please consult the documentation of the SK-files for the
|  references.
|
|===============================================================================

Reading input file 'dftb_in.hsd'
Parser version: 14

--------------------------------------------------------------------------------
ERROR!
-> SK file with generated name 'pbc-0-3/Si-Si.skf' does not exist.
Path: dftbplusinput/Hamiltonian/DFTB/SlaterKosterFiles/Type2FileNames
Line: 16-20 (File: dftb_in.hsd)

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

错误提示sk文件路径不对，调整目录结构，再次运行，依旧报错：

WARNING!
-> Dipole printed for extended system : value printed is not well defined
MPI processes:               1
OpenMP threads:              6

ERROR!
-> You must explicitely enable OpenMP threads (UseOmpThreads = Yes) if you wish to run an MPI-parallelised binary with OpenMP threads. If not, make sure that the environment variable OMP_NUM_THREADS is set to 1.

错误信息提示一个mpi进程，6个openMP线程，查询可知：

DFTB+ 24.1在MPI构建中存在一个运行时检查机制：

  1. 代码逻辑：当检测到MPI并行构建时（WITH_MPI=ON），程序会强制检查OpenMP线程配置
  2. 检查条件：如果OMP_NUM_THREADS未设置或值>1，且输入文件中没有UseOmpThreads = Yes，程序会报错终止
    我们先设置环境变量进行测试：

    [qihuanye@QHY SiC.0064]$ export OMP_NUM_THREADS=1
[qihuanye@QHY SiC.0064]$ DFTBPLUS_PARAM_DIR=~/opt/slakos dftb+

    得到如下输出：

    
Mode:                        Static calculation
Self consistent charges:     Yes
SCC-tolerance:                 0.100000E-04
Max. scc iterations:                    100
Shell resolved Hubbard:      No
Spin polarisation:           No
Nr. of up electrons:           128.000000
Nr. of down electrons:         128.000000
Periodic boundaries:         Yes
Electronic solver:           Relatively robust
Mixer:                       Broyden mixer
Mixing parameter:                  0.200000
Maximal SCC-cycles:                     100
Nr. of chrg. vec. in memory:            100
Electronic temperature:              0.126673E-03 H      0.344694E-02 eV
Initial charges:             Set automatically (system chrg:   0.000E+00)
Included shells:            Si:  s, p
C:  s, p
K-points and weights:           1:  0.125000  0.125000  0.125000     0.031250
2:  0.125000  0.125000  0.375000     0.031250
3:  0.125000  0.125000  0.625000     0.031250
4:  0.125000  0.125000  0.875000     0.031250
5:  0.125000  0.375000  0.125000     0.031250
6:  0.125000  0.375000  0.375000     0.031250
7:  0.125000  0.375000  0.625000     0.031250
8:  0.125000  0.375000  0.875000     0.031250
9:  0.125000  0.625000  0.125000     0.031250
10:  0.125000  0.625000  0.375000     0.031250
11:  0.125000  0.625000  0.625000     0.031250
12:  0.125000  0.625000  0.875000     0.031250
13:  0.125000  0.875000  0.125000     0.031250
14:  0.125000  0.875000  0.375000     0.031250
15:  0.125000  0.875000  0.625000     0.031250
16:  0.125000  0.875000  0.875000     0.031250
17:  0.375000  0.125000  0.125000     0.031250
18:  0.375000  0.125000  0.375000     0.031250
19:  0.375000  0.125000  0.625000     0.031250
20:  0.375000  0.125000  0.875000     0.031250
21:  0.375000  0.375000  0.125000     0.031250
22:  0.375000  0.375000  0.375000     0.031250
23:  0.375000  0.375000  0.625000     0.031250
24:  0.375000  0.375000  0.875000     0.031250
25:  0.375000  0.625000  0.125000     0.031250
26:  0.375000  0.625000  0.375000     0.031250
27:  0.375000  0.625000  0.625000     0.031250
28:  0.375000  0.625000  0.875000     0.031250
29:  0.375000  0.875000  0.125000     0.031250
30:  0.375000  0.875000  0.375000     0.031250
31:  0.375000  0.875000  0.625000     0.031250
32:  0.375000  0.875000  0.875000     0.031250

 

发表评论