# GPAW编译与安装 注： 手动方式安装 `gpaw`最重要的是修改 `customize.py`文件，在文件里把要关联的库路径添加修改正确，并把 `False`改为 `True`。只有把 `customize.py`文件看懂，才能正确编译 `gpaw` - 官方要求的安装必要软件包 官网安装说明链接[https://wiki.fysik.dtu.dk/gpaw/install.html](https://wiki.fysik.dtu.dk/gpaw/install.html#) - Python 3.5 or later（使用python3.5以上版本是因为ase需要的python版本已经是3.5了） - NumPy 1.9 or later (base N-dimensional array package) - SciPy 0.14 or later (library for scientific computing) - ASE 3.18.0 or later (atomic simulation environment) - a C-compiler - LibXC 3.x or 4.x - BLAS and LAPACK libraries Optional, but highly recommended: - an MPI library (required for parallel calculations) - FFTW (for increased performance) - BLACS and ScaLAPACK ## 1. 安装依赖库 安装 `anaconda3`之后，一些 `python`库就可以安装了，`Python`、`Numpy`、`Scipy`、`ASE`、`matplotlib`均可安装在库中 ```bash pip install **** ``` ### 1.1 安装 `BLAS`、`LAPACK`（Ubuntu系统直接安装，不需要自行编译） ```bash 参考Octopus安装说明 ``` ### 1.2 安装SCALAPACK（可选择系统直接安装，不需要自行编译） ```bash tar xvf scalapack_installer.tgz cd scalapack_installer ``` 修改 `setup.py`文件，把 `prefix`改为 `/home/gn/gpaw2160/scalapack`，把 `f90`改为 `gfortran`，把 `downall`改为 `True`，保存退出 ```bash ./setup.py --prefix=/home/gn/gpaw2160/scalapack --f90=gfortran --downall ``` 创建软链接: 把编译的 `libscalapack.a`拷贝到 `/usr/lib64`目录下，并链接为 `libscalapack-openmpi.a` ```bash ln -s /usr/lib64/libscalapack.a /usr/lib64/libscalapack-openmpi.a ``` ### 1.3 安装 `FFTW`（需要重新编译） 大多数软件并不需要fftw编译并行，但gpaw需要libfftw3_mpi.so * 点击此处下载源码： [fftw-3.3.5.tar.gz](ftp://ftp.fftw.org/pub/fftw/fftw-3.3.5.tar.gz) 安装 ```bash tar xvf fftw-3.3.5.tar.gz cd fftw-3.3.5 ./configure --prefix=/opt/libraries/gnu8-fftw/3.3.4 --enable-mpi --enable-shared=yes make make install ``` 查看 `/opt/libraries/gnu8-fftw/3.3.4/lib`目录中，如果有 `libfftw3_mpi`文件即为成功。 ### 1.4 安装 `openmpi`（需要重新编译） * 点击此处下载源码： [openmpi-4.1.1.tar.gz](https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz) 安装 ```bash tar xvf openmpi-4.1.1.tar.gz cd openmpi-4.1.1 ./configure --prefix=/opt/libraries/gnu8-openmpi/4.1.4 make all install -j vi ~/.bashrc export PATH=$PATH:/sob/openmpi313/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sob/openmpi313/lib source ~/.bashrc ``` ### 1.5 安装 `libxc`（需要重新编译） * 点击此处下载源码： [libxc-4.3.4.tar.gz](https://gitlab.com/libxc/libxc/-/archive/4.3.4/libxc-4.3.4.tar.gz) 安装 ```bash tar xvf libxc-4.3.4.tar.gz cd libxc-4.3.4 ./configure --prefix=/opt/libraries/gnu8-libxc/4.3.4 --enable-shared && make && make install ``` 这是一个密度泛函理论(`DFT`)的交换关联泛函库，其中你可以找到不同类型的泛函，例如：`LDA`, `GGA`, `hybrids`, 和 `mGGA`。 `Libxc`库也可以用于 `Abinit`软件，目前最新版本为6.1.0。 ### 1.6 安装 `ELPA`（需要重新编译） * 点击此处下载源码： [elpa-2021.05.001.tar.gz](https://elpa.mpcdf.mpg.de/html/Releases/2021.05.001/elpa-2021.05.001.tar.gz) 安装 ```bash ./configure --prefix=/opt/libraries/gnu8-elpa/2021.05.002 FC=mpiifort CC=mpiicc CXX=mpiicpc CFLAGS="-O3 -xHost" CXXFLAGS="-O3 -xHost" FCFLAGS="-O3 -xHost" --enable-openmp make && make install && make clean ``` ### 1.7 安装 `libvdwxc`（需要重新编译） ```bash yum install fftw3 fftw3-devel ``` * 点击此处下载源码： [libvdwxc-0.4.0.tar.gz](https://gitlab.com/libvdwxc/libvdwxc/-/archive/0.4.0/libvdwxc-0.4.0.tar.gz) 安装 ```bash ./configure --prefix=/opt/libraries/gnu8-libvdwxc/0.4.0 CC="gcc" FC="gfortran" CFLAGS="-O3 -march=native" FCFLAGS="-g -O2" make -j && make install ``` ## 2. 安装 `gpaw` ### 2.1 下载 `gpaw`源码 * 点击此处下载源码： [gpaw-22.8.0.tar.gz](https://pypi.org/packages/source/g/gpaw/gpaw-22.8.0.tar.gz) [![Download](https://img.shields.io/badge/download-gpaw22.8.0%20-blue.svg)](https://pypi.org/packages/source/g/gpaw/gpaw-22.8.0.tar.gz) Download gpaw-22.8.0 * 或者您可以下载本站的资源包： [资源下载](../../Other/download/dl) ```bash wget https://gitlab.com/gpaw/gpaw/-/archive/master/gpaw-master.tar.gz tar xvf gpaw-22.8.0.tar.gz cd gpaw-22.8.0 ``` ### 2.2 修改 `siteconfig.py`文件 复制 `siteconfig.py.example`文件为 `siteconfig.py`文件 ```bash cp siteconfig.py.example siteconfig.py ``` 修改 `siteconfig.py`文件 ```bash nano siteconfig.py ``` 改为如下内容 ```bash """User provided customizations. Here one changes the default arguments for compiling _gpaw.so. Here are all the lists that can be modified: * libraries List of libraries to link: -l -l ... * library_dirs Library search directories: -L -L ... * include_dirs Header search directories: -I -I ... * extra_link_args Arguments forwarded directly to linker * extra_compile_args Arguments forwarded directly to compiler * runtime_library_dirs Runtime library search directories: -Wl,-rpath= -Wl,-rpath= ... * extra_objects * define_macros The following lists work like above, but are only linked when compiling the parallel interpreter: * mpi_libraries * mpi_library_dirs * mpi_include_dirs * mpi_runtime_library_dirs * mpi_define_macros To override use the form: libraries = ['somelib', 'otherlib'] To append use the form libraries += ['somelib', 'otherlib'] """ # flake8: noqa # compiler = 'gcc' # mpicompiler = 'mpicc' # mpilinker = 'mpicc' # platform_id = '' # FFTW3: fftw = True if fftw: libraries += ['fftw3'] library_dirs += ['/opt/ohpc/pub/libs/gnu8/openmpi3/fftw/3.3.8/lib/'] # ScaLAPACK (version 2.0.1+ required): scalapack = True if scalapack: libraries += ['scalapack','openblas'] library_dirs += ['/opt/ohpc/pub/libs/gnu8/openmpi3/scalapack/2.0.2/lib/','/opt/ohpc/pub/libs/gnu8/openblas/0.3.7/lib/'] # Use Elpa (requires ScaLAPACK and Elpa API 20171201): if 0: elpa = True elpadir = '/opt/libraries/gnu8-elpa/2021.05.002' libraries += ['elpa'] library_dirs += ['{}/lib'.format(elpadir)] extra_link_args += ['-Wl,-rpath={}/lib'.format(elpadir)] include_dirs += ['{}/include/elpa_openmp-2021.05.002'.format(elpadir)] # LibXC: # In order to link libxc installed in a non-standard location # (e.g.: configure --prefix=/home/user/libxc-2.0.1-1), use: # - static linking: if 0: xc = '/opt/libraries/gnu8-libxc/4.3.4/' include_dirs += [xc + 'include'] extra_link_args += [xc + 'lib/libxc.a'] if 'xc' in libraries: libraries.remove('xc') # - dynamic linking (requires rpath or setting LD_LIBRARY_PATH at runtime): if 0: xc = '/opt/libraries/gnu8-libxc/4.3.4/' include_dirs += [xc + 'include'] library_dirs += [xc + 'lib'] # You can use rpath to avoid changing LD_LIBRARY_PATH: extra_link_args += ['-Wl,-rpath={xc}/lib'.format(xc=xc)] if 'xc' not in libraries: libraries.append('xc') # libvdwxc: if 0: libvdwxc = True path = '/opt/libraries/gnu8-libvdwxc/0.4.0' extra_link_args += ['-Wl,-rpath=%s/lib' % path] library_dirs += ['%s/lib' % path] include_dirs += ['%s/include' % path] libraries += ['vdwxc'] extra_compile_args += ['-fopenmp'] extra_link_args += ['-fopenmp'] ``` 注：`fftw`、`scalapack`、`elpa`、`libxc`、`libvdwxc`这些库的路径需要根据实际情况修改。 如果是在服务器上编译（有ophc和PBS） 写好siteconfig.py文件之后保存退出 加载所有能用到的库 然后开始编译 ``python3 setup.py install`` (这样才能把所有的库安装上) 如果使用pip，则不能安装所有的库，会失败 以后更新gpaw，直接下载源码，编写siteconfig.py文件，进行编译即可，切记要升级一些依赖的库。 ## 3. 安装 `gpaw`所需的赝势文件（Install PAW datasets） ```bash gpaw install-data ~/gpaw-21.6.0/datasets ``` ## 4. 测试 `gpaw` ```bash cd path_to_gpaw/gpaw-22.8.0 python3 -c "import gpaw; print(gpaw.__version__)" ``` ## 5. 最终软件的环境变量（仅作参考） ```bash #GPAW# conda activate gpaw export MPI_HOME=/opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4 && \ export PATH=$MPI_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH && \ export INCLUDE=$MPI_HOME/include:$INCLUDE && \ export MANPATH=$MPI_HOME/share/man:$MANPATH && \ export LIBXC_HOME=/opt/libraries/gnu8-libxc/4.3.4 && \ export PATH=$LIBXC_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$LIBXC_HOME/lib:$LD_LIBRARY_PATH && \ export LIBRARY_PATH=$LIBXC_HOME/lib:$LIBRARY_PATH && \ export INCLUDE=$LIBXC_HOME/include:$INCLUDE && \ export C_INCLUDE_PATH=$LIBXC_HOME/include:$C_INCLUDE_PATH && \ export FFTW_HOME=/opt/ohpc/pub/libs/gnu8/openmpi3/fftw/3.3.8 && \ export PATH=$FFTW_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$FFTW_HOME/lib:$LD_LIBRARY_PATH && \ export INCLUDE=$FFTW_HOME/include:$INCLUDE && \ export MANPATH=$FFTW_HOME/share/man:$MANPATH && \ export C_INCLUDE_PATH=$FFTW_HOME/include:$C_INCLUDE_PATH && \ export OPENBLAS_HOME=/opt/ohpc/pub/libs/gnu8/openblas/0.3.7 && \ export PATH=$OPENBLAS_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$OPENBLAS_HOME/lib:$LD_LIBRARY_PATH && \ export LIBRARY_PATH=$OPENBLAS_HOME/lib:$LIBRARY_PATH && \ export INCLUDE=$OPENBLAS_HOME/include:$INCLUDE && \ export SCALAPACK_HOME=/opt/ohpc/pub/libs/gnu8/openmpi3/scalapack/2.0.2 && \ export PATH=$SCALAPACK_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$SCALAPACK_HOME/lib:$LD_LIBRARY_PATH && \ export LIBRARY_PATH=$SCALAPACK_HOME/lib:$LIBRARY_PATH && \ export INCLUDE=$SCALAPACK_HOME/include:$INCLUDE && \ export ELPA_HOME=/opt/libraries/gnu8-elpa/2021.05.002 && \ export PATH=$ELPA_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$ELPA_HOME/lib:$LD_LIBRARY_PATH && \ export INCLUDE=$ELPA_HOME/include:$INCLUDE && \ export MANPATH=$ELPA_HOME/share/man:$MANPATH && \ export C_INCLUDE_PATH=$ELPA_HOME//include/elpa_openmp-2021.05.002/elpa/:$C_INCLUDE_PATH && \ export LIBVDWXC_HOME=/opt/libraries/gnu8-libvdwxc/0.4.0 && \ export PATH=$LIBVDWXC_HOME/bin:$PATH && \ export LD_LIBRARY_PATH=$LIBVDWXC_HOME:$LD_LIBRARY_PATH && \ export LIBRARY_PATH=$LIBVDWXC_HOME:$LIBRARY_PATH && \ export INCLUDE=$LIBVDWXC_HOME/include:$INCLUDE #gpaw-tools export PATH="/opt/apps/tools/gpaw-tools-23.2.0:$PATH" ``` ## 6. 安装 `gpaw-tools` ```bash conda activate gpaw pip install gpaw-tools ``` ## 7. 激活环境变量后再次测试 `gpaw` ```bash gpaw info gpaw info | grep -i 'libxc' gpaw test gpaw test --parallel=2 ``` ## 8. 编者注 - 由于作者时间有限，本文中的安装流程没有经过严格的测试，仅供参考。如果有问题，欢迎提出issue，或者直接联系作者。 - 本文存在很多问题，读者切不可照搬，待作者有时间一定进行修正。