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centos6.5 gcc Openmpi 编译octopus-4.1.2

2018-09-15
cndaqiang
DFT
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编译方法主要参考@sculxb
环境centos6.5,软件版本gcc-4.4.7,libXC-2.0.0,gsl-1.14,openmpi-1.10.3,fftw-3.3.3 scalapack-2,octopus-4.1.2
gcc使用系统默认的gcc-4.4.7,其他软件分别编译



根据Basic Configuration of Octopus 4.1.2 with OpenMPI on CentOS 6的建议:
octopus-4.1.2只能使用libxc-2.0.x或2.1.x
gsl只能用1.14或更早


遇到的问题:
gcc-4.4.7编译openmpi-1.6.4报错,使用openmpi-1.10.3
gcc-4.8.4编译libxc-2.0.0出错,使用libxc-2.0.3
centos7最后编译octopus时configure没问题,make时报错,解决方案centos7 gun 编译octopus-4.1.2遇到问题和解决方案

依赖关系

  • 使用gcc编译libXC-2.0.0,gsl-1.14,openmpi-1.10.3
  • 编译openmpi-1.10.3得到的并行编译器(mpicc,mpif90等)和库用于编译fftw-3.3.3 scalapack-2,octopus-4.1.2
    因此在测试不同openmpi版本时,不用重新编译libxc和gsl

此文直接将在我计算机上的编译过程输入的命令复制了过来,请适当更改

下载

wget http://ftp.gnu.org/gnu/gsl/gsl-1.14.tar.gz
wget http://www.tddft.org/programs/octopus/down.php?file=libxc/2.0.0/libxc-2.0.0.tar.gz
wget https://download.open-mpi.org/release/open-mpi/v1.10/openmpi-1.10.3.tar.gz
wget http://www.netlib.org/scalapack/scalapack_installer.tgz
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gz
wget http://www.tddft.org/programs/octopus/down.php?file=4.1.2/octopus-4.1.2.tar.gz

如果编译gcc

如果指定某版本的gcc编译器,可以参考gcc Openmpi 编译siesta
编译libXC时要指定FCCPP为gcc-4.8.4的cpp,默认是系统的/usr/bin/cpp

libXC-2.0.0

cd ..
tar xzvf libxc-2.0.0.tar.gz 
cd libxc-2.0.0
./configure --prefix=/home/cndaqiang/soft/libxc-2.0.0/ CC=gcc CXX=g++ FC=gfortran
make -j8
make install
export LD_LIBRARY_PATH=/home/cndaqiang/soft/libxc-2.0.0/lib:$LD_LIBRARY_PATH

gsl-1.14

cd ..
tar xzvf gsl-1.14.tar.gz 
cd gsl-1.14
mkdir build-gsl
cd build-gsl/
../configure --prefix=/home/cndaqiang/soft/gsl-1.14
make -j8
make install
export PATH=/home/cndaqiang/soft/gsl-1.14/bin:$PATH
export LD_LIBRARY_PATH=/home/cndaqiang/soft/gsl-1.14/lib:$LD_LIBRARY_PATH

openmpi-1.10.3

tar xzvf openmpi-1.10.3.tar.gz 
cd openmpi-1.10.3
./configure --prefix=/home/cndaqiang/soft/openmpi-1.10.3 CC=gcc FC=gfortran CXX=g++
make -j8
make install
export LD_LIBRARY_PATH=/home/cndaqiang/soft/openmpi-1.10.3/lib:$LD_LIBRARY_PATH
export PATH=/home/cndaqiang/soft/openmpi-1.10.3/bin:$PATH

fftw-3.3.3

cd ..
tar xzvf fftw-3.3.3.tar.gz 
cd fftw-3.3.3
./configure --prefix=/home/cndaqiang/soft/fftw-3.3.3 --enable-mpi
make -j8
make install
export LD_LIBRARY_PATH=/home/cndaqiang/soft/fftw-3.3.3/lib:$LD_LIBRARY_PATH
export PATH=/home/cndaqiang/soft/fftw-3.3.3/bin:$PATH

scalapack

cd ..
tar xzvf scalapack_installer.tgz 
cd scalapack_installer
./setup.py --prefix=/home/cndaqiang/soft/scalapack --downall

octopus-4.1.2

cd ..
tar xzvf octopus-4.1.2.tar.gz 
cd octopus-4.1.2
 ./configure --prefix=/home/cndaqiang/soft/octopus-4.1.2 --with-blas='-L/home/cndaqiang/soft/scalapack/lib -lrefblas' --with-lapack='-L/home/cndaqiang/soft/scalapack/lib -ltmg -lreflapack' --with-scalapack='-L/home/cndaqiang/soft/scalapack/lib -lscalapack' --with-libxc-prefix=/home/cndaqiang/soft/libxc-2.0.0 --with-gsl-prefix=/home/cndaqiang/soft/gsl-1.14  --with-fft-lib=/home/cndaqiang/soft/fftw-3.3.3/lib/libfftw3.a --enable-mpi
make -j8
make install

测试

EXEC=/home/cndaqiang/soft/octopus-4.1.2/bin/octopus_mpi 
cd ~/soft/octopus-test/
mpirun -np 8 $EXEC  <inp> result
grep rel_dens result

备注

每次运行octopus需执行下列命令,即在交作业脚本中加入以下内容,或者添加到.bashrc

export LD_LIBRARY_PATH=/home/cndaqiang/soft/openmpi-1.10.3/lib:$LD_LIBRARY_PATH
export PATH=/home/cndaqiang/soft/openmpi-1.10.3/bin:$PATH
export LD_LIBRARY_PATH=/home/cndaqiang/soft/libxc-2.0.0/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/cndaqiang/soft/gsl-1.14/lib:$LD_LIBRARY_PATH
export PATH=/home/cndaqiang/soft/gsl-1.14/bin:$PATH
export LD_LIBRARY_PATH=/home/cndaqiang/soft/fftw-3.3.3/lib:$LD_LIBRARY_PATH
export PATH=/home/cndaqiang/soft/fftw-3.3.3/bin:$PATH

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