服务器安装octopus-非root用户

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前言

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一、依赖库安装

1.gsl

./configure CC=gcc --prefix=/home/li/bin/local/gsl24-1 --disable-shared --enable-static

1.math

./setup.py --prefix=/home/li/bin/local/octopus_old/math --downall --mpiincdir=/home/li/bin/local/octopus_old/openmpi164/include

1.gcc

../configure -v --prefix=/home/li/bin/local/octopus_old/gcc830 -enable-checking=release -enable-languages=c,c++ -disable-multilib --with-gmp=/home/li/bin/lib/gcclib/gmp610 --with-mpfr=/home/li/bin/lib/gcclib/mpfr314  --with-mpc=/home/li/bin/lib/gcclib/mpc103

报错：g++: error: unrecognized command line option '-qversion'

解决：

>重置
unset LIBRARY_PATH CPATH C_INCLUDE_PATH PKG_CONFIG_PATH CPLUS_INCLUDE_PATH INCLUDE PATH

一、安装octopus4.1.0

1.环境搭建

软件版本：gnu8/8.3.0；openmpi164；fftw333; scalapack; libxc220

2.代码显示

ROOT=/home/li/bin/local/octopus_old
MATHDIR=$ROOT/math/lib
export LD_LIBRARY_PATH=$ROOT/libxc200gcc830/lib:\$LD_LIBRARY_PATH
export PATH=$ROOT/gsl114/bin:\$PATH
export LD_LIBRARY_PATH=$ROOT/gsl114/lib:\$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$ROOT/fftw333/lib:\$LD_LIBRARY_PATH
export PATH=$ROOT/fftw333/bin:\$PATH

../configure --prefix=/home/li/bin/local/octopus_old/octopus410 \
    --with-blas="-L/home/li/bin/local/octopus_old/math/lib -lrefblas" \
    --with-lapack="-L/home/li/bin/local/octopus_old/math/lib -ltmg -lreflapack"  \
    --with-scalapack="-L/home/li/bin/local/octopus_old/math/lib -lscalapack" \
    --with-libxc-prefix=/home/li/bin/local/octopus_old/libxc200gcc830    \
    --with-gsl-prefix=/home/li/bin/local/octopus_old/gsl114  \
    --with-fft-lib=/home/li/bin/local/octopus_old/fftw333/lib/libfftw3f.a  \
    --with-libxc-include=/usr/lib64/gfortran/modules \
    --with-libxc-lib=/home/li/bin/local/octopus_old/libxc200gcc830/lib/libxc.a \
    --with-blas=-lopenblas --with-lapack=-llapack \
    CC=gcc  FC=gfortran  FCFLAGS="-O3" CFLAGS="-O3" \
    --enable-mpi

3.报错信息

checking for MPI_init in ... no
checking for MPI_Init in -lmpi... no
configure: error: cannot call MPI from C

配置不报错，make报错，不好解决。

../configure --prefix=/home/li/bin/local/octopus_old/octopus410 --with-libxc-prefix=/home/li/bin/local/octopus_old/libxc200 --with-libxc-include=/home/li/bin/local/octopus_old/libxc200/include --with-gsl-prefix=/home/li/bin/local/octopus_old/gsl114 --with-blas="-L/home/li/bin/lib/lib" --with-lapack="-L/home/li/bin/lib/lib" --with-arpack="-L/home/li/bin/lib/lib" --with-fft-include=/home/li/bin/local/octopus_old/fftw333/include --with-fft-prefix="/home/li/bin/local/octopus_old/fftw333" -with-fft-lib="-L/home/li/bin/local/fftw335/lib" CC=gcc  FC=gfortran  FCFLAGS="-O3" CFLAGS="-O3"

3.标识解析

软件编译时候./configure  --help可以看到如下参数
Some influential environment variables:
 CC         C compiler command
 CFLAGS     C compiler flags
 LDFLAGS    linker flags, e.g. -L if you have libraries in a
             nonstandard directory
 LIBS       libraries to pass to the linker, e.g. -l
 CPPFLAGS   (Objective) C/C++ preprocessor flags, e.g. -I if
             you have headers in a nonstandard directory
 CPP        C preprocessor
 CXX        C++ compiler command
 CXXFLAGS    C++ compiler flags
 CXXCPP     C++ preprocessor
 CCAS       assembler compiler command (defaults to CC)
  CCASFLAGS  assembler compiler flags (defaults to CFLAGS)
 FC         Fortran compiler command
 FCFLAGS    Fortran compiler flags
CFLAGS， 表示用于 C 编译器的选项，
CXXFLAGS， 表示用于 C++ 编译器的选项,
FFLAGS, 表示用于 Fortran编译器的选项,
LDFLAGS, 库路径
LIBS ， 库名

intel
CC=icc  CXX=icpc F77=ifort  FC=ifort  
gnu
CC=gcc CXX=g++ F77=gfortran FC=gfortran
--disable-fortran --disable-mpi
CC=icc MPICC=icc CFLAGS=-O3 F77=ifort FFLAGS=-O3

4.本章小结

make时会各种报错，不建议使用。

二、安装octopus10.4(gcc版)

1.环境搭建

软件版本：gnu8/8.3.0；openmpi412；fftw334; libxc434

2.代码显示

ROOT=/home/li/bin/local/octopus_old
MATHDIR=$ROOT/math/lib
export LD_LIBRARY_PATH=$ROOT/libxc200gcc830/lib:$LD_LIBRARY_PATH
export PATH=$ROOT/gsl114/bin:$PATH
export LD_LIBRARY_PATH=$ROOT/gsl114/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$ROOT/fftw333/lib:$LD_LIBRARY_PATH
export PATH=/home/li/bin/local/fftw335/bin:$PATH

../configure --prefix=$ROOT/octopus104 \
    --with-blas="-L$ROOT/math/lib -lrefblas" \
    --with-lapack="-L$ROOT/math/lib -ltmg -lreflapack"  \
    --with-scalapack="-L$ROOT/math/lib -lscalapack" \
    --with-libxc-prefix=/home/li/bin/local/libxc434gcc830    \
    --with-gsl-prefix=$ROOT/gsl114  \
    --with-fftw-prefix=/home/li/bin/local/fftw335  \
    --enable-mpi

2.报错

代码如下（示例）：

Error: Assumed-shape array 'ff' at (1) cannot be an argument to the procedure 'c_loc' because it is not C interoperable
basic/io_binary_f_inc.F90:298.34:
    Included at basic/io_binary_f.F90:282:
 call read_binary(np, 0, c_loc(ff(1,1)), 3, ierr, iio, string_f_to_c(fname))

checking for libxc... no (-I /home/li/bin/lib/libxc434/include -L/home/li/bin/lib/libxc434/lib -lxcf03 -lxc)
configure: error: Could not find required libxc library ( >= v 3.0.0).

解决：没卵用

./configure --with-libxc-include=/usr/lib64/gfortran/modules --with-blas=-lopenblas --with-lapack=-llapack

2.总结

1. 使用编译器gcc830, 总是报错。

报错：c编译器不能执行

2. 使用gcc474,也会报错。

configure: error: Could not find required libxc library ( >= v 3.0.0).

代码如下（示例）：

data = pd.read_csv(
    'https://labfile.oss.aliyuncs.com/courses/1283/adult.data.csv')
print(data.head())

二、安装octopus10.4(intel版)

1.环境搭建

软件版本：intel/parallel_studio_xe_2019/psxevars.sh；math,mpi；fftw(intel自带)，; libxc434;gsl114

2.代码显示

MATHDIR=$ROOT/math/lib
export LD_LIBRARY_PATH=/home/li/bin/local/libxc434-intel/lib:\$LD_LIBRARY_PATH

MKL_DIR=$(echo $MKLROOT | awk -F: '{ print $1 }')
echo $MKL_DIR
../configure -v CC=mpiicc CXX=mpiicpc FC=mpiifort \
    --prefix=/home/li/bin/local/octopus104-intel \
    --with-libxc-prefix=/home/li/bin/local/libxc434-intel \
    FCFLAGS_FFTW=-I$MKL_DIR/include/fftw  \
    --with-blas="-L$MKL_DIR/lib/intel64 -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread -lmkl_blacs_intelmpi_lp64 -lmkl_scalapack_lp64 " \
    --with-gsl-prefix=/home/li/bin/local/gsl114-intel  \
    --enable-mpi

3.本章小结

总是报错：c编译器不能执行
暂时没法解决。

总结

提示：这里对文章进行总结：
具体参照：
https://cndaqiang.gitee.io/2020/10/19/huairou-octopus/#intelsslab%E5%AE%89

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