eigen库安装_超算安装precice

1、安装OpenFOAM-5.x

2、安装petsc-3.8.4

module load petsc/3.8.4-icc17-gcc620
module load boost/1.69.0-gcc620
export CPLUS_INCLUDE_PATH=$BOOST_INCDIR:$CPLUS_INCLUDE_PATH
module load cmake/3.13.4

3、安装Eigen 3.3.7

tar xvf ../eigen-eigen-323c052e1731.tar.gz
cd /PARA/blsc401/fsi_software/tmp/eigen-eigen-323c052e1731
mkdir build
cd build/
export CC=/WORK/paratera_share/gcc/6.2.0/bin/gcc
export CXX=/WORK/paratera_share/gcc/6.2.0/bin/g++
cmake ../ -DCMAKE_INSTALL_PREFIX=/PARA/blsc401/fsi_software/install/eigen
make
make install
mv tmp/eigen-eigen-323c052e1731/ ~/eigen3
export EIGEN3_ROOT_DIR="$HOME/eigen3"

4、安装preCICE

unzip precice-1.4.0.zip
mkdir build
cd build/

无法搜索到Eigen3，在缺省位置建立了一个符号链接

cd ~/include
ln -fs /PARA/blsc401/fsi_software/install/eigen/include/eigen3/ eigen3
 
CXX=mpicxx cmake -DPETSC=ON -DPYTHON=OFF -DPETSC_EXECUTABLE_RUNS=YES -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-O3 -DNDEBUG -std=gnu++11 -DBOOST_NO_CXX11_DEFAULTED_FUNCTIONS" -DCMAKE_INSTALL_PREFIX=/PARA/blsc401/fsi_software/install/precice ..
make
make install
 

5、cgx编译安装

cd CalculiX/cgx_2.13

根据INSTALL文件，修改一下cgx.h中的#define HELPFILE定义

不需要加载环境变量，直接编译

make

成功

cd /PARA/blsc401/fsi_software/install
mkdir calculix/bin -p
cp ../calculix/CalculiX/cgx_2.13/src/cgx calculix/bin/
export PATH=/PARA/blsc401/fsi_software/ calculix/bin:$PATH
cgx -b dummy.fbd

需要图形界面才能启动

暂时不能测试！！！

6、spooles安装

mkdir /PARA/blsc401/fsi_software/install/SPOOLES.2.2
cd /PARA/blsc401/fsi_software/install/SPOOLES.2.2
tar xvf spooles.2.2.tgz

修改Make.inc文件，定义CC = gcc

修改~/SPOOLES.2.2/Tree/src/makeGlobalLib文件中的drawTree.c为draw.c

make lib

7、ARPACK安装

cd /PARA/blsc401/fsi_software/install
tar xvf arpack96.tar.gz
tar xvf patch.tar.gz
cd ARPACK/

注释掉文件UTIL/second.f的24行

* EXTERNAL ETIME

修改ARmake.inc

home = /PARA/blsc401/fsi_software/install/ARPACK
PLAT = INTEL
#
MAKE = /usr/bin/make
FC = gfortran
#FFLAGS = -O -cg89
make lib

8、yaml-cpp安装

unzip yaml-cpp-yaml-cpp-0.6.2.zip
cd yaml-cpp-yaml-cpp-0.6.2
mkdir build
cd build/
cmake .. -DCMAKE_INSTALL_PREFIX=/PARA/blsc401/fsi_software/install/yaml-cpp
make
make install

OpenFOAM adaptor需要动态库，通过执行

ccmake .

打开BUILD_SHARED_LIBS，重新

make
make install

9、ccx安装

cd /PARA/blsc401/fsi_software/install
tar xvjf ccx_2.13.src.tar.bz2
cd CalculiX/ccx_2.13/src
CC=gcc
FC=gfortran

设置好spooles和arpack路径

不需要编译，下一步一起编译

10、CalculiX adapter for version 2.15

unzip calculix-adapter-master.zip
cd install/calculix-adapter-master

修改Makefile

CCX = /PARA/blsc401/fsi_software/install/CalculiX/ccx_2.15/src
# Path to SPOOLES main directory (e.g.   $(HOME)/SPOOLES.2.2 )
SPOOLES =   /PARA/blsc401/fsi_software/install/SPOOLES.2.2
# Path to ARPACK main directory (e.g.   $(HOME)/ARPACK )
ARPACK =   /PARA/blsc401/fsi_software/install/ARPACK
# Path to yaml-cpp prefix (e.g.   $(HOME)/yaml-cpp, should contain "include" and "build")
YAML =   /PARA/blsc401/fsi_software/install/yaml-cpp-yaml-cpp-0.6.2
LIBS = 
 $(SPOOLES)/spooles.a 
 $(PKGCONF_LIBS) 
 -lstdc++ -lxml2
 -L$(YAML)/build -lyaml-cpp 
 -L/PARA/app/boost/1_69_0-gcc/lib   -lboost_log -lboost_log_setup -lboost_program_options
 -L/PARA/app/petsc/3.8.4-icc17-gcc620/lib -lpetsc 
 -L/WORK/paratera_share/gcc/6.2.0/lib64 -lgfortran
$(OBJDIR)/ccx_preCICE: $(OBJDIR)   $(OCCXMAIN) $(OBJDIR)/ccx_2.15.a
 $(FC) -fopenmp -Wall -O3 -o $@ $(OCCXMAIN) $(OBJDIR)/ccx_2.15.a   $(LIBS) -nofor_main
export PKG_CONFIG_PATH=/PARA/blsc401/fsi_software/install/precice/lib/pkgconfig
make

11、OpenFOAM adaptor

unzip openfoam-adapter-master.zip
cd openfoam-adapter-master/

修改Allwmake

ADAPTER_PRECICE_DEP="-L/PARA/app/boost/1_69_0-gcc/lib   -lboost_system -lboost_filesystem -lboost_log -lboost_log_setup   -lboost_thread -lboost_program_options -L/PARA/app/petsc/3.8.4-icc17-gcc620/lib   -lpetsc -lpthread -lxml2"
source /PARA/blsc401/fsi_software/install/OpenFOAM/OpenFOAM-5.x/etc/rebashrc
export CPLUS_INCLUDE_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/include:$CPLUS_INCLUDE_PATH
export LD_LIBRARY_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/lib:$LD_LIBRARY_PATH
./Allwmake 2>&1 | tee Allwmake.log

显示成功

总结编译需要用到的module和环境: /PARA/blsc401/fsi_software/install/base.sh

module load MPI/Intel/MPICH/3.2-icc2017-dyn
module load gcc/6.2.0
module load petsc/3.8.4-icc17-gcc620
module load boost/1.69.0-gcc620
module load cmake/3.13.4
export CPLUS_INCLUDE_PATH=$BOOST_INCDIR:$CPLUS_INCLUDE_PATH
export EIGEN3_ROOT_DIR="$HOME/eigen3"
export PKG_CONFIG_PATH=/PARA/blsc401/fsi_software/install/precice/lib/pkgconfig
source /PARA/blsc401/fsi_software/install/OpenFOAM/OpenFOAM-5.x/etc/rebashrc
export CPLUS_INCLUDE_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/include:$CPLUS_INCLUDE_PATH
export LD_LIBRARY_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/lib:$LD_LIBRARY_PATH

测试

把Allrun命令改成超算需要的命令。比如节点的设置、添加环境变量等，

#!/bin/bash
#SBATCH -p paratera
#SBATCH -n 24
#SBATCH -N 1
RUNDIR=$PWD
PARTITON=paratera
source /PARA/blsc401/fsi_software/install/base.sh
 

但还是会出现问题：

在我./Allclean 之后测试其他的算例也出现同样的问题

我觉得主要是找不到cgx的环境变量，cgx都无法运行

在base.sh中添加好环境变量，即可运行

module load MPI/Intel/MPICH/3.2-icc2017-dyn
module load gcc/6.2.0
module load petsc/3.8.4-icc17-gcc620
module load boost/1.69.0-gcc620
module load cmake/3.13.4
export CPLUS_INCLUDE_PATH=$BOOST_INCDIR:$CPLUS_INCLUDE_PATH
export EIGEN3_ROOT_DIR="$HOME/eigen3"
export PKG_CONFIG_PATH=/PARA/blsc401/fsi_software/install/precice/lib/pkgconfig
source /PARA/blsc401/fsi_software/install/OpenFOAM/OpenFOAM-5.x/etc/rebashrc
export CPLUS_INCLUDE_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/include:$CPLUS_INCLUDE_PATH
export LD_LIBRARY_PATH=/PARA/blsc401/fsi_software/install/yaml-cpp/lib:$LD_LIBRARY_PATH
export ccx_PATH=/PARA/blsc401/fsi_software/install/calculix-adapter-master/bin:$ccx_PATH
export PATH=/PARA/blsc401/fsi_software/install/calculix/bin:$PATH
export LD_LIBRARY_PATH=/PARA/blsc401/fsi_software/install/calculix/lib:$LD_LIBRARY_PATH
export PATH=/PARA/blsc401/fsi_software/install/calculix-adapter-master/bin:$PATH
export GLEX_USE_ZC_RNDV=0

pc上算了30小时，超算也算了11小时23分