Advanced Simulation Library（ASL）&& An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method (IBAMR)

时间：2018-04-25 00:21:09 阅读：323 评论：0 收藏：0 [点我收藏+]

标签：https 配置 opengl dev sof let inf slap pen

ASL 和 IBAMR 都是有限元分析的工具，流体力学等，ASL可以使用GPU加速计算，

主机配置，i7 6代，1060, 32G，500G，ubuntu1604。

安装ASL、配置依赖、安装、运行测试：

1.GPU DRIVER && CUDA SDK OpenCL

　　在Ubuntu 软件源下载GPU驱动。

　　NVIDIA 官网下载cuda run安装包，安装时候不要选择图形图像显示驱动的安装。

装一些依赖：

1 sudo apt-get install clinfo dkms xz-utils openssl libnuma1 libpciaccess0 bc curl libssl-dev lsb-core libicu-dev -y

1 sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
2 echo "deb http://download.mono-project.com/repo/debian wheezy main" | sudo tee /etc/apt/sources.list.d/mono-xamarin.list
3 sudo apt-get install mono-complete -y

2.CMAKE

1 sudo apt-get install libncurses5-dev cmake-curses-gui -y

1 sudo apt-get install build-essential -y
2 wget http://www.cmake.org/files/v3.2/cmake-3.2.2.tar.gz
3 tar xf cmake-3.11.1.tar.gz && cd cmake-3.11.1 && ./configure
4 make -j8 && sudo make install

3.OpenGL

1 sudo apt-get install build-essential libgl1-mesa-dev freeglut3-dev libglew-dev libsdl2-dev libsdl2-image-dev libglm-dev libfreetype6-dev gfortran  doxygen graphviz -y

4.VTK

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization.

又是一个神乎其技的开源工具。

1 sudo apt-get install libvtk6.2
2 wget https://www.vtk.org/files/release/6.3/VTK-6.3.0.zip
3 unzip VTK-6.3.0.zip
4 mkdir VTK-build && cd VTK-build&&ccmake ../VTK-6.3.0

然后按“c”确认配置生成可编译文件，直到“g”选项出现，然后按“g”即可

1 make -j8
2 sudo make install

5.BOOST

首先安装一个低版本的boost，这个是给ASL用的。

1 sudo apt-get install libboost1.58-all-dev -y

6.ASL

1 unzip ASL-0.1.7.zip
2 mkdir build-asl && cd build-asl
3 cmake -D OpenCL_INCLUDE_DIR=/usr/local/cuda-9.0/include/ -G "Unix Makefiles" ../ASL-0.1.7
4 cmake -D OpenCL_LIBRARY=/usr/local/cuda-9.0/lib64/libOpenCL.so -G "Unix Makefiles" ../ASL-0.1.7
5 make -j8
6 sudo make install

运行实例：

1 cd examples/flow/locomotive
2 wget http://asl.org.il/input_data/locomotive.stl
3 ./asl-locomotive --input locomotive.stl

安装IBAMR、配置依赖、安装、运行测试：

1.安装BOOST

1 mkdir sfw && cd sfw && mkdir linux && cd linux && mkdir boost && cd boost
2 unzip boost_1_60_0.zip
3 mv boost_1_60_0 1.6.0
4 export BOOST_ROOT=$HOME/sfw/linux/boost/1.6.0
5 mkdir $BOOST_ROOT/include
6 ln -s $BOOST_ROOT/boost $BOOST_ROOT/include

2.安装eigen

1 cd sfw && cd linux && mkdir eigen && cd eigen 
2 下载 eigen 3.3.1
3 tar -jxvf 3.3.1.tar.bz2
4 cmake eigen-eigen-f562a193118d
5 make -j8 && sudo make install

3.安装HDF5

1 cd sfw/linux && mkdir hdf5 && cd hdf5
2 下载 hdf5-1.8.16.tar.bz2
3 tar xvjf ~/hdf5-1.8.16.tar.bz2
4 cd hdf5-1.8.16

./configure   CC=gcc   CXX=g++   FC=gfortran   F77=gfortran   --enable-production   --disable-debug   --prefix=$HOME/sfw/linux/hdf5/1.8.16

1 make -j8 && make check && sudo make install

4.安装SILO

1 cd $HOME/sfw/linux
2 tar xvfz silo-4.10.tar.gz && cd silo-4.10

./configure   CC=gcc   CXX=g++   FC=gfortran   F77=gfortran   --prefix=$HOME/sfw/linux/silo/4.10   --disable-silex

1 make -j8 && sudo make install

5.安装MUPARSER

1 sudo apt-get install libmuparser-dev -y

6.安装OpenMPI

1 cd $HOME/sfw/linux

2 tar xvfj openmpi-1.10.2.tar.bz2
3 cd openmpi-1.10.2

./configure 
  CC=gcc 
  CXX=g++ 
  FC=gfortran 
  F77=gfortran 
  --prefix=$HOME/sfw/linux/openmpi/1.10.2 
  --disable-mpi-cxx-seek 
  --disable-heterogeneous 
  --enable-orterun-prefix-by-default

1 make -j8 && make check && sudo make install

7.安装PETSC

　　7.1首先编译debug 版：

1 sudo apt-get install libblas-dev liblapack-dev -y

2 cd $HOME/sfw && mkdir petsc && cd petsc

3 wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.2.tar.gz

4 tar xvfz petsc-3.7.2.tar.gz

5 mv petsc-3.7.2 3.7.2 && cd 3.7.2

6 export PETSC_DIR=$PWD

7 export PETSC_ARCH=linux-debug

./config/configure.py 
  --CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  --CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  --FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  --LDFLAGS="-L$HOME/sfw/linux/openmpi/1.10.2/lib -Wl,-rpath,$HOME/sfw/linux/openmpi/1.10.2/lib" 
  --with-debugging=1 
  --with-c++-support 
  --download-hypre=1

1 make && make test

　　7.2再编译optimize版：

1 export PETSC_DIR=$PWD

2 export PETSC_ARCH=linux-opt

./config/configure.py 
  --CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  --CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  --FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  --COPTFLAGS="-O3" 
  --CXXOPTFLAGS="-O3" 
  --FOPTFLAGS="-O3" 
  --LDFLAGS="-L$HOME/sfw/linux/openmpi/1.10.2/lib -Wl,-rpath,$HOME/sfw/linux/openmpi/1.10.2/lib" 
  --with-default-arch=0 
  --PETSC_ARCH=$PETSC_ARCH 
  --with-debugging=0 
  --with-c++-support 
  --with-hypre=1 
  --download-hypre=1 
  --with-x=0
1 make && make test

8.安装SAMRAI

1 cd $HOME/sfw && mkdir samrai && cd samrai && mkdir 2.4.4&& cd 2.4.4

2 tar xvfz SAMRAI-v2.4.4.tar.gz && mv SAMRAI SAMRAI-2.4.4

然后要打一个补丁

1 wget https://github.com/IBAMR/IBAMR/releases/download/v0.1-rc1/SAMRAI-v2.4.4-patch-121212.gz

2 cd SAMRAI-2.4.4

3 gunzip -c ../SAMRAI-v2.4.4-patch-121212.gz | patch -p2

4 ./source/scripts/includes --link

5 cd $HOME/sfw/samrai/2.4.4

6 mkdir objs-debug && cd objs-debug

../SAMRAI-2.4.4/configure 
  --prefix=$HOME/sfw/samrai/2.4.4/linux-g++-debug 
  --with-CC=gcc 
  --with-CXX=g++ 
  --with-F77=gfortran 
  --with-MPICC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  --with-hdf5=$HOME/sfw/linux/hdf5/1.8.16 
  --without-hypre 
  --with-silo=$HOME/sfw/linux/silo/4.10 
  --without-blaslapack 
  --without-cubes 
  --without-eleven 
  --without-kinsol 
  --without-petsc 
  --without-sundials 
  --without-x 
  --with-doxygen 
  --with-dot 
  --enable-debug 
  --disable-opt 
  --enable-implicit-template-instantiation 
  --disable-deprecated

1 make -j8 &&  sudo make install

优化版本：

1 cd $HOME/sfw/samrai/2.4.4 &&mkdir objs-opt &&cd objs-opt

../SAMRAI-2.4.4/configure 
  CFLAGS="-O3" 
  CXXFLAGS="-O3" 
  FFLAGS="-O3" 
  --prefix=$HOME/sfw/samrai/2.4.4/linux-g++-opt 
  --with-CC=gcc 
  --with-CXX=g++ 
  --with-F77=gfortran 
  --with-MPICC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  --with-hdf5=$HOME/sfw/linux/hdf5/1.8.16 
  --without-hypre 
  --with-silo=$HOME/sfw/linux/silo/4.10 
  --without-blaslapack 
  --without-cubes 
  --without-eleven 
  --without-kinsol 
  --without-petsc 
  --without-sundials 
  --without-x 
  --with-doxygen 
  --with-dot 
  --disable-debug 
  --enable-opt 
  --enable-implicit-template-instantiation 
  --disable-deprecated

1 make -j8 && sudo make install

9.安装libMesh

1 cd $HOME/sfw/linux &&mkdir libmesh &&cd libmesh &&mkdir 1.0.0 &&cd 1.0.0

2 wget https://github.com/libMesh/libmesh/releases/download/v1.0.0/libmesh-1.0.0.tar.gz

3 THEN:4 tar xvfz libmesh-1.0.0.tar.gz && mv libmesh-1.0.0 LIBMESH &&cd $HOME/sfw/linux/libmesh/1.0.0 && mkdir objs-debug && cd objs-debug

5 export BOOST_ROOT=$HOME/sfw/linux/boost/1.6.0

../LIBMESH/configure 
  --prefix=$HOME/sfw/linux/libmesh/1.0.0/1.0.0-debug 
  --with-methods=dbg 
  PETSC_DIR=$HOME/sfw/petsc/3.7.2 
  PETSC_ARCH=linux-debug 
  CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  F77=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  --enable-triangle 
  --disable-cxx11 
  --disable-openmp 
  --disable-perflog 
  --disable-strict-lgpl 
  --disable-pthreads 
  --disable-cppthreads 
  --disable-unique-ptr

1 make -j8 && sudo make install

然后安装优化版：

1 cd $HOME/sfw/linux/libmesh/1.0.0 &&mkdir objs-opt &&cd objs-opt

2 export BOOST_ROOT=$HOME/sfw/linux/boost/1.6.0

../LIBMESH/configure 
  --prefix=$HOME/sfw/linux/libmesh/1.0.0/1.0.0-opt 
  --with-methods=opt 
  PETSC_DIR=$HOME/sfw/petsc/3.7.2 
  PETSC_ARCH=linux-opt 
  CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  F77=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  --enable-triangle 
  --disable-cxx11 
  --disable-openmp 
  --disable-perflog 
  --disable-strict-lgpl 
  --disable-pthreads 
  --disable-cppthreads 
  --disable-unique-ptr

1 make -j8 && sudo make install

终于到了主角，10.安装IBAMR

1 cd $HOME/sfw && mkdir ibamr && cd ibamr

2 git clone https://github.com/IBAMR/IBAMR.git

3 THEN:4 tar xvfj ibamr.tar.bz2 && cd $HOME/sfw/ibamr && mkdir ibamr-objs-dbg && cd ibamr-objs-dbg

5 export BOOST_ROOT=$HOME/sfw/linux/boost/1.6.0 && export PETSC_ARCH=linux-debug && export PETSC_DIR=$HOME/sfw/petsc/3.7.2

../IBAMR/configure 
  CFLAGS="-g -O1 -Wall" 
  CXXFLAGS="-g -O1 -Wall" 
  FCFLAGS="-g -O1 -Wall" 
  CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  CPPFLAGS="-DOMPI_SKIP_MPICXX" 
  --with-hypre=$PETSC_DIR/$PETSC_ARCH 
  --with-samrai=$HOME/sfw/samrai/2.4.4/linux-g++-debug 
  --with-hdf5=$HOME/sfw/linux/hdf5/1.8.16 
  --with-silo=$HOME/sfw/linux/silo/4.10 
  --with-boost=$HOME/sfw/linux/boost/1.6.0 
  --enable-libmesh 
  --with-libmesh=$HOME/sfw/linux/libmesh/1.0.0/1.0.0-debug 
  --with-libmesh-method=dbg

1 make lib -j8 && make examples -j8

然后安装优化版本

1 cd $HOME/sfw/ibamr && mkdir ibamr-objs-opt && cd ibamr-objs-opt && export PETSC_ARCH=linux-opt && export PETSC_DIR=$HOME/sfw/petsc/3.7.2

../IBAMR/configure 
  CC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  CXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  F77=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  FC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpif90 
  MPICC=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicc 
  MPICXX=$HOME/sfw/linux/openmpi/1.10.2/bin/mpicxx 
  CFLAGS="-O3 -Wall" 
  CXXFLAGS="-O3 -Wall -std=gnu++11" 
  FFLAGS="-O3 -Wall" 
  FCFLAGS="-O3 -Wall" 
  CPPFLAGS="-DOMPI_SKIP_MPICXX" 
  --with-hypre=$PETSC_DIR/$PETSC_ARCH 
  --with-samrai=$HOME/sfw/samrai/2.4.4/linux-g++-opt 
  --with-hdf5=$HOME/sfw/linux/hdf5/1.8.16 
  --with-silo=$HOME/sfw/linux/silo/4.10 
  --with-boost=$HOME/sfw/linux/boost/1.6.0 
  --enable-libmesh 
  --with-libmesh=$HOME/sfw/linux/libmesh/1.0.0/1.0.0-opt 
  --with-libmesh-method=opt

make -j8 &&make check

运行实例程序：

1 cd $HOME/sfw/ibamr/ibamr-objs-opt/examples/IB/staggered_grid/explicit/ex1

2 make examples

3 ./main2d input2d

技术分享图片

完，qsy。

Advanced Simulation Library（ASL）&& An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method (IBAMR)

标签：https 配置 opengl dev sof let inf slap pen

原文地址：https://www.cnblogs.com/pandaroll/p/8934405.html

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