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NAMD编译

NAMD编译

作者: 全村滴希望 | 来源:发表于2020-02-18 10:20 被阅读0次

http://www.ks.uiuc.edu/Research/namd/2.13/notes.html

For version 2.12

  1. OPENMP 多核编译:
    1.1 tar xzf NAMD_2.12_Source.tar.gz
    1.2 cd NAMD_2.12_Source
    1.3 tar xf charm-6.7.1.tar
    1.4 cd charm-6.7.1
    1.5 ./build charm++ multicore-linux64 --with-production
    1.6 cd multicore-linux64/tests/charm++/megatest
    1.7 make pgm
    1.8 ./pgm +p4
    1.9 cd ../../../../..
    1.10 wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
    1.11 tar xzf fftw-linux-x86_64.tar.gz
    1.12 mv linux-x86_64 fftw
    1.13 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
    1.14 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.15 tar xzf tcl8.5.9-linux-x86_64.tar.gz
    1.16 tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.17 mv tcl8.5.9-linux-x86_64 tcl
    1.18 mv tcl8.5.9-linux-x86_64-threaded tcl-threaded

1.19 ./config Linux-x86_64-g++ --charm-arch multicore-linux64
1.20 cd Linux-x86_64-g++
1.21. make

  1. MPI version:
    1.1 tar xzf NAMD_2.12_Source.tar.gz
    1.2 cd NAMD_2.12_Source
    1.3 tar xf charm-6.7.1.tar
    1.4 cd charm-6.7.1
    1.5 env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
    //注释:env MPICXX=mpicxx 如果已经确定好 mpicxx 的路径,则不需要加这一句话。
    1.6 cd mpi-linux-x86_64/tests/charm++/megatest
    1.7 make pgm
    1.8 mpiexec -n 4 ./pgm (run as any other MPI program on your cluster)
    1.9 cd ../../../../..
    1.10 wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
    1.11 tar xzf fftw-linux-x86_64.tar.gz
    1.12 mv linux-x86_64 fftw
    1.13 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
    1.14 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.15 tar xzf tcl8.5.9-linux-x86_64.tar.gz
    1.16 tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.17 mv tcl8.5.9-linux-x86_64 tcl
    1.18 mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
    1.19 ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64
    1.20 cd Linux-x86_64-g++
    1.21. make
  2. InfiniBand version
    1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 1.13
    tar xzf NAMD_2.12_Source.tar.gz cd NAMD_2.12_Source
    tar xf charm-6.7.1.tar
    cd charm-6.7.1
    ./build charm++ verbs-linux-x86_64 --with-production cd verbs-linux-x86_64/tests/charm++/megatest
    make pgm
    ./charmrun ++mpiexec +p4 ./pgm
    cd ../../../../..
    wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
    tar xzf fftw-linux-x86_64.tar.gz
    mv linux-x86_64 fftw
    wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz

1.14 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
1.15 tar xzf tcl8.5.9-linux-x86_64.tar.gz
1.16 tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
1.17 mv tcl8.5.9-linux-x86_64 tcl
1.18 mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
1.19 ./config Linux-x86_64-g++ --charm-arch verbs-linux-x86_64
1.20 cd Linux-x86_64-g++
1.21. make

  1. CUDA version (GPU)
    1.1 tar xzf NAMD_2.12_Source.tar.gz
    1.2 cd NAMD_2.12_Source
    1.3 tar xf charm-6.7.1.tar
    1.4 cd charm-6.7.1
    1.5 ./build charm++ multicore-linux64 --with-production
    1.6 cd multicore-linux64/tests/charm++/megatest
    1.7 make pgm
    1.8 ./pgm +p4
    1.9 cd ../../../../..
    1.10 wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
    1.11 tar xzf fftw-linux-x86_64.tar.gz
    1.12 mv linux-x86_64 fftw
    1.13 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
    1.14 wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.15 tar xzf tcl8.5.9-linux-x86_64.tar.gz
    1.16 tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
    1.17 mv tcl8.5.9-linux-x86_64 tcl
    1.18 mv tcl8.5.9-linux-x86_64-threaded tcl-threaded
    1.19. ./config Linux-x86_64-g++ --charm-arch multicore-linux64 --with-cuda --cuda-prefix /usr/local/cuda
    1.20 cd Linux-x86_64-g++
    1.21. make

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