NAMD编译

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

2. 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
3. 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

4. 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