http://www.ks.uiuc.edu/Research/namd/2.13/notes.html
For version 2.12
- 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
- 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 - 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
- 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
