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HiPC

至尊木虫 (初入文坛)

thinker

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在线: 41.5小时
虫号: 443627
注册: 2007-10-27
性别: GG
专业: 计算机应用技术

[交流] 【原创】编译、测试NAMD分子动力学仿真软件编译【已搜无重复】

试验环境：ubuntu系统

1、下载TCL和FFTW库：
   mkdir fftw
   cd fftw

   wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux.tar.gz
   tar xzf fftw-linux.tar.gz

   cd ..
   mkdir tcl
   cd tcl

   wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux.tar.gz
   tar xzf tcl-linux.tar.gz

2、解NAMD包
   tar xzf NAMD_2.6_Source.tar.gz
   cd NAMD_2.6_Source
   tar xf charm-5.9.tar
   cd charm-5.9

3、编译并测试Charm++/Converse库
   ./build charm++ net-linux --no-shared -O -DCMK_OPTIMIZE=1
   cd net-linux/pgms/charm++/megatest/
   make pgm
   ./charmrun ++local +p4 ./pgm (also try running on multiple
nodes)
   cd ../../../../..

4、编辑各种配置文件
   vi Make.charm  (set CHARMBASE to .rootdir/charm-5.9 or full path
to charm)
   vi arch/Linux-i686.fftw    (fix library name and path to files)
   vi arch/Linux-i686.tcl    (fix library version and path to TCL
files)

5、编译
   ./config tcl fftw Linux-i686-g++
   cd Linux-i686-g++
   make

6、快速测试
   ./namd2
   ./namd2 src/alanin
   ./charmrun ++local +p2 ./namd2
   ./charmrun ++local +p2 ./namd2 src/alanin

参考：
http://www.ks.uiuc.edu/Research/namd/development.html

补充：

3、编译并测试Charm++/Converse库
   ./build charm++ net-linux --no-shared -O -DCMK_OPTIMIZE=1
   cd net-linux/pgms/charm++/megatest/
   make pgm
   ./charmrun ++local +p4 ./pgm (also try running on multiple
nodes)
   cd ../../../../..

根据最新版本(charm-5.9)，上面一步校正为：

3、编译并测试Charm++/Converse库
   ./build charm++ net-linux --no-shared -O -DCMK_OPTIMIZE=1
   cd  net-linux/examples/charm++/hello
   make
   cd 1darray/
   ./charmrun ++local +p4 ./hello (also try running on multiple
nodes)
   cd  ../../../../../..

NAMD 简介

NAMD Molecular Dynamics Software(NAMD分子动力学计算软件)
自由,开源开发团队:Illinois大学,Illinois 贝克曼研究所,理论生物物理小组.
NAMD 官方主页: http://www.ks.uiuc.edu/Research/namd

公布论文:
Laxmikant Kale,Robert Skeel,Milind Bhandarkar,Robert Brunner,Attila
Gursoy,Neal Krawetz,James Ohillips,Aritomo Shinozaki,Krishnan
Varadarajan,and Klaus Schulten.

NAMD2: Greater scalability for parallel molecular dynamics.J. Comp.
Phys.,151:283-312,1999.

[ Last edited by HiPC on 2007-11-16 at 00:32 ]

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