namd安装运行测试

1、namd 的安装与编译浪潮方案与实施部编制：当前版本：V1.0编写人：编写日期2013.11.1人：日期级别：目录NAMD 简介2所需列表2安装步骤2解压. 3编译 CHARMM3编译NAMD5NAMD 作业. 6namd 简介NAMD（NAnoscale Molecular Dynamics）是用于在大规模并行计算机上快速模拟大分子体系的并行分子动力学代码。NAMD 用经验力场，如Amber，CHARMM 和Dreiding，通过数值求解运动方程计算原子轨迹安装环境所需列表编译namd 之前先设置好root 用户的el 编译器环境变量sourcepilervars.shel64source

2、/opt/el/mkl/bin/el64/mklvars_el64.sh source /opt/ el/impi/4.1.0/bin64/mpivars.shNAMD_2.9_Source. fftw-linux-x86_64. tcl-linux-x86_64.安装步骤硬件环境CPU：el Xeon CPU E5-2670 2.60GHzNETWORK：56Gbps Infiniband环境操作系统版本：Redhat6.3_x86_64编译器：el comerxe- 2013.1.117解压编译 CHARMM编辑 conv-mach.sh 文件如下rootmu01 mpi-linux-x8

3、6_64# cat conv-mach.sh# user enviorn var: MPICXX and MPICC# or, use the definition in file $CHARMINC/MPIOPTS if test -x $CHARMINC/MPIOPTSthen. $CHARMINC/MPIOPTSelseMPICXX_DEF=mpiicpc MPICC_DEF=mpiiccfitest -z $MPICXX & MPICXX=$MPICXX_DEFtest -z $MPICC & MPICC=$MPICC_DEFtest $MPICXX != $MPICXX_DEF &

4、/bin/rm -f $CHARMINC/MPIOPTS if test ! -f $CHARMINC/MPIOPTSthenecho MPICXX_DEF=$MPICXX $CHARMINC/MPIOPTS echo MPICC_DEF=$MPICC $CHARMINC/MPIOPTSod +x $CHARMINC/MPIOPTSfiPILER=$MPICXX -show 2/dev/null | cut -d -f1 case $PILER ing+) CMK_AMD64=-m64 -fPIC ;pgCC) CMK_AMD64=-fPIC -DCMK_FIND_OF_PREDICATE=1

5、 ;解压charmtar xvf charm-6.4.0.tarcd charm-6.4.0/src/arpi-linux-x86_64把NAMD_2.9_Source.解压到/opt/soft/下fftw-linux-x86_64. 和 tcl-linux-x86_64. 到/opt/soft/NAMD_2.9_Source 下 tar zxv tw-linux-x86_64. tar zxvf tcl-linux-x86_64.Namd 安装目录情况如下rootmu01 NAMD_2.9_Source# lsannounce.txtfftw-linux-x86_64.Make.charmp

6、sfgen archlibMake.dependsREADME.txtcharm-6.4.0license.txtMakefilesrccharm-6.4.0.tarlinux-x86_64notes.txttcl-linux- x86_64.configLinux-x86_64-iccpluginsugcharmc) echo Error charmc can not callesacIs mpicxx/mpiCC wrapper! Please fix your PATH.; exit 1 ;CMK_CPP_CHARM=/lib/cpp -P CMK_CPP_C=$MPICC -E CMK

7、_CC=$MPICC $CMK_AMD64 CMK_CXX=$MPICXX $CMK_AMD64 CMK_CXXPP=$MPICXX -E $CMK_AMD64 #CMK_SYSLIBS=-lmpich CMK_LIBS=-lckqt $CMK_SYSLIBS CMK_LD_LIBRARY_PATH=-Wl,-rpath,$CHARMLIBSO/CMK_NATIVE_CC=icc $CMK_AMD64 CMK_NATIVE_LD=icc $CMK_AMD64 CMK_NATIVE_CXX=icpc $CMK_AMD64 CMK_NATIVE_LDXX=icpc $CMK_AMD64 CMK_N

8、ATIVE_LIBS=# fortran compiler CMK_CF90=which f95 2/dev/null if test -n $CMK_CF90then# # # # # # #CMK_FPP=/lib/cpp -P -CCCMK_CF90=$CMK_CF90 -fpic -fautomatic -fdollar-ok CMK_CF90_FIXED=$CMK_CF90 -ffixed-form CMK_F90LIBS=-lgfortran CMK_F90_USE_MODDIR=1CMK_F90_MODINC=-I CMK_MOD_NAME_ALLCAPS= CMK_MOD_EX

9、T=mod. $CHARMINC/conv-mach-gfortran.shelseCMK_CF77=g77 CMK_CF90=f90 CMK_CF90_FIXED=$CMK_CF90 -W132 CMK_F90LIBS=-L/usr/absoft/lib -L/opt/absoft/lib -lf90math -lfio -lU77 -lf77math CMK_F77LIBS=-lg2c CMK_F90_USE_MODDIR=1 CMK_F90_MODINC=-pfiCMK_QT=generic64CMK RANLIB=ranlibrootmu01 mpi-linux-x86_64#开始编译

10、charm编译 namd进入arch 目录cd arch编辑 Linux-x86_64.tcl 文件，指定 tcl 库路径 rootmu01 arch# cinux-x86_64.tcl #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 TCLDIR=/opt/soft/NAMD_2.9_Source/linux-x86_64TCLINCL=-I$(TCLDIR)/include #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldlTCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread

11、 TCLFLAGS=-DNAMD_TCL TCL=$(TCLINCL) $(TCLFLAGS)编辑 Linux-x86_64.fftw 文件，指定 fftw 库路径rootmu01 arch# cinux-x86 fftw FFTDIR=/opt/soft/NAMD_2.9_Source/linux-x86_64 FFTINCL=-I$(FFTDIR)/includeFFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw FFTFLAGS=-DNAMD_FFTW FFT=$(FFTINCL) $(FFTFLAGS)编辑 Linux-x86_64-icc.arch 文件r

12、ootmu01 arch# cinux-x86_64-icc.arch NAMD_ARCH = Linux-x86_64 CHARMARCH = mpi-linux-x86_64FLOATOPTS = -ip -fno-rtti -no-vec -xAVX CXX = mpiicpcCXXOPTS = -i-s ic -O2 $(FLOATOPTS) CXXNOALIASOPTS = -O3 -xAVX -fno-alias $(FLOATOPTS)CC = mpiiccCOPTS = -i-s ic -O3 -xAVX $(FLOATOPTS)编译完charm 后，修改Make.charm

13、文件，指定charm 路径rootmu01 NAMD_2.9_Source# cat Make.charm # Set CHARMBASE to the top level charm directory.# The config script will override this setting if there is a directory # called charm-6.4.0 or charmhe NAMD base directory.CHARMBASE = /opt/soft/NAMD_2.9_Source/charm-6.4.0cd /opt/soft/NAMD_2.9_Sou

14、rce./build charm+ mpi-linux-x86_64开始编译 namdcd /opt/soft/NAMD_2.9_Source./config tcl fftw Linux-x86_64-icc cd Linux-x86_64-iccmake编译成功后在当前目录生成 namd2 可执行文件namd 作业#!/bin/bash#PBS -N namd_test #PBS -l nodes=1:ppn=16#PBS -l walltime=1200:00:00 #PBS -q batch#PBS -V#PBS -S /bin/bash# NAMD pbs #cd $PBS_O_WORKDIR namd=/opt/soft/NAMD_2.9_Source/Linux-x86_64-icc/namd2 charmrun=/opt/soft/NAMD_2.9_Source/charm-6.4.0/bin/char