namd安裝運(yùn)行測試

1、namd 的安裝與編譯浪潮方案與實(shí)施部編制：當(dāng)前版本：V1.0編寫人：編寫日期2013.11.1人：日期級(jí)別：目錄NAMD 簡介2所需列表2安裝步驟2解壓. 3編譯 CHARMM3編譯NAMD5NAMD 作業(yè). 6namd 簡介NAMD（NAnoscale Molecular Dynamics）是用于在大規(guī)模并行計(jì)算機(jī)上快速模擬大分子體系的并行分子動(dòng)力學(xué)代碼。NAMD 用經(jīng)驗(yàn)力場，如Amber，CHARMM 和Dreiding，通過數(shù)值求解運(yùn)動(dòng)方程計(jì)算原子軌跡安裝環(huán)境所需列表編譯namd 之前先設(shè)置好root 用戶的el 編譯器環(huán)境變量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.安裝步驟硬件環(huán)境CPU：el Xeon CPU E5-2670 2.60GHzNETWORK：56Gbps Infiniband環(huán)境操作系統(tǒng)版本：Redhat6.3_x86_64編譯器：el comerxe- 2013.1.117解壓編譯 CHARMM編輯 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、 ;解壓charmtar xvf charm-6.4.0.tarcd charm-6.4.0/src/arpi-linux-x86_64把NAMD_2.9_Source.解壓到/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 安裝目錄情況如下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#開始編譯

10、charm編譯 namd進(jìn)入arch 目錄cd arch編輯 Linux-x86_64.tcl 文件，指定 tcl 庫路徑 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) $(TCLFLAGS)編輯 Linux-x86_64.fftw 文件，指定 fftw 庫路徑rootmu01 arch# cinux-x86 fftw FFTDIR=/opt/soft/NAMD_2.9_Source/linux-x86_64 FFTINCL=-I$(FFTDIR)/includeFFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw FFTFLAGS=-DNAMD_FFTW FFT=$(FFTINCL) $(FFTFLAGS)編輯 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)編譯完charm 后，修改Make.charm

13、文件，指定charm 路徑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開始編譯 namdcd /opt/soft/NAMD_2.9_Source./config tcl fftw Linux-x86_64-icc cd Linux-x86_64-iccmake編譯成功后在當(dāng)前目錄生成 namd2 可執(zhí)行文件namd 作業(yè)#!/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