Gromacs 4.0.3、4.5.5版安装方法

Gromacs 4.0.3、4.5.5版安装方法

文/Sobereva    Last update: 2012-Jan-6


下面是gromacs4.0.3安装方法。4.5.5版安装方法见本文后半。


gmx4.0.3安装方法

平台:F7-64bit、Q6600、gcc4.1.2、mpich2-1.0.7、root、ifort 10.1.015,软件版本gromacs4.0.3,安装在/sob/gromacs
安装的是并行版本、单精度版本。

指定编译器和编译选项:
export CC=gcc
export CXX=g++
export CFLAGS="-O3 -msse -msse2 -msse3 -mssse3 -march=core2"
export CXXFLAGS="-O3 -msse -msse2 -msse3 -mssse3 -march=core2"
export FFLAGS="-O3 -axT" //用C编译器编译内核的话不用这步

复制mpich2-1.0.7.tar.gz到/sob,解压到/sob/mpich2-1.0.7,进入此目录,运行:
./configure
make
make install

运行
touch /etc/mpd.conf
chmod 700 /etc/mpd.conf
将下面加入mpd.conf:
secretword=<secretword> (比如secretword=ltwd)


解压fftw3.1.2压缩包到/sob下,进入fftw-3.1.2目录
./configure --enable-float --with-gcc-arch=core2
make
make install
默认安在了/usr/local/include(lib)下。


解压gromacs-4.0压缩包到/sob下,进入gromacs-4.0目录,
./configure --prefix=/sob/gromacs --enable-mpi -enable-fortran
make
make install

在/root/.bashrc中添加PATH=$PATH:/sob/gromacs/bin,MANPATH=$MANPATH:/sob/gromacs/share/man。输入bash使环境变量生效

此时可删掉/sob下的fftw3.1.2目录、gromacs-4.0目录和mpich2-1.0.7目录。留下安好的gromacs目录。

*******
如果我们要进行QMMM计算,需要编译时设定,目前gromacs支持gamess-UK、mopac7、gaussian98/03,这里介绍把mopac7编进gromacs的方法。
下载http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f
下载http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/SGI/mopac7.tar.gz
把mopac7.tar.gz解压,把刚下载的dcart.f放进去替换原文件,把目录下的mopac.f、moldat.f、deriv.f删掉。运行:
ifort -O2 -c *.f
ar rcv libmopac.a *.o
ranlib libmopac.a然后把libmopac.a放到/lib下
export CPPFLAGS=-DUSE_MOPAC
export LIBS=-lmopac
之后同样进行configure步骤,但多加一个参数--with-qmmm-mopac,即运行:
./configure --prefix=/sob/gromacs --enable-mpi -enable-fortran --with-qmmm-mopac
之后make、make install即可。
********


PS:

用mkl的话,先修改./configure
把两处LIBS="-lmkl $LIBS"改成LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core $LIBS"
然后运行./configure --prefix=/sob/gromacs4mkl --enable-mpi -enable-fortran --with-fft=mkl CPPFLAGS=-I/opt/intel/mkl/10.0.4.023/include LDFLAGS=-L/opt/intel/mkl/10.0.4.023/lib/em64t,串行版本比fftw有提升,但是并行版本相对fftw却没有提升。如果是32bit平台,-lmkl_intel_lp64改为lmkl_intel,把.../lib/em64t改为.../lib/32

如果硬盘空间紧张,可以在./configure时加入--enable-shared来使用共享库,最终得到的bin非常小,gmx4.0中只有2.3MB,远小于使用静态库的172.65MB,只不过gromacs/lib文件夹里面会多出4约20MB。另外需要再添加环境变量LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sob/gromacs/lib。使用静态库或者动态库对运行速度基本没有影响。

gmx的内核有C语言和fortran两套版本,默认是C语言编译,如果用了-enable-fortran就是用fortran编译器编译,此时建议用ifort。用这个选项对gmx3.3.x来说并不会使性能有所多少提升,但对gmx 4.0.x来说性能提升明显。./configure的时候可以在后面加F77=xxx来指定fortran编译器。用gfortran可能会报错。

没必要用icc,性能相比用gcc不会有丝毫提升。

如果已经make过了,之后想./configure接新的选项重新编译,应当先执行make distclean

--program-suffix=[suffix]给出来的程序名加个后缀,可以区分单双精度版本、串行并行版本。比如先不加--enable-mpi编译一遍,然后make distclean,再加上--enable-mpi和--program-suffix=_mpi编译一遍,这样mdrun和mdrun_mpi串并行版本互不干扰。实际上没有必要单独编译串行版本,如果只是1个CPU用,就当成-np 1即可。

--disable-float或--enable-double可以编译成双精度版本(默认采用的是单精度),双精度版本速度约为单精度60%,对常规分子动力学来说单精度就够了,除了简正振动分析等情况。


老gmx版本有一些问题,在gmx4.0.3皆已修正,写在这里作为参考。
gmx4.0.0开-enable-fortran编译出错:把src/gmxlib/libxdrf.c的第1156行#define XDR_INT_SIZE 4挪到第68行,即在#ifdef GMX_FORTRAN之前。
编译得到的g_spatial和g_cluster完全一样:把src/tools/g_spatial.c里面的gmx_cluster改成gmx_spatial(gmx4.0.3已修正)


在configure文件中可以看到:

CC C compiler command 一般这个环境变量就是gcc
CFLAGS C compiler flags 编译时的参数,一般是-O3
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir> 库文件目录
LIBS libraries to pass to the linker, e.g. -l<library> 设的时候不用“-l xxx”,无需引号
CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
F77 Fortran 77 compiler command 一般这个环境变量就是gfortran或ifort
FFLAGS Fortran 77 compiler flags 编译时的参数,一般是-O3
CCAS assembler compiler command (defaults to CC)
CCASFLAGS assembler compiler flags (defaults to CFLAGS)
CPP C preprocessor
CXX C++ compiler command 一般是g++
CXXFLAGS C++ compiler flags
CXXCPP C++ preprocessor
XMKMF Path to xmkmf, Makefile generator for X Window System


Optional Features:
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--enable-shared[=PKGS] build shared libraries [default=no]
--disable-float use double instead of single precision
--enable-double same effect as --disable-float
--enable-fortran use fortran (default on sgi,ibm,sun,axp)
--enable-mpi compile for parallel runs using MPI
--disable-threads don't try to use multithreading
--enable-mpi-environment=VAR only start parallel runs when VAR is set
--disable-ia32-3dnow don't build 3DNow! assembly loops on ia32
--disable-ia32-sse don't build SSE/SSE2 assembly loops on ia32
--disable-x86-64-sse don't build SSE assembly loops on X86_64
--disable-ppc-altivec don't build Altivec loops on PowerPC
--disable-ia64-asm don't build assembly loops on ia64
--disable-cpu-optimization no detection or tuning flags for cpu version
--disable-software-sqrt no software 1/sqrt (disabled on sgi,ibm,ia64)
--enable-prefetch-forces prefetch forces in innerloops
--enable-all-static make completely static binaries
--disable-dependency-tracking speeds up one-time build
--enable-dependency-tracking do not reject slow dependency extractors
--enable-static[=PKGS] build static libraries [default=yes]
--enable-fast-install[=PKGS]
optimize for fast installation [default=yes]
--disable-libtool-lock avoid locking (might break parallel builds)
--disable-largefile omit support for large files

Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
--with-fft=[fftw3/fftw2/mkl(>=6.0)/fftpack]
FFT library to use. fftw3 is default, fftpack built
in.
--with-external-blas Use system BLAS library (add to LIBS). Automatic on
OS X.
--with-external-lapack Use system LAPACK library (add to LIBS). Automatic
on OS X.
--without-qmmm-gaussian Interface to mod. Gaussian0x for QM-MM (see website)
--with-qmmm-gamess use modified Gamess-UK for QM-MM (see website)
--with-qmmm-mopac use modified Mopac 7 for QM-MM (see website)
--with-gnu-ld assume the C compiler uses GNU ld [default=no]
--with-pic try to use only PIC/non-PIC objects [default=use
both]
--with-tags[=TAGS] include additional configurations [automatic]
--with-dmalloc use dmalloc, as in
http://www.dmalloc.com/dmalloc.tar.gz
--with-x use the X Window System
--with-motif-includes=DIR Motif include files are in DIR
--with-motif-libraries=DIR Motif libraries are in DIR
--without-gsl do not link to the GNU scientific library, prevents certain analysis tools from being built
--with-xml Link to the xml2 library, experimental




gmx4.5.5安装方法

RHEL6-U1 64bit, 2630QM, root

#Install Intel Fortran Composer XE(Linux) 2011.1.107 to default folder (/opt/intel)

#This step can be skipped if you want to use threats parallelization
#In mpich2 1.4.1 folder:
./configure
make
make install
#Now mpich2 1.4.1 folder can be deleted

#In fftw-3.3:
./configure --enable-threads --enable-single --enable-sse2 --enable-avx F77=ifort --prefix=/sob/fftw3.3
make -j 4
make install
#Now fftw-3.3 folder can be deleted

#In gromacs-4.5.5 folder
#If you prefer to use MPI parallelization, add --enable-mpi to below command
./configure --with-fft=fftw3 --prefix=/sob/gromacs455 LDFLAGS="-L/sob/fftw3.3/lib" CPPFLAGS="-I/sob/fftw3.3/include" -enable-shared=no
make -j 4
make install
#Now gromacs-4.5.5 folder can be deleted
#Add "export PATH=$PATH:/sob/gromacs455/bin" to /root/.bashrc

注:如果想用fortran编译内核,先export F77=ifort,并在./configure中加上--enable-fortran。然而性能并不会有丝毫提升,甚至还略微下降。threads并行和MPI并行在单机上效率差不多,前者并没体现出额外优势,只是方便了。

已有 2 条评论

  1. dalong

    编译gaussian的接口,可以直接使用二进制的高斯吗

  2. Neo

    sob老师,5.0版本的QM-MM编译mopac怎么编译呢?用cmake按照上述配置没有搞定

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