vasp5.3安装方法.doc

1. 采用Centos 6.4光盘安装系统。安装系统时，将有如下几个配置可供先择：(1) Desktop, (2) Minimal Desktop, (3)Minimal, (4) Basic Server, (5) Database Server, (6) Web Sever, (7) Virtual Host, (8) Software Development Workstation。任选一个选项即可。选择一个选项后，对系统进行配置。语言配置只选英语。除语言配置外，其余所有配置全部选上。选上所有其它配置之原因，是使系统文件更全面，以减少后续安装软件时由于软件依赖所带来的麻烦。所有安装软件都在 /home 目录下。安装目录可以任意，但在 /home目录下容易管理。为使安装软件时拥有最大的系统操作权限，用 root 身份安装。2. 安装Python。版本为Python-2.5.2。在 /home 下建 Python文件夹，则安装命令如下：# tar jxvf Python-2.5.2.tar.bz2 解压# cd Python-2.5.2 进入解压后的文件目录# ./configure 配置文件，不要指定路径，直接覆盖# make 编译# make install 安装检测是否安装成功：在任意目录下的命令行输入 python，如果出现python的解析器，则表示已正确安装，如未出现，则未正确安装，需重新安装。安装Python是为了系统能够识别后续将要安装的 mpich 编译器。3. GCC编译器采用Centos 6.4系统自带的即可，不用安装。对于Centos 6.4 系统，安装系统时，除语言配置外，如果选择了其余全部系统配置软件，并且第2步已正确安装 Python的话，安装完Python时，在命令行输入python以检验是否安装成功时，如果Python已安装成功，则可同时显示Python和与之本匹配的GCC版本信息。对于Centos 6.4系统内已预定安装的所有GCC版本中，与Python相匹配的版本为 GCC 4.4.7 (Red Hat 4.4.7-3)。如果在任意目录下的命令行输入rpm qa | grep gcc，则可列出系统内所有已安装的GCC的信息。预安装的GCC版本较多。4. 安装MPI编译器。此步骤极为关键，即使已安装好MPI后，路径配置不正确的话，将会导致后续安装的VASP不能正常运行。采用mpich-3.2.1版本。首先在 /home下建一个mpich的文件夹，将mpich-3.2.1.tar.gz放入mpich文件夹中。安装时，由于需要配置安装文件的路径，因此，安装后的软件不一事实上在mpich文件夹中，这由安装过程具体配置的路径确定。本安装的mpich文件配置路径为 /home/mpichexe，则安装命令如下：# tar -zxvf mpich-3.2.1.tar.gz 解压# cd mpich-3.2.1 进入解压后的文件目录# export F90=ifort FC=ifort 引入环境变量# ./configure -prefix=/ home/mpichexe / -enable-f90 -enable-f77 指定安装路径，并指定可使用mpif90及mpi77编译器 红色的是解压目录# make 编译# make install 安装# vi /.bashrc 修改环境变量，在bashrc文件的最后加入以下三行后，保存退出export PATH=/usr/local/mpi/:$PATHexport LD_LIBRARY_PATH=/usr/local/mpi/lib/:$LD_LIBRARY_PATHulimit -s unlimited# source /.bashrc 永久保存# exportPATH=$PATH:/opt/mpich3/bin 添加环境变量# exportLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mpich3/lib#source/etc/profile然后，在/etc/目录中新建一个名为mpd.conf的文本文件，在里面填写上：MPD_SECRETWORD=mr45-j9z，最后保存退出#chmod600/etc/mpd.conf 增加权限安装完毕后，检查环境变量是否正确：# which mpicc 显示路径则表示正确# which mpirun 显示路径则表示正确以下为网上某安装mpich的方法，复制于下，以作参考：安装mpich3:将mpich3压缩包解压，然后进入，执行：root#./configure-prefix=/opt/mpich3-enable-fortran=all-enable-cxxF77=ifortFC=ifortFCFLAGS=-O2-xHostFFLAGS=-O2-xHostCC=iccCXX=icpcCFLAGS=-O2xHostCXXFLAGS=-O2-xHost-enable-threads=multiple-enable-fast=all-enable-mpit-pvars=allroot#make-j8root#makeinstall然后添加环境变量：exportPATH=$PATH:/opt/mpich3/binexportLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mpich3/lib然后在终端执行：root#source/etc/profile注意，安装完并行库(不论是openmpi还是mpich)后，都要设置一下：在/etc/目录中新建一个名为mpd.conf的文本文件，在里面填写上：MPD_SECRETWORD=mr45-j9z然后保存退出，给这个文件加上权限：root#chmod600/etc/mpd.conf5.安装Intel编译器。文件为parallel_studio_xe_2018_update1_composer_edition_for_fortran.tgz。安装不难，按网上各年的版本安装即可，但中间涉及的文件很长很长，不写于下。安装完毕后，配置环境变量如下：# vi /.bashrc 修改环境变量，在bashrc文件的最后加入以下三行后，保存退出export PATH=/usr/local/mpi/:$PATHexport LD_LIBRARY_PATH=/usr/local/mpi/lib/:$LD_LIBRARY_PATHulimit -s unlimited# source /.bashrc 永久保存跟配置MPI的配置一样即可。安装完毕后，# rpm qa | grep mpi 出现版本号即表示安装成功6. 安装fftw傅里叶变换库。安装目录为 /home/fftw。命令如下。# tar -zxvf fftw-3.3.4.tar.gz# cd fftw-3.3.4# ./configure -prefix=/home/fftw CC=ifort F77=ifort -enable-mpi# make# make install至此，fftw安装完毕。7. 编译vasp。此过程分两部分。所用vasp版本为vasp.5.3.5。此处，由于vasp编译过程繁锁，且编译文默认的引用库路径为相对路径，因此，把vasp.5.3.5.tar.gz和vasp.5.3.5.lib.tar.gz解压后，放在同一目录下，且目录的路径尽量浅。本安装将vasp.5.3.5.tar.gz和vasp.5.3.5.lib.tar.gz解压后共同放在 /home/vasp下面。下面是安装过程。7.1 编译vasp.lib。# tar -zxvf vasp.5.3.5.lib.tar.gz 解压，并把解压文件放在/home/vasp下面。因此，文件路径为/home/vasp/vasp.5.3.5.lib# cd vasp.5.3.5.lib 进入解压目录。由于文件解压后经过移动，具体进入的命令会不同# ls 显示所有文件的列表# cp make.linux_ifort_P4 makefile 复制make.linux_ifort_P4文件，并重命名为 makefile# vi makefile 修改编译文件，文件主要内容及修改如下：#C-preprocessor 此处的#是文件中的注释，不执行CPP = gcc -E -P -C $*.F $*.fFC=ifc将FC=ifc 修改为FC=ifort，保存退出。# make 编译7.2 编译vasp主程序。# tar -zxvf vasp.5.3.5. tar.gz 解压，并把解压文件放在/home/vasp下面。因此，文件路径为/home/vasp/vasp.5.3.5# cd vasp.5.3.5 进入解压目录。由于文件解压后经过移动，具体进入的命令会不同# ls 显示所有文件的列表# ls 显示所有文件的列表# cp make.linux_ifort_P4 makefile 复制make.linux_ifort_P4文件，并重命名为 makefile此时，将/hom /fftw-3.3.4/api/fftw3.f 拷贝到解压后的VASP 安装源代码文件夹下（/home/ vasp/vasp.5.3.5）。# vi makefile 修改makefile文件。具体修改过程非常复杂，需要很细致的过程。下面是第二次安装vasp时的makefile文件。红色的为执持语句，#为注释，不是执行语句。Makefile修改完毕后，输入如下操作：# make 编译过程需要大约半小时，编译过程会出现多次错误，导致编译无法继续进行，需要不断修改makefile并不断make，直到提示 make: vaspis up to date. ，则表示已成功编译。编译成功后，在安装目录生成可执行的二进制文件，文件名为vasp。测试vasp是否可用：将典型物质的或正确的INCAR, POSCAR, KPOINTS, POTCAR放于同一文件中，并将可执行的vasp复制后与INCAR, POSCAR, KPOINTS, POTCAR放置于同一文件中，在命令行输入：# ./vasp 单机单核运行或输入# mpirun np y ./vasp y为想让vasp运行的cpu核数目，例如，mpirun np 4 ./vasp为单机四核运行vasp能正常运行则表明已真正成功编译。以下是第二次成功地在手提电脑安装vasp的vasp.5.3.5的makefile的全部内容：.SUFFIXES: .inc .f .f90 .F#-# Makefile for Intel Fortran compiler for Pentium/Athlon/Opteron # based systems# we recommend this makefile for both Intel as well as AMD systems# for AMD based systems appropriate BLAS (libgoto) and fftw libraries are# however mandatory (whereas they are optional for Intel platforms)# For Athlon we recommend # ) to link against libgoto (and mkl as a backup for missing routines)# ) odd enough link in libfftw3xf_intel.a (fftw interface for mkl)# feedback is greatly appreciated# The makefile was tested only under Linux on Intel and AMD platforms# the following compiler versions have been tested:# - ifc.7.1 works stable somewhat slow but reliably# - ifc.8.1 fails to compile the code properly# - ifc.9.1 recommended (both for 32 and 64 bit)# - ifc.10.1 partially recommended (both for 32 and 64 bit)# tested build 20080312 Package ID: l_fc_p_10.1.015# the gamma only mpi version can not be compiles# using ifc.10.1# - ifc.11.1 partially recommended (some problems with Gamma only and intel fftw)# Build 20090630 Package ID: l_cprof_p_11.1.046# - ifort.12.1 strongly recommended (we use this to compile vasp)# Version 39 Build 20120612# it might be required to change some of library path ways, since# LINUX installations vary a lot# Hence check *ALL* options in this makefile very carefully#-# BLAS must be installed on the machine# there are several options:# 1) very slow but works:# retrieve the lapackage from # and compile the blas routines (BLAS/SRC directory)# please use g77 or f77 for the compilation. When I tried to# use pgf77 or pgf90 for BLAS, VASP hang up when calling# ZHEEV (however this was with lapack 1.1 now I use lapack 2.0)# 2) more desirable: get an optimized BLAS # the two most reliable packages around are presently:# 2a) Intels own optimised BLAS (PIII, P4, PD, PC2, Itanium)# /software/products/mkl/# this is really excellent, if you use Intel CPUs# 2b) probably fastest SSE2 (4 GFlops on P4, 2.53 GHz, 16 GFlops PD, # around 30 GFlops on Quad core)# Kazushige Gotos BLAS# /users/kgoto/signup_first.html# /resources/software/#-# all CPP processed fortran files have the extension .f90SUFFIX=.f90#-# fortran compiler and linker#-FC=ifort # fortran linkerFCL=$(FC)#-# whereis CPP ? (I need CPP, cant use gcc with proper options)# thats the location of gcc for SUSE 5.3# CPP_ = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C # thats probably the right line for some Red Hat distribution:# CPP_ = /usr/lib/gcc-lib/i386-redhat-linux//cpp -P -C# SUSE X.X, maybe some Red Hat distributions:CPP_ = ./preprocess $*$(SUFFIX)# this release should be fpp clean# we now recommend fpp as preprocessor# if this fails go back to cppCPP_=fpp -f_com=no -free -w0 $*.F $*$(SUFFIX) #-# possible options for CPP:# NGXhalf charge density reduced in X direction# wNGXhalf gamma point only reduced in X direction# avoidalloc avoid ALLOCATE if possible# PGF90 work around some for some PGF90 / IFC bugs# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4, PD# RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (depends on used BLAS)# RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (depends on used BLAS)# tbdyn MD package of Tomas Bucko#-CPP = $(CPP_) -DHOST=LinuxIFC -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc -DNGXhalf -DRPROMU_DGEMV -DRACCMU_DGEMV#-# general fortran flags (there must a trailing blank on this line)# byterecl is strictly required for ifc, since otherwise# the WAVECAR file becomes huge#-FFLAGS = -FR -names lowercase -assume byterecl -heap-arrays 64 #-# optimization# we have tested whether higher optimisation improves performance# -axK SSE1 optimization, but also generate code executable on all mach.# xK improves performance somewhat on XP, and a is required in order# to run the code on older Athlons as well# -xW SSE2 optimization# -axW SSE2 optimization, but also generate code executable on all mach.# -tpp6 P3 optimization# -tpp7 P4 optimization#-# ifc.9.1, ifc.10.1 recommendedOFLAG=-O2 -ip OFLAG_HIGH = $(OFLAG)OBJ_HIGH = OBJ_NOOPT = DEBUG = -FR -O0INLINE = $(OFLAG)#-# the following lines specify the position of BLAS and LAPACK# we recommend to use mkl, that is simple and most likely # fastest in Intel based machines#-# mkl path for ifc 11 compiler#MKL_PATH=$(MKLROOT)/lib/em64t# mkl path for ifc 12 compilerMKL_PATH=$(MKLROOT)/lib/intel64MKL_FFTW_PATH=$(MKLROOT)/interfaces/fftw3xf/# BLAS# setting -DRPROMU_DGEMV -DRACCMU_DGEMV in the CPP lines usually speeds up program execution# BLAS= -Wl,-start-group $(MKL_PATH)/libmkl_intel_lp64.a $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,-end-group -lguide # faster linking and available from at least version 11BLAS=-mkl=sequential # LAPACK, use vasp.5.lib/lapack_double#LAPACK= ./vasp.5.lib/lapack_double.o# LAPACK from mkl, usually faster and contains scaLAPACK as wellLAPACK= $(MKL_PATH)/libmkl_intel_lp64.a # here a tricky version, link in libgoto and use mkl as a backup# also needs a special line for LAPACK# this is the best thing you can do on AMD based systems !#BLAS = -Wl,-start-group /opt/libs/libgoto/libgoto.so $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,-end-group -liomp5#LAPACK= /opt/libs/libgoto/libgoto.so $(MKL_PATH)/libmkl_intel_lp64.a#-LIB = -L ./vasp.5.lib -ldmy /home/vasp/vasp.5.lib/linpack_double.o $(LAPACK) $(BLAS) 指定linpack_double.o文件的路径。./为相对路径，/为绝对路径。此处为绝对路径。# options for linking, nothing is required (usually)#LINK =#-# fft libraries:# VASP.5.2 can use fftw.3.1.X ()# since this version is faster on P4 machines, we recommend to use it#-FFT3D = fft3dfurth.o fft3dlib.o# alternatively: fftw.3.1.X is slighly faster and should be used if available#FFT3D = fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a# you may also try to use the fftw wrapper to mkl (but the path might vary a lot)# it seems this is best for AMD based systems#FFT3D = fftw3d.o fft3dlib.o $(MKL_FFTW_PATH)/libfftw3xf_intel.a#INCS = -I$(MKLROOT)/include/fftw #=# MPI section, uncomment the following lines until # general rules and compile lines# presently we recommend OPENMPI, since it seems to offer better# performance than lam or mpich# # ! Please do not send me any queries on how to install MPI, I will# certainly not answer them !#=#-# fortran linker for mpi#-FC=mpif90FCL=$(FC) -mkl=sequential#-# additional options for CPP in parallel version (see also above):# NGZhalf charge density reduced in Z direction# wNGZhalf gamma point only reduced in Z direction# scaLAPACK use scaLAPACK (recommended if mkl is available)# avoidalloc avoid ALLOCATE if possible# PGF90 work around some for some PGF90 / IFC bugs# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4, PD# RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (depends on used BLAS)# RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (depends on used BLAS)# tbdyn MD package of Tomas Bucko#-#-CPP = $(CPP_) -DMPI -DHOST=LinuxIFC -DIFC -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DRPROMU_DGEMV -DRACCMU_DGEMV#-# location of SCALAPACK# if you do not use SCALAPACK simply leave this section commented out#-# usually simplest link in mkl scaLAPACK#BLACS= -lmkl_blacs_openmpi_lp64#SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)SCA= $MKLROOT/lib/intel64/libmkl_scalapack_lp64.a -Wl,-start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_core.a $MKLROOT/lib/intel64/libmkl_sequential.a -Wl,-end-group $MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm#-# libraries#-LIB = -L./vasp.5.lib -ldmy ./vasp.5.lib/linpack_double.o $(SCA) $(LAPACK) $(BLAS) 指定linpack_double.o文件的路径。./为相对路径，/为绝对路径。此处为相对路径。#-# parallel FFT#-# FFT: fftmpi.o with fft3dlib of Juergen Furthmueller#FFT3D = fftmpi.o fftmpi_map.o fft3dfurth.o fft3dlib.o # alternatively: fftw.3.1.X is slighly faster and should be used if available#FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a# you may also try to use the fftw wrapper to mkl (but the path might vary a lot)# it seems this is best for AMD based systems#FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $(MKL_FFTW_PATH)/libfftw3xf_intel.aINCS = -I$(MKLROOT)/include/fftw #-# general rules and compile lines#-BASIC= symmetry.o symlib.o lattlib.o random.o SOURCE= base.o mpi.o smart_allocate.o xml.o constant.o jacobi.o main_mpi.o scala.o asa.o lattice.o poscar.o ini.o mgrid.o xclib.o vdw_nl.o xclib_grad.o radial.o pseudo.o gridq.o ebs.o mkpoints.o wave.o wave_mpi.o wave_high.o spinsym.o $(BASIC) nonl.o nonlr.o nonl_high.o dfast.o choleski2.o mix.o hamil.o xcgrad.o xcspin.o potex1.o potex2.o constrmag.o cl_shift.o relativistic.o LDApU.o paw_base.o metagga.o egrad.o pawsym.o pawfock.o pawlhf.o rhfatm.o hyperfine.o paw.o mkpoints_full.o charge.o Lebedev-Laikov.o stockholder.o dipol.o pot.o dos.o elf.o tet.o tetweight.o hamil_rot.o chain.o dyna.o k-proj.o sphpro.o us.o core_rel.o aedens.o wavpre.o wavpre_noio.o broyden.o dynbr.o hamil_high.o rmm-diis.o reader.o writer.o tutor.o xml_writer.o brent.o stufak.o fileio.o opergrid.o stepver.o chgloc.o fast_aug.o fock_multipole.o fock.o mkpoints_change.o sym_grad.o mymath.o internals.o npt_dynamics.o dynconstr.o dimer_heyden.o dvvtrajectory.o subdftd3.o vdwforcefield.o nmr.o pead.o subrot.o subrot_scf.o paircorrection.o force.o pwlhf.o gw_model.o optreal.o steep.o davidson.o david_inner.o electron.o rot.o electron_all.o shm.o pardens.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o hamil_lr.o rmm-diis_lr.o subrot_cluster.o subrot_lr.o lr_helper.o hamil_