首页 > 代码库 > 搭建高性能计算环境(五)、应用软件的安装之VASP
搭建高性能计算环境(五)、应用软件的安装之VASP
1,将需要的软件包上传vasp.5.2.12.tar.gz、vasp.5.lib.tar.gz、benchmark.Hg.tar.gz。
2,创建vasp目录并解压软件包。
mkdir /opt/vaspcd /opt/vasptar xvf ~/vasp.5.lib.tar.gztar xvf ~/vasp.5.2.12.tar.gz
3,编译lib
cd vasp.5.lib/cp makefile.linux_ifc_P4 makefile
修改makefilemake
修改后的makefile:
.SUFFIXES: .inc .f .F#-----------------------------------------------------------------------# Makefile for Portland Group F90/HPF compiler# the makefile was tested only under Linux on Intel platforms# however it might work on other platforms as well## this release of vasp.4.lib contains lapack v2.0# this can be compiled with pgf90 compiler if the option -O1 is used## Mind: one user reported that he had to copy preclib.F diolib.F# dlexlib.F and drdatab.F to the directory vasp.4.4, compile the files# there and link them directly into vasp# for no obvious reason these files could not be linked from the library##-----------------------------------------------------------------------# C-preprocessorCPP = gcc -E -P -C $*.F >$*.fFC=ifortCFLAGS = -O3FFLAGS = -O3 -ipo -no-prec-div -xAVX -FIFREE = -FRDOBJ = preclib.o timing_.o derrf_.o dclock_.o diolib.o dlexlib.o drdatab.o#-----------------------------------------------------------------------# general rules#-----------------------------------------------------------------------libdmy.a: $(DOBJ) lapack_double.o linpack_double.o lapack_atlas.o -rm libdmy.a ar vq libdmy.a $(DOBJ)# files which do not require autodouble lapack_min.o: lapack_min.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_min.flapack_double.o: lapack_double.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_double.flapack_single.o: lapack_single.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_single.flapack_atlas.o: lapack_atlas.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_atlas.flinpack_double.o: linpack_double.f $(FC) $(FFLAGS) $(NOFREE) -c linpack_double.flinpack_single.o: linpack_single.f $(FC) $(FFLAGS) $(NOFREE) -c linpack_single.f.c.o: $(CC) $(CFLAGS) -c $*.c.F.o: $(CPP) $(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f.F.f: $(CPP) .f.o: $(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f
4,编译vasp
cd ../vasp.5.2/cp makefile.linux_ifc_P4 makefile
修改makefilemake
修改后的makefile:
.SUFFIXES: .inc .f .f90 .F#-----------------------------------------------------------------------# Makefile for Intel Fortran compiler for Pentium/Athlon/Opteron # bases systems# we recommend this makefile for both Intel as well as AMD systems# for AMD based systems appropriate BLAS and fftw libraries are# however mandatory (whereas they are optional for Intel platforms)## 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## it might be required to change some of library pathes, since# LINUX installation 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 ftp.netlib.org# 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)# http://developer.intel.com/software/products/mkl/# this is really excellent, if you use Intel CPU‘s## 2b) probably fastest SSE2 (4 GFlops on P4, 2.53 GHz, 16 GFlops PD, # around 30 GFlops on Quad core)# Kazushige Goto‘s BLAS# http://www.cs.utexas.edu/users/kgoto/signup_first.html# http://www.tacc.utexas.edu/resources/software/##-----------------------------------------------------------------------# all CPP processed fortran files have the extension .f90SUFFIX=.f90#-----------------------------------------------------------------------# fortran compiler and linker#-----------------------------------------------------------------------FC=ifc # fortran linkerFCL=$(FC)#-----------------------------------------------------------------------# whereis CPP ?? (I need CPP, can‘t use gcc with proper options)# that‘s the location of gcc for SUSE 5.3## CPP_ = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C ## that‘s probably the right line for some Red Hat distribution:## CPP_ = /usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P -C## SUSE X.X, maybe some Red Hat distributions:CPP_ = ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(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 = -O3 -no-prec-div -ipo -xAVX#-----------------------------------------------------------------------# 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=OFLAG_HIGH = $(OFLAG)OBJ_HIGH = OBJ_NOOPT = DEBUG = -FR -O0INLINE = $(OFLAG)#-----------------------------------------------------------------------# the following lines specify the position of BLAS and LAPACK# VASP works fastest with the libgoto library# so that‘s what we recommend#-----------------------------------------------------------------------# mkl.10.0# set -DRPROMU_DGEMV -DRACCMU_DGEMV in the CPP linesBLAS=-L/opt/intel/mkl/lib/intel64 -lmkl_core -lmkl_sequential -lmkl_intel_lp64 # even faster for VASP Kazushige Goto‘s BLAS# http://www.cs.utexas.edu/users/kgoto/signup_first.html# parallel goto version requires sometimes -libverbs#BLAS= /opt/libs/libgoto/libgoto.so# LAPACK, simplest use vasp.5.lib/lapack_doubleLAPACK= ../vasp.5.lib/lapack_double.o# use the mkl Intel lapack#LAPACK= -lmkl_lapack#-----------------------------------------------------------------------LIB = -L../vasp.5.lib -ldmy ../vasp.5.lib/linpack_double.o $(LAPACK) $(BLAS)# options for linking, nothing is required (usually)LINK = #-----------------------------------------------------------------------# fft libraries:# VASP.5.2 can use fftw.3.1.X (http://www.fftw.org)# since this version is faster on P4 machines, we recommend to use it#-----------------------------------------------------------------------FFT3D = fft3dfurth.o fft3dlib.o# alternatively: fftw.3.1.X is slighly faster and should be used if available#FFT3D = fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a#=======================================================================# MPI section, uncomment the following lines until # general rules and compile lines# presently we recommend OPENMPI, since it seems to offer better# performance than lam or mpich# # !!! Please do not send me any queries on how to install MPI, I will# certainly not answer them !!!!#=======================================================================#-----------------------------------------------------------------------# fortran linker for mpi#-----------------------------------------------------------------------FC=mpiifortFCL=$(FC)#-----------------------------------------------------------------------# 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 (usually slower on 100 Mbit Net)# 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 = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc -DNGZhalf -DMPI_BLOCK=8000 # -DRPROMU_DGEMV -DRACCMU_DGEMV#-----------------------------------------------------------------------# location of SCALAPACK# if you do not use SCALAPACK simply leave that section commented out#-----------------------------------------------------------------------#BLACS=$(HOME)/archives/SCALAPACK/BLACS/#SCA_=$(HOME)/archives/SCALAPACK/SCALAPACK#SCA= $(SCA_)/libscalapack.a # $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.a $(BLACS)/LIB/blacs_MPI-LINUX-0.a $(BLACS)/LIB/blacsF77init_MPI-LINUX-0.aSCA=#-----------------------------------------------------------------------# libraries for mpi#-----------------------------------------------------------------------LIB = -L../vasp.5.lib -ldmy ../vasp.5.lib/linpack_double.o $(LAPACK) $(SCA) $(BLAS)# FFT: fftmpi.o with fft3dlib of Juergen FurthmuellerFFT3D = 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#-----------------------------------------------------------------------# 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 $(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 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 steep.o chain.o dyna.o sphpro.o us.o core_rel.o aedens.o wavpre.o wavpre_noio.o broyden.o dynbr.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.o mkpoints_change.o sym_grad.o mymath.o internals.o dynconstr.o dimer_heyden.o dvvtrajectory.o vdwforcefield.o hamil_high.o nmr.o pead.o mlwf.o subrot.o subrot_scf.o force.o pwlhf.o gw_model.o optreal.o davidson.o david_inner.o electron.o rot.o electron_all.o shm.o pardens.o paircorrection.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_lrf.o elinear_response.o ilinear_response.o linear_optics.o linear_response.o setlocalpp.o wannier.o electron_OEP.o electron_lhf.o twoelectron4o.o ratpol.o screened_2e.o wave_cacher.o chi_base.o wpot.o local_field.o ump2.o bse_te.o bse.o acfdt.o chi.o sydmat.o dmft.o rmm-diis_mlr.o linear_response_NMR.ovasp: $(SOURCE) $(FFT3D) $(INC) main.o rm -f vasp $(FCL) -o vasp main.o $(SOURCE) $(FFT3D) $(LIB) $(LINK)makeparam: $(SOURCE) $(FFT3D) makeparam.o main.F $(INC) $(FCL) -o makeparam $(LINK) makeparam.o $(SOURCE) $(FFT3D) $(LIB)zgemmtest: zgemmtest.o base.o random.o $(INC) $(FCL) -o zgemmtest $(LINK) zgemmtest.o random.o base.o $(LIB)dgemmtest: dgemmtest.o base.o random.o $(INC) $(FCL) -o dgemmtest $(LINK) dgemmtest.o random.o base.o $(LIB) ffttest: base.o smart_allocate.o mpi.o mgrid.o random.o ffttest.o $(FFT3D) $(INC) $(FCL) -o ffttest $(LINK) ffttest.o mpi.o mgrid.o random.o smart_allocate.o base.o $(FFT3D) $(LIB)kpoints: $(SOURCE) $(FFT3D) makekpoints.o main.F $(INC) $(FCL) -o kpoints $(LINK) makekpoints.o $(SOURCE) $(FFT3D) $(LIB)clean: -rm -f *.g *.f *.o *.L *.mod ; touch *.Fmain.o: main$(SUFFIX) $(FC) $(FFLAGS)$(DEBUG) $(INCS) -c main$(SUFFIX)xcgrad.o: xcgrad$(SUFFIX) $(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcgrad$(SUFFIX)xcspin.o: xcspin$(SUFFIX) $(FC) $(FFLAGS) $(INLINE) $(INCS) -c xcspin$(SUFFIX)makeparam.o: makeparam$(SUFFIX) $(FC) $(FFLAGS)$(DEBUG) $(INCS) -c makeparam$(SUFFIX)makeparam$(SUFFIX): makeparam.F main.F ## MIND: I do not have a full dependency list for the include# and MODULES: here are only the minimal basic dependencies# if one strucuture is changed then touch_dep must be called# with the corresponding name of the structure#base.o: base.inc base.Fmgrid.o: mgrid.inc mgrid.Fconstant.o: constant.inc constant.Flattice.o: lattice.inc lattice.Fsetex.o: setexm.inc setex.Fpseudo.o: pseudo.inc pseudo.Fposcar.o: poscar.inc poscar.Fmkpoints.o: mkpoints.inc mkpoints.Fwave.o: wave.Fnonl.o: nonl.inc nonl.Fnonlr.o: nonlr.inc nonlr.F$(OBJ_HIGH): $(CPP) $(FC) $(FFLAGS) $(OFLAG_HIGH) $(INCS) -c $*$(SUFFIX)$(OBJ_NOOPT): $(CPP) $(FC) $(FFLAGS) $(INCS) -c $*$(SUFFIX)fft3dlib_f77.o: fft3dlib_f77.F $(CPP) $(F77) $(FFLAGS_F77) -c $*$(SUFFIX).F.o: $(CPP) $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX).F$(SUFFIX): $(CPP)$(SUFFIX).o: $(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)# special rules#-----------------------------------------------------------------------# these special rules are cummulative (that is once failed# in one compiler version, stays in the list forever)# -tpp5|6|7 P, PII-PIII, PIV# -xW use SIMD (does not pay of on PII, since fft3d uses double prec)# all other options do no affect the code performance since -O1 is usedfft3dlib.o : fft3dlib.F $(CPP) $(FC) -FR -lowercase -O2 -c $*$(SUFFIX)fft3dfurth.o : fft3dfurth.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)fftw3d.o : fftw3d.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)wave_high.o : wave_high.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)radial.o : radial.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)symlib.o : symlib.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)symmetry.o : symmetry.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)wave_mpi.o : wave_mpi.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)wave.o : wave.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)dynbr.o : dynbr.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)asa.o : asa.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)broyden.o : broyden.F $(CPP) $(FC) -FR -lowercase -O2 -c $*$(SUFFIX)us.o : us.F $(CPP) $(FC) -FR -lowercase -O1 -c $*$(SUFFIX)LDApU.o : LDApU.F $(CPP) $(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
5,添加环境变量
在/etc/profile文件末尾添加如下内容,需要重新登录后生效
export PATH=/opt/vasp/vasp5.2:$PATH
6,测试
准备测试文件vasp.Hg,进入算例目录,输入:
mpirun -np 4 vasp
如能正常计算完毕,说明软件安装成功。
补充软件下载地址(仅供测试使用):
链接: http://pan.baidu.com/s/1qWv4k7i 密码: rsgh
搭建高性能计算环境(五)、应用软件的安装之VASP
声明:以上内容来自用户投稿及互联网公开渠道收集整理发布,本网站不拥有所有权,未作人工编辑处理,也不承担相关法律责任,若内容有误或涉及侵权可进行投诉: 投诉/举报 工作人员会在5个工作日内联系你,一经查实,本站将立刻删除涉嫌侵权内容。