搭建高性能计算环境（四）、应用软件的安装之VASP-白红宇

搭建高性能计算环境（四）、应用软件的安装之VASP

阅读量：4670 次

发布时间：2019-06-09

本文共 17139 字，大约阅读时间需要 57 分钟。

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 -ip -no-prec-div -funrool-loops -xHost -heap-arrays 64 FREE   =  -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 -ip -no-prec-div -funroll-loops -xHost -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=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