搭建高性能计算环境（四）、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/vasp

cd /opt/vasp

tar xvf ~/vasp.5.lib.tar.gz

tar xvf ~/vasp.5.2.12.tar.gz

3,编译lib

cd vasp.5.lib/

cp makefile.linux_ifc_P4 makefile
修改makefile

make

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-preprocessor

CPP     = gcc -E -P -C $*.F >$*.f

FC=ifort



CFLAGS = -O3

FFLAGS = -O3 -ip -no-prec-div -funrool-loops -xHost -heap-arrays 64 

FREE   =  -FR



DOBJ =  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.f

lapack_double.o: lapack_double.f

        $(FC) $(FFLAGS) $(NOFREE) -c lapack_double.f

lapack_single.o: lapack_single.f

        $(FC) $(FFLAGS) $(NOFREE) -c lapack_single.f

lapack_atlas.o: lapack_atlas.f

        $(FC) $(FFLAGS) $(NOFREE) -c lapack_atlas.f

linpack_double.o: linpack_double.f

        $(FC) $(FFLAGS) $(NOFREE) -c linpack_double.f

linpack_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makefile

make

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 .f90

SUFFIX=.f90



#-----------------------------------------------------------------------

# fortran compiler and linker

#-----------------------------------------------------------------------

FC=ifc 

# fortran linker

FCL=$(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 recommended

OFLAG=



OFLAG_HIGH = $(OFLAG)

OBJ_HIGH = 

OBJ_NOOPT = 

DEBUG  = -FR -O0

INLINE = $(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 lines

BLAS=-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_double

LAPACK= ../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=mpiifort

FCL=$(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.a



SCA=



#-----------------------------------------------------------------------

# 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 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



#-----------------------------------------------------------------------

# 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.o



vasp: $(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 *.F



main.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.F

mgrid.o: mgrid.inc mgrid.F

constant.o: constant.inc constant.F

lattice.o: lattice.inc lattice.F

setex.o: setexm.inc setex.F

pseudo.o: pseudo.inc pseudo.F

poscar.o: poscar.inc poscar.F

mkpoints.o: mkpoints.inc mkpoints.F

wave.o: wave.F

nonl.o: nonl.inc nonl.F

nonlr.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 used



fft3dlib.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