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BountyHunter

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[交流] 求助：VASP編譯問題已有2人參與

各位大神，VASP.5.2編譯遇到問題，求幫助，謝謝大家！
系統(tǒng)：ubuntu-14.04-desktop-amd64；ifort, icc, icpc, mpif90都沒有問題。
vasp.5.lib也沒有問題（出現(xiàn)make: ‘libdmy.a’ is up to date）。
在編譯vasp時有問題：
/home/ubuntu-1/vasp_setups/openmpi-1.6.5/bin/mpif90 -FR -lowercase -assume byterecl  -O3  -c base.f90
/home/ubuntu-1/vasp_setups/openmpi-1.6.5/bin/mpif90: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
make: *** [base.o] Error 127

說找不到libimf.so，我查了下這個文件在：/opt/intel/composer_xe_2011_sp1.11.339/compiler/lib/intel64。加到mpi的library里面沒有用，還是這個提示！
大家看看，makefile如下：

.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=/opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/ifort
# 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)
#-----------------------------------------------------------------------

CPP    = $(CPP_)  -DHOST=\"LinuxIFC\" \
      -Dkind8 -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 -lowercase -assume byterecl

#-----------------------------------------------------------------------
# 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=-O3

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/mkl100/lib/em64t -lmkl -lpthread

# 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=  /home/ubuntu-1/vasp_setups/GotoBLAS2/libgoto2.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 = -limf -lm -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=/home/ubuntu-1/vasp_setups/openmpi-1.6.5/bin/mpif90
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)
#-----------------------------------------------------------------------

CPP = $(CPP_) -DMPI  -DHOST=\"LinuxIFC\" -DIFC \
   -Dkind8 -DCACHE_SIZE=4000 -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
#-----------------------------------------------------------------------

MKL_PATH=/opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64

BLAS= -L$(MKL_PATH) -libmkl_blas95_lp64
LAPACK= -L$(MKL_PATH) -libmkl_intel_lp64  -libmkl_sequential -libmkl_core -libmkl_pgi_thread
SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(MKL_PATH)/libmkl_blacs_openmpi_lp64.a

#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/opt/intel/composer_xe_2011_sp1.11.339/compiler/lib/intel64 -libimf -limf -lm \
   -limf -lm -L../vasp.5.lib -ldmy  \
   ../vasp.5.lib/linpack_double.o $(LAPACK) \
   $(SCA) $(BLAS) $(BLACS) \

# 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 = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o  /opt/libs/fftw-3.1.2/lib/libfftw3.a
FFT3D = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o  /opt/intel/composer_xe_2011_sp1.11.339/mkl/interfaces/fftw3xf/libfftw3xf_intel.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    xclib.o    xclib_grad.o \
      radial.o pseudo.o mgrid.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  \
      metagga.o constrmag.o cl_shift.o relativistic.o LDApU.o \
      paw_base.o egrad.o pawsym.o pawfock.o  pawlhf.o paw.o \
      mkpoints_full.o    charge.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 dimer_heyden.o dvvtrajectory.o vdwforcefield.o \
      hamil_high.o nmr.o force.o \
      pead.o    subrot.o subrot_scf.o pwlhf.o  gw_model.o optreal.o davidson.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.o acfdt.o chi.o sydmat.o

INC=

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.inc 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)

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)

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1樓 2014-11-04 16:36:54

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KalaShayminS

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檢查intel的環(huán)境變量，最好用它自帶的腳本設置。

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2樓2014-11-04 19:45:25

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BountyHunter

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什么是自帶的腳本設置？我只改了需要改的部分，其他部分看不懂，也沒動。
安裝后都設置環(huán)境變量，都是用intel編譯的。
mpif90也是用ifort編譯的，都沒出問題。

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3樓2014-11-05 10:13:41

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BountyHunter

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我剛開始學，大家?guī)兔纯�，謝謝啦

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4樓2014-11-05 10:14:53

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llh2010

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ljw4010: 金幣+1, 謝謝指導解答！ 2014-11-05 22:07:46

libimf.so是mpi的庫文件，在bashrc中將openmpi的lib導入到LD_LIBRARY_PATH路徑下就不會出這個問題了。

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知識引導人生，學習成就未來

5樓2014-11-05 13:38:02

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KalaShayminS

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引用回帖:

3樓: Originally posted by BountyHunter at 2014-11-05 10:13:41
什么是自帶的腳本設置？我只改了需要改的部分，其他部分看不懂，也沒動。
安裝后都設置環(huán)境變量，都是用intel編譯的。
mpif90也是用ifort編譯的，都沒出問題。

安裝Intel的時候應該會有提示的，將這個加入.bashrc
source /opt/intel/composer_xe_2011_sp1.11.339/bin/compilervars.sh intel64

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6樓2014-11-05 14:16:46

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BountyHunter

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5樓: Originally posted by llh2010 at 2014-11-05 13:38:02
libimf.so是mpi的庫文件，在bashrc中將openmpi的lib導入到LD_LIBRARY_PATH路徑下就不會出這個問題了。

謝謝回復，在~/.bashrc中加了，還是沒有變。
下面是~/.bashrc中的設置：
export LD_LIBRARY_PATH=/home/ubuntu-1/vasp_setups/openmpi-1.6.5/bin:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/ubuntu-1/vasp_setups/openmpi-1.6.5/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/ubuntu-1/vasp_setups/openmpi-1.6.5:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/intel/composer_xe_2011_sp1.11.339/compiler/lib/intel64:$LD_LIBRARY_PATH
source /opt/intel/composer_xe_2011_sp1.11.339/bin/compilervars.sh intel64

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7樓2014-11-05 15:08:09

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7樓: Originally posted by BountyHunter at 2014-11-05 15:08:09
謝謝回復，在~/.bashrc中加了，還是沒有變。
下面是~/.bashrc中的設置：
export LD_LIBRARY_PATH=/home/ubuntu-1/vasp_setups/openmpi-1.6.5/bin:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/ubuntu-1/vasp ...

不需要這么多，只要
source /opt/intel/composer_xe_2011_sp1.11.339/bin/compilervars.sh intel64
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/ubuntu-1/vasp_setups/openmpi-1.6.5/lib
這兩行就夠了，另外你的openmpi是安裝在/home/ubuntu-1/vasp_setups/openmpi-1.6.5路徑下嗎？默認是安裝在/opt/路徑下。
如果是安裝在你寫的路徑下，修改完bashrc后source ~/.bashrc一下，讓修改生效。
你的Makefile也有些問題，不知道你是要串行版本還是并行版本，要是并行版本的最好把串行部分注釋掉。還有就是既然用libgoto2數(shù)學庫，就不需要Intel的mkl數(shù)學庫。你的Makefile里指定了兩種數(shù)學庫，編譯就搞亂了。建議使用Intel的數(shù)學庫

把
# mkl.10.0
# set -DRPROMU_DGEMV  -DRACCMU_DGEMV in the CPP lines
#BLAS=-L/opt/intel/mkl100/lib/em64t -lmkl -lpthread
改成
BLAS=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64  -lmkl_sequential -lmkl_core -lpthread
并行部分的
刪除
MKL_PATH=/opt/intel/composer_xe_2011_sp1.11.339/mkl/lib/intel64

BLAS= -L$(MKL_PATH) -libmkl_blas95_lp64
LAPACK= -L$(MKL_PATH) -libmkl_intel_lp64  -libmkl_sequential -libmkl_core -libmkl_pgi_thread
SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(MKL_PATH)/libmkl_blacs_openmpi_lp64.a
把
LIB = -L/opt/intel/composer_xe_2011_sp1.11.339/compiler/lib/intel64 -libimf -limf -lm \
   -limf -lm -L../vasp.5.lib -ldmy  \
   ../vasp.5.lib/linpack_double.o $(LAPACK) \
   $(SCA) $(BLAS) $(BLACS) \
改成
LIB    = -L../vasp.5.lib -ldmy  \
   ../vasp.5.lib/linpack_double.o $(LAPACK) \
   $(SCA) $(BLAS)

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8樓2014-11-05 15:22:09

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8樓: Originally posted by llh2010 at 2014-11-05 15:22:09
不需要這么多，只要
source /opt/intel/composer_xe_2011_sp1.11.339/bin/compilervars.sh intel64
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/ubuntu-1/vasp_setups/openmpi-1.6.5/lib
這兩行就夠了 ...

我的openmpi確實安裝在/home/ubuntu-1/vasp_setups/openmpi-1.6.5，
修改后，source ~/.bashrc，還是不行。

我用的是VMware的虛擬機，這個有影響嗎？

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9樓2014-11-05 15:48:31

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9樓: Originally posted by BountyHunter at 2014-11-05 15:48:31
我的openmpi確實安裝在/home/ubuntu-1/vasp_setups/openmpi-1.6.5，
修改后，source ~/.bashrc，還是不行。

我用的是VMware的虛擬機，這個有影響嗎？...

你看看我給你改的Makefile，
虛擬機跟真機是一模一樣的，編譯沒有任何問題！

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10樓2014-11-05 15:53:15

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