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sdwawa

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专业: 金属材料的力学行为

[求助] VASP5.2编译成功后运行出错

在fedora17上编译VASP5.2单机版，装的编译器是ifort，下载版本是l_fcompxe_intel64_2013.1.117.tgz.

编译成功后找了文件运行后出错，错误内容是：
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image             PC             Routine          Line       Source
libmkl_avx.so    00002B4D4F5E20BB  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E0EFE  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E17D4  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4D6E141E  Unknown             Unknown  Unknown
libmkl_core.so    00002B4D4DB47183  Unknown             Unknown  Unknown
vasp             00000000004A9F8C  Unknown             Unknown  Unknown
vasp             000000000062FA7E  Unknown             Unknown  Unknown
vasp             0000000000408DA6  Unknown             Unknown  Unknown
vasp             000000000040467C  Unknown             Unknown  Unknown
libc.so.6       00002B4D4E9F5735  Unknown             Unknown  Unknown
vasp             0000000000404559  Unknown             Unknown  Unknown

采用了网上的一些方案如在FFLAGS后加入-heap-arrarys 64不可行。试着更换ifort版本如ifort11.1，但在fedora17中并不支持。请求解决方案。非常感谢。

使用的VASP 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=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 -heap-arrarys 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=-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=  /opt/libs/libgoto/libgoto.so
BLAS=

# LAPACK, simplest use vasp.5.lib/lapack_double
#LAPACK= ../vasp.5.lib/lapack_double.o

# use the mkl Intel lapack
#LAPACK= -lmkl_lapack
LAPACK= -L$(MKLROOT)/lib/intel64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -
lpthread

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

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=mpif77
#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
#-----------------------------------------------------------------------

#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 $(BLA
CS)/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 = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o  /opt/libs/fftw-3.1.2/lib/l
ibfftw3.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 davi
dson.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_allocat
e.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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iamikaruk

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franch: 金币+2, 谢谢回帖交流， 2012-12-17 15:40:17

引用回帖:

12楼: Originally posted by sdwawa at 2012-12-17 13:27:45
我在Intel官网上看到关于fedora安装intel编译器的内容，说fedora11-15是支持的，最新版和测试版可能不支持，且要安装最新版的编译器。我用fedora17安装ifort11.1说需要安装libstdc++.so.5，但用yum安装得到的最新版 ...

不可能吧？
我用centos 6.3，安装的libstdc++是5.0.7和6.0.13，按理来说fedora会有的