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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Vasp&MedeA » 并行vasp安装后运行出错
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dk1013

木虫 (正式写手)

[求助] 并行vasp安装后运行出错

刚刚在ubuntu 12.04 LTS (64 bit)上面安装了并行的vasp 5.2.12。
GotoBLAS2 + FFTW3 + gcc + ifort + openmpi
编译过程没有报错，成功生成vasp程序。
于是把从网上找来的一个example 放进vasp.5.2文件夹里面去，然后运行vasp。
接着就出现下面的错误：

running on    1 nodes
distr:  one band on    1 nodes,    1 groups
vasp.5.2.12 26May11 complex
POSCAR found :  1 types and       1 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: small aliasing (wrap around) errors must be expected
FFT: planning ...(           1 )
WAVECAR not read
entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
Segmentation fault (core dumped)

因为刚自学还不会使用vasp，所以也不明白产生的原因是什么（见笑了）。
请高手来给小弟帮帮忙吧！！
先谢过了！！


makefile 和输入文件都贴在下面：

.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)
# 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 =  -FR -names 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=-O2 -ip -ftz
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=~/vasp-install/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  = -L../vasp.5.lib -ldmy \
     ../vasp.5.lib/linpack_double.o $(LAPACK) \
     $(BLAS)
# options for linking, nothing is required (usually)
LINK    =
#-----------------------------------------------------------------------
# fft libraries:
# VASP.5.2 can use fftw.3.1.X (http://www.fftw.org)
# since this version is faster on P4 machines, we recommend to use it
#-----------------------------------------------------------------------
#FFT3D   = fft3dfurth.o fft3dlib.o
# alternatively: fftw.3.1.X is slighly faster and should be used if available
#FFT3D   = fftw3d.o fft3dlib.o   /opt/libs/fftw-3.1.2/lib/libfftw3.a
#=======================================================================
# MPI section, uncomment the following lines until
#    general  rules and compile lines
# presently we recommend OPENMPI, since it seems to offer better
# performance than lam or mpich
#
# !!! Please do not send me any queries on how to install MPI, I will
# certainly not answer them !!!!
#=======================================================================
#-----------------------------------------------------------------------
# fortran linker for mpi
#-----------------------------------------------------------------------
FC=/opt/openmpi/bin/mpif77
FCL=$(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)
# 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    = $(CPP_) -DMPI  -DHOST=\"LinuxIFC\" -DIFC \
     -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \
     -DMPI_BLOCK=8000
##    -DRPROMU_DGEMV  -DRACCMU_DGEMV
#-----------------------------------------------------------------------
# location of SCALAPACK
# if you do not use SCALAPACK simply leave that section commented out
#-----------------------------------------------------------------------
#BLACS=$(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 $(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
INCS = -I/opt/fftw3/include
# 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/fftw3/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)


INCAR：

SYSTEM = O atom in a box
ISMEAR = 0  ! Gaussian smearing

KPOINTS:

Gamma-point only
1        ! one k-point
rec       ! in units of the reciprocal lattice vector
0 0 0 1  ! 3 coordinates and weight

POSCAR:

O atom in a box
1.0          ! universal scaling parameters
8.0 0.0 0.0  ! lattice vector  a(1)
0.0 8.0 0.0  ! lattice vector  a(2)
0.0 0.0 8.0  ! lattice vector  a(3)
1             ! number of atoms
cart          ! positions in cartesian coordinates
0 0 0

POTCAR:
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到得还来别无事 庐山烟雨浙江潮
1楼 2012-11-30 00:19:35
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

emilyoyang

木虫 (正式写手)

【答案】应助回帖

★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
感谢参与，应助指数 +1
dk1013: 金币+29, ★★★★★最佳答案, 多谢了！！改了FFLAGS，运行时忘加ulimit -s unlimited居然也能得出结果。 2012-11-30 12:00:52
对提示段错误或者内存不足的
在FFLAGS 选项的赋值中增加  -heap-arrays  64
运行的时候加 ulimit -s unlimited
再make得到vasp,运行即可
另外课参考贺版主的百度空间：http://hi.baidu.com/heyi87/item/c9e517345419a3d66d15e9e3
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2楼2012-11-30 10:26:54
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dk1013

木虫 (正式写手)
引用回帖:
2楼: Originally posted by emilyoyang at 2012-11-30 10:26:54
对提示段错误或者内存不足的
在FFLAGS 选项的赋值中增加  -heap-arrays  64
运行的时候加 ulimit -s unlimited
再make得到vasp,运行即可
另外课参考贺版主的百度空间：http://hi.baidu.com/heyi87/item/c9e5173 ...

好的，多谢了！
我马上试试！
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到得还来别无事 庐山烟雨浙江潮
3楼2012-11-30 10:54:15
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dk1013

木虫 (正式写手)
引用回帖:
2楼: Originally posted by emilyoyang at 2012-11-30 10:26:54
对提示段错误或者内存不足的
在FFLAGS 选项的赋值中增加  -heap-arrays  64
运行的时候加 ulimit -s unlimited
再make得到vasp,运行即可
另外课参考贺版主的百度空间：http://hi.baidu.com/heyi87/item/c9e5173 ...

再问一个问题：

“运行的时候加 ulimit -s unlimited”

是指在make后面加？还是指在vasp后面加？
我都没有加，跑起来没出错，莫非是换个模型可能会出错吗？
赞一下 回复此楼
到得还来别无事 庐山烟雨浙江潮
4楼2012-11-30 12:10:29
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emilyoyang

木虫 (正式写手)
引用回帖:
4楼: Originally posted by dk1013 at 2012-11-30 12:10:29
再问一个问题：

“运行的时候加 ulimit -s unlimited”

是指在make后面加？还是指在vasp后面加？
我都没有加，跑起来没出错，莫非是换个模型可能会出错吗？...

他那个帖子上说的有点模糊  我也没太明白  嘿嘿~~~

一般都是把ulimit -s unlimited 添加到环境变量中（比如，.bashrc .profile等文件文件中 source 一下 就OK了
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5楼2012-11-30 14:37:26
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dk1013

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5楼: Originally posted by emilyoyang at 2012-11-30 14:37:26
他那个帖子上说的有点模糊  我也没太明白  嘿嘿~~~

一般都是把ulimit -s unlimited 添加到环境变量中（比如，.bashrc .profile等文件文件中 source 一下 就OK了...

在网上查了查，好像可以通过 ulimit -a来查看系统资源限制情况
我在我的ubuntu下面得到下面的输出：
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 11940
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 11940
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

发现貌似stack size是被限制了的。
stack size              (kbytes, -s) 8192
顺序执行ulimit -s unlimited和ulimit -a之后发现stack size 就变成 unlimited了。
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到得还来别无事 庐山烟雨浙江潮
6楼2012-11-30 15:12:55
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love5264

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谋定而动
7楼2013-01-08 21:17:56
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wmy8802217

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楼主。。。最后就是运行了一下那个命令就解决了么？
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凝聚态理论与计算物理
8楼2014-05-02 22:30:24
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