Segmentation fault

Problems running VASP: crashes, internal errors, "wrong" results.


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Gu Chenjie
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Segmentation fault

#1 Post by Gu Chenjie » Wed Dec 29, 2010 8:30 am

Dear Sir,
when I run the example from the handson1, the following error happen:

Code: Select all

 running on    1 nodes
 distr:  one band on    1 nodes,    1 groups
 vasp.5.2.8 07Jul10 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 )
 reading WAVECAR
 WARNING: random wavefunctions but no delay for mixing, default for NELMDL
 entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
Segmentation fault

I know this should be a compilation problem, because I use Intel's fortran compiler 11,
but for the mpi, I use mpif90, from mpich2.
however is there any way to solve this problem?
thanks a lot.
INCAR

Code: Select all

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

KPOINTS

Code: Select all

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


POSCAR

Code: Select all

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


and finally the makefile

Code: Select all

.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 = -I/home/enola/lib/intel/icc/mkl/include/fftw -FR -lowercase 

#-----------------------------------------------------------------------
# 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=-L/home/enola/lib/intel/icc/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread
# LAPACK, simplest use vasp.5.lib/lapack_double
LAPACK= -L/home/enola/lib/intel/icc/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread

# 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
FFT3D   =  fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o  /home/enola/lib/intel/icc/mkl/lib/intel64/libfftw3xf_intel.a 
# 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=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
#-----------------------------------------------------------------------

#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       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  \
         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   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.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)


&|
<span class='smallblacktext'>[ Edited ]</span>
Last edited by Gu Chenjie on Wed Dec 29, 2010 8:30 am, edited 1 time in total.

forsdan
Sr. Member
Sr. Member
Posts: 339
Joined: Mon Apr 24, 2006 9:07 am
License Nr.: 173
Location: Gothenburg, Sweden

Segmentation fault

#2 Post by forsdan » Wed Dec 29, 2010 7:10 pm

1. Please note that mpif90 is just a wrapper compiler for MPI and does not compile or link applications itself. It only adds in command line flags and invokes the underlying fortran 90 compiler. You can usually check the command line that would be executed to compile the program by "mpif90 -showme".

2. In your previous thread I saw that you have switched from vasp 4.6 to vasp 5.2. Have you accounted for that large arrays now is loaded from the stack in vasp 5.2 instead of the heap in vasp 4.6 ? Please see

http://cms.mpi.univie.ac.at/vasp-forum/ ... php?2.7459

If your stacksize is too small you will get a seg. fault.

Otherwise if this is accounted for, you should go through the standard procedure to check if the serial version works, the linking is correct, and if the MPI libraries, compilers, and system are set up properly. A debugger is always helpful as well.

Cheers,
/Dan


<span class='smallblacktext'>[ Edited Wed Dec 29 2010, 08:17PM ]</span>
Last edited by forsdan on Wed Dec 29, 2010 7:10 pm, edited 1 time in total.

Gu Chenjie
Newbie
Newbie
Posts: 18
Joined: Thu Nov 25, 2010 5:41 am

Segmentation fault

#3 Post by Gu Chenjie » Thu Jan 06, 2011 7:01 am

Hi frosdan, thanks a lot for your reply.
yes, if I set the stack to unlimit, the vasp.5 can work on the single node, which contain 24 cores. However, when I try to link two nodes together to do the calculation, it failed.

Code: Select all

Fatal error in MPI_Waitall: Other MPI error, error stack:
MPI_Waitall(261)..................: MPI_Waitall(count=46, req_array=0x7fffeeca46a0, status_array=0x7fffeeca4760) failed
MPIDI_CH3I_Progress(150)..........: 
MPID_nem_mpich2_blocking_recv(948): 
MPID_nem_tcp_connpoll(1709).......: Communication error
rank 23 in job 1  node0_55860   caused collective abort of all ranks
  exit status of rank 23: killed by signal 9

I think the problem still comes from the stack, though I already set both of the stack of these two nodes to unlimited.

Thanks a lot,
Have a nice day.
Chenjie GU
Last edited by Gu Chenjie on Thu Jan 06, 2011 7:01 am, edited 1 time in total.

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