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segmentation fault -- IBRION=1 SIGSEV

Posted: Fri Aug 29, 2008 8:39 pm
by piquini
I have compiled the vasp 4.6.31 in a Core 2 Duo using

Compiler: ifort 10 and icc 10
mkl 10 libraries
OpenMpi 1.2.6
mkl fftw3

It runs well if I use IBRION = 0, 2, 3 but it gives a segmentation fault bug (SIGSEV) when I use IBRION=1.
I have debugged the code and the error appears to be in the dynbr.F in the subroutines brion_ and brzero_

The makefiles I used follow below

.SUFFIXES: .inc .f .f90 .F
#-----------------------------------------------------------------------
# Makefile for Intel Fortran compiler for Operton systems
#
# The makefile was tested only under Linux on Intel platforms
# (Suse 5.3- Suse 9.2)
# the followin compiler versions have been tested
# 5.0, 6.0, 7.0 and 7.1 (some 8.0 versions seem to fail compiling the code,
# 8.1 is slower than 8.0)
# presently we recommend version 7.1 or 7.0, since these
# releases have been used to compile the present code versions
#
# 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:
# Kazushige Goto's BLAS is required
# http://www.cs.utexas.edu/users/kgoto/signup_first.html
# (see below libgoto comments)
#
# FFT:
# the fftw.3.0.1 must be available and installed, since
# the ifc compiler creates crap code if the build in fft routines are used
# (see below fftw comments)
#-----------------------------------------------------------------------

# all CPP processed fortran files have the extension .f90
SUFFIX=.f90

#-----------------------------------------------------------------------
# fortran compiler and linker
#-----------------------------------------------------------------------
FC=mpif90
# 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
# IFC work around some IFC bugs
# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4
# 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\" -I/opt/lab/include/fftw
# -Dkind8 -DNGXhalf -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \
# -Duse_cray_ptr
# -DRPROMU_DGEMV -DRACCMU_DGEMV
# "
#-----------------------------------------------------------------------
# general fortran flags (there must a trailing blank on this line)
#-----------------------------------------------------------------------

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

OFLAG=-O0 -axW
OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =

OBJ_NOOPT =
DEBUG = -FR -O0
INLINE = $(OFLAG)


#-----------------------------------------------------------------------
# the following lines specify the position of BLAS and LAPACK
# on Operton, you really need the libgoto library
#-----------------------------------------------------------------------

#BLAS= $(HOME)/OPT/src/vasp.4.6/libgoto_opteron-32-r0.99.so -lpthread
#$(HOME)/OPT/src/vasp.4.6/libgoto_opt32-r0.96.so -lpthread
#BLAS = /opt/libs/libgoto/libgoto_p4_512-r0.6.so
# LAPACK, simplest use vasp.4.lib/lapack_double
#-----------------------------------------------------------------------

#-lmkl_blas95 -lmkl_core -lmkl_solver -lmkl_ia32
# -lmkl_core -lmkl_cdft_core -lmkl_solver
# -lmkl_blas95 -lmkl_lapack -lmkl_intel
#-L/opt/lab/lib/32 $(MKLS)
# options for linking (for compiler version 6.X, 7.1) nothing is required
#LINK =
# compiler version 7.0 generates some vector statments which are located
# in the svml library, add the LIBPATH and the library (just in case)
#LINK = -L/opt/intel/compiler70/ia32/lib/ -lsvml

#-----------------------------------------------------------------------
# fft libraries:
# On Operton you really have to used fftw.3.0.X (http://www.fftw.org)
# the ifc compiler creates suboptimal performance on the Opteron for
# the build in fft routines
#
# fftw.3.0.1 was compiled using the following command lines:
# > export CC="gcc -m32"
# > export F77="f77 -m32"
# > ./configure --enable-sse2 --prefix=/home/kresse/ifc_opt/fftw-3.0.1/
# > make
# > make install
# PLEASE do not send querries related to fftw to the vasp site
#-----------------------------------------------------------------------

#FFT3D = fft3dfurth.o fft3dlib.o
#FFT3D = fftw3d.o fft3dlib.o ../libfftw3.a

#=======================================================================
# MPI section, uncomment the following lines
#
# one comment for users of mpich or lam:
# You must *not* compile mpi with g77/f77, because f77/g77
# appends *two* underscores to symbols that contain already an
# underscore (i.e. MPI_SEND becomes mpi_send__). The pgf90/ifc
# compilers however append only one underscore.
# Precompiled mpi version will also not work !!!
#
# We found that mpich.1.2.1 and lam-6.5.X to lam-7.0.4 are stable
# mpich.1.2.1 was configured with
# ./configure -prefix=/usr/local/mpich_nodvdbg -fc="pgf77 -Mx,119,0x200000" \
# -f90="pgf90 " \
# --without-romio --without-mpe -opt=-O \
#
# lam was configured with the line
# ./configure -prefix /opt/libs/lam-7.0.4 --with-cflags=-O -with-fc=ifc \
# --with-f77flags=-O --without-romio
#
# please note that you might be able to use a lam or mpich version
# compiled with f77/g77, but then you need to add the following
# options: -Msecond_underscore (compilation) and -g77libs (linking)
#
# !!! Please do not send me any queries on how to install MPI, I will
# certainly not answer them !!!!
#=======================================================================
#-----------------------------------------------------------------------
# fortran linker for mpi: if you use LAM and compiled it with the options
# suggested above, you can use the following line
#-----------------------------------------------------------------------

FC=mpif90
# -L/opt/lab/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -I/opt/lab/include/
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)
#-----------------------------------------------------------------------

#-DMPI

CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
-Dkind8 -DNGZhalf -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc \
-DMPI_BLOCK=2000 \
-Duse_cray_ptr
# -DRPROMU_DGEMV -DRACCMU_DGEMV
# "

#-----------------------------------------------------------------------
# location of SCALAPACK
# if you do not use SCALAPACK simply uncomment the line SCA
#-----------------------------------------------------------------------

#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= $(P)/libmkl_scalapack.a $(P)/libmkl_scalapack_core.a

#-----------------------------------------------------------------------
# libraries for mpi
#-----------------------------------------------------------------------

P = /opt/mkl/lib/32

MKLS = ../vasp.4.lib/libdmy.a \
../vasp.4.lib/linpack_double.o \
-L/opt/mkl/lib/32 \
-L/opt/ifort/lib \
-lsvml \
-lmkl \
-lmkl_core \
-lmkl_intel \
-lmkl_blas95 \
-lmkl_lapack \
-lmkl_intel_thread \
-lguide -lpthread

#
#LIB = ../vasp.4.lib/linpack_double.o -L/opt/lab/lib/32 -L/opt/lab/lib $(MKLS)

LIB = $(MKLS) $(LAPACK) $(SCA) $(BLAS)

#-L../vasp.4.lib -ldmy \
# ../vasp.4.lib/linpack_double.o $(LAPACK) $(SCA) $(BLAS)

# FFT: fftmpi.o with fft3dlib of Juergen Furthmueller
#FFT3D = fftmpi.o fftmpi_map.o fft3dlib.o

# fftw.3.0.1 is much faster on Opteron
FFT3D = fftmpiw.o fftmpi_map.o fft3dlib.o ../libfftw3.a

# /opt/mkl/lib/32/libfftw3xf_intel.a /opt/mkl/lib/32/libfftw3xc_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 setex.o radial.o \
pseudo.o mgrid.o mkpoints.o wave.o wave_mpi.o $(BASIC) \
nonl.o nonlr.o dfast.o choleski2.o \
mix.o charge.o xcgrad.o xcspin.o potex1.o potex2.o \
metagga.o constrmag.o pot.o cl_shift.o force.o dos.o elf.o \
tet.o hamil.o steep.o \
chain.o dyna.o relativistic.o LDApU.o sphpro.o paw.o us.o \
ebs.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 \
dipol.o xclib.o chgloc.o subrot.o optreal.o davidson.o \
edtest.o electron.o shm.o pardens.o paircorrection.o \
optics.o constr_cell_relax.o stm.o finite_diff.o \
elpol.o setlocalpp.o aedens.o

INC=

vasp: $(SOURCE) $(FFT3D) $(INC) main.o
rm -f vasp
$(FCL) -o vasp $(LINK) main.o $(SOURCE) $(FFT3D) $(LIB)
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 -O1 -xW -unroll0 -vec_report3 -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)

dynbr.o : dynbr.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)

wave.o : wave.F
$(CPP)
$(FC) -FR -lowercase -O0 -c $*$(SUFFIX)

LDApU.o : LDApU.F
$(CPP)
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)

_____________________________________________________________

.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 = icc -E -P -C $*.F >$*.f
FC = ifort

CFLAGS = -O
FFLAGS = -O0 -FI
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

--------------------------------------------------------------------------------------------------------------------

Re: segmentation fault -- IBRION=1 SIGSEV

Posted: Wed Sep 04, 2024 2:04 pm
by support_vasp

Hi,

We're sorry that we didn’t answer your question. This does not live up to the quality of support that we aim to provide. The team has since expanded. If we can still help with your problem, please ask again in a new post, linking to this one, and we will answer as quickly as possible.

Best wishes,

VASP