My Community

Hello,

I'm trying to set up a small calculation (CeO2, primitive cell) using 4x4x4 k-points with the serial version of VASP 5.2.2 on my linux machine. The only non-VASP part in the VASP compile is the Goto BLAS.
After starting the calculation the DFT steps run smoothly, but at the start of the hybrid part I get a segmentation fault.
I also did some attempts for calculations of alpha Ce, and those worked(i.e. didn't crash for this reason) for kpointsets up to 5x5x5 before suffering the same fate.

Could someone tell me the origin of this problem? And a way to fix it?
according to PRB 75, 045121 (2007) this HSE calculation should be possible even with a 6x6x6 kpointset.

thx
Danny

the machine is an intel core2 quad
makefile:
.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

#-----------------------------------------------------------------------
# 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 -xHost

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= /home/danny/programs/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 = -L/opt/intel/Compiler/11.1/064/lib/intel64 -lsvml

#-----------------------------------------------------------------------
# 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 $(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 = fftmpi.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 \
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) -pg -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)

<span class='smallblacktext'>[ Edited Fri Mar 05 2010, 02:14PM ]</span>

The INCAR file:

general:
SYSTEM = fcc_alpha_Ce_bulk
!ISTART = 0 ! start from 0: scratch, 1: previous WAVECAR
ICHARG = 1 ! 1: read old CHGCAR, 2: superposition from atom positions
ISMEAR = 0 ! 0: Gaussian; 1-N: MP; -5: Tetra+Blochl
SIGMA = 0.1
EDIFF = 1.0E-8
PREC = High ! to make ROPT=2.0E-4 for LREAL=Auto
ENCUT = 500 ! ENCUT for O
LWAVE = .FALSE.
LCHARGE = .TRUE.
LVTOT = .FALSE.
ISPIN = 2 ! include spin
!MAGMOM = ! put spins of Ce in same direction
NBANDS = 24 ! fix number of bands manually
VOSKOWN = 1 ! important for GGA (PW91) for interpolation of XC
LMAXMIX = 6
HSE Calculation:
ISTART = 1
LHFCALC = .TRUE. ; HFSCREEN = 0.2
NBANDS = 24
ALGO = Damped ; TIME = 0.5
LMAXFOCK = 5 ! default 4, but we have f electrons=> +1
ENCUTFOCK = 0 !omit flag for High Quality Calcs
NKRED = 4 !omit Flag for High Quality Calcs
dynamic:
IBRION = -1 ! -1: Fix atoms; 0: MD; 2: ConjGrad relax
NSW = 0 ! Number electronic steps
parallel:
LPLANE = .TRUE.
!NPAR = 1 ; NSIM = 8

memory problems? Maybe you are running a 32bit system. Check with less kpoints first ...

Hth

alex

64 bit system
still a few Gb free memory

It works with less k-points (1x1x1, 2x2x2 and 3x3x3 run without a glitch, they even converge...4x4x4 seg faults out, I even tried NKRED=4 (and 2))

please check your stack size limits (ulimit -s) , it has to be (set to) unlimited

thx a lot, this seems to cure the problem.

Danny

bump

having similar problems with larger runs, trying this now, hopefully it will work.