gamma version problem

Questions regarding compilation of VASP on various platforms.

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Posts: 4
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License Nr.: ATU37586901

gamma version problem

#1 Post by 5-524 » Thu May 01, 2014 10:22 am

Hello admin,
i have installed VASP, its is running fine for bulk but for single gamma point calculations its giving problem for parallel version.
The error is
rashant@xena test2]$ mpirun -np 2 vasp.5.3.gamma.par
running on 2 total cores
distrk: each k-point on 2 cores, 1 groups
distr: one band on 1 cores, 2 groups
using from now: INCAR
vasp.5.3.3 18Dez12 (build Jan 24 2014 16:40:54) gamma-only

POSCAR found : 1 types and 2 ions
scaLAPACK will be used
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 ...
WAVECAR not read
entering main loop
N E dE d eps ncg rms rms(c)
mpirun noticed that process rank 0 with PID 9427 on node xena exited on signal 11 (Segmentation fault).
2 total processes killed (some possibly by mpirun during cleanup)
he makefile
: .inc .f .f90 .F
CPP_ = ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX)
FFLAGS = -FR -names lowercase -assume byterecl
OFLAG= -O2 -ip

BLAS=-L$(MKL_PATH) -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
-DCACHE_SIZE=12000 -DPGF90 -Davoidalloc -DwNGZhalf \
-DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK \
-Duse_collective -DscaLAPACK
BLACS= -lmkl_blacs_openmpi_lp64
SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)
LIB = -L../vasp.5.lib -ldmy \
../vasp.5.lib/linpack_double.o $(SCA) $(LAPACK) $(BLAS)

FFT3D = fftmpi.o fftmpi_map.o fft3dfurth.o fft3dlib.o $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a

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 spinsym.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 hyperfine.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 \
chain.o dyna.o k-proj.o sphpro.o us.o core_rel.o \
aedens.o wavpre.o wavpre_noio.o broyden.o \
dynbr.o hamil_high.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_multipole.o fock.o mkpoints_change.o sym_grad.o \
mymath.o internals.o npt_dynamics.o dynconstr.o dimer_heyden.o dvvtrajectory.o vdwforcefield.o \
nmr.o pead.o subrot.o subrot_scf.o \
force.o pwlhf.o gw_model.o optreal.o steep.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 \
setlocalpp.o wannier.o electron_OEP.o electron_lhf.o twoelectron4o.o \
mlwf.o ratpol.o screened_2e.o wave_cacher.o chi_base.o wpot.o \
local_field.o ump2.o ump2kpar.o fcidump.o ump2no.o \
bse_te.o bse.o acfdt.o chi.o sydmat.o dmft.o \
rmm-diis_mlr.o linear_response_NMR.o wannier_interpol.o linear_response.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)

-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.F
mgrid.o: mgrid.F
constant.o: constant.F
lattice.o: lattice.F
setex.o: setex.F
pseudo.o: pseudo.F
mkpoints.o: mkpoints.F
wave.o: wave.F
nonl.o: nonl.F
nonlr.o: nonlr.F

$(FC) $(FFLAGS) $(INCS) -c $*$(SUFFIX)

fft3dlib_f77.o: fft3dlib_f77.F
$(F77) $(FFLAGS_F77) -c $*$(SUFFIX)

$(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)
$(FC) $(FFLAGS) $(OFLAG) $(INCS) -c $*$(SUFFIX)

# special rules
# these special rules have been tested for ifc.11 and ifc.12 only

fft3dlib.o : fft3dlib.F
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
fft3dfurth.o : fft3dfurth.F
$(FC) -FR -lowercase -O1 -c $*$(SUFFIX)
fftw3d.o : fftw3d.F
$(FC) -FR -lowercase -O1 $(INCS) -c $*$(SUFFIX)
fftmpi.o : fftmpi.F
$(FC) -FR -lowercase -O1 -c $*$(SUFFIX)
fftmpiw.o : fftmpiw.F
$(FC) -FR -lowercase -O1 $(INCS) -c $*$(SUFFIX)
wave_high.o : wave_high.F
$(FC) -FR -lowercase -O1 -c $*$(SUFFIX)
# the following rules are probably no longer required (-O3 seems to work)
wave.o : wave.F
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
paw.o : paw.F
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
cl_shift.o : cl_shift.F
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
us.o : us.F
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)
$(FC) -FR -lowercase -O2 -c $*$(SUFFIX)

please help
Last edited by 5-524 on Thu May 01, 2014 10:22 am, edited 1 time in total.

Posts: 4
Joined: Thu May 01, 2014 9:50 am
License Nr.: ATU37586901

gamma version problem

#2 Post by 5-524 » Wed Jun 04, 2014 6:34 am

Hello Admin, please reply.
Last edited by 5-524 on Wed Jun 04, 2014 6:34 am, edited 1 time in total.

Posts: 4
Joined: Thu May 01, 2014 9:50 am
License Nr.: ATU37586901

gamma version problem

#3 Post by 5-524 » Thu Jun 05, 2014 9:08 am

the output of OUTCAR file at the end is;

use seriel FFT for wavefunctions x direction half grid
k-point 1 : 0.0000 0.0000 0.0000 plane waves: 31659

maximum and minimum number of plane-waves per node : 31659 31659

maximum number of plane-waves: 31659
maximum index in each direction:
IXMIN= 0 IYMIN= -24 IZMIN= -24

WARNING: aliasing errors must be expected set NGX to 98 to avoid them
WARNING: aliasing errors must be expected set NGY to 98 to avoid them
WARNING: aliasing errors must be expected set NGZ to 98 to avoid them
aliasing errors are usually negligible using standard VASP settings
and one can safely disregard these warnings

serial 3D FFT for wavefunctions
parallel 3D FFT for charge:
minimum data exchange during FFTs selected (reduces bandwidth)

total amount of memory used by VASP on root node 371612. kBytes

base : 30000. kBytes
nonl-proj : 5571. kBytes
fftplans : 144408. kBytes
grid : 176414. kBytes
one-center: 15. kBytes
wavefun : 15204. kBytes

Broyden mixing: mesh for mixing (old mesh)
NGX = 49 NGY = 49 NGZ = 49
(NGX =126 NGY =126 NGZ =126)
gives a total of 117649 points

initial charge density was supplied:
charge density of overlapping atoms calculated
number of electron 22.0000000 magnetization
keeping initial charge density in first step
Maximum index for augmentation-charges 1855 (set IRDMAX)
First call to EWALD: gamma= 0.089
Maximum number of real-space cells 3x 3x 3
Maximum number of reciprocal cells 3x 3x 3

FEWALD executed in parallel
FEWALD: cpu time 0.00: real time 0.00

----------------------------------------- Iteration 1( 1) ---------------------------------------

POTLOK: cpu time 2.29: real time 2.29
SETDIJ: cpu time 0.00: real time 0.00
EDDIAG: cpu time 1.20: real time 1.20
Last edited by 5-524 on Thu Jun 05, 2014 9:08 am, edited 1 time in total.

Posts: 2921
Joined: Tue Aug 03, 2004 8:18 am
License Nr.: 458

gamma version problem

#4 Post by admin » Thu Jun 05, 2014 11:31 am

Is your stack size large enough (ulimit -s has to return unlimited)?
Last edited by admin on Thu Jun 05, 2014 11:31 am, edited 1 time in total.

Posts: 4
Joined: Thu May 01, 2014 9:50 am
License Nr.: ATU37586901

Re: gamma version problem

#5 Post by 5-524 » Wed Sep 10, 2014 7:21 am

Hello admin,
[prashant@xena M_DISTR]$ ulimit -s
[prashant@xena M_DISTR]$ ulimit

my system is scientific linux 6


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