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VASP 5.2.2 Seg Faults on some problems

Posted: Thu Jun 11, 2009 7:09 pm
by d-farrell2
I was able to successfully compile the serial version of VASP 5.2.2 on 2 of our local machines (both Opterons) using the following compilers and libraries:

1) ifort 10.1 20070913, mkl 10.0.011

2) ifort 10.1 20080801, mkl 10.0.4.023

and I ran 5 test problems of different types. One is an old benchmark that I think came with a vasp distribution (50 Hg atoms), One relaxation of the primitive cell for BCC-V (1 atom), two Li4BN3H10 systems (1 72 atom relax, 1 144 atom MD ) and 1 Mg-Al system (29 atoms, relaxation).

the 50 Hg atom and BCC-V tests ran without any problems. The other 3 would seg fault in what seems like the first electronic step with the following backtrace:

#0 0x00000000005950a4 in hamil_mp_hamiltmu_ ()
#1 0x000000000090d1fc in david_mp_eddav_ ()
#2 0x00000000009162e8 in elmin (*arguments deleted*)
#3 0x00000000004286cd in vamp () at main.f90:2287
#4 0x0000000000404d96 in main ()

all of these problems run fine under VASP 4.6.32.

VASP 5.2.2 Seg Faults on some problems

Posted: Thu Jun 11, 2009 7:11 pm
by d-farrell2
here is the makefile used on machine # 2 above:

.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)

#MKL_PATH = /opt/intel/mkl/10.0.5.025/lib/em64t
#INT_KIND=8

#-----------------------------------------------------------------------
# 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 = $(CPP_) -DHOST=\"LinuxIFC\" \
# -Dkind${INT_KIND} -DCACHE_SIZE=12000 -DIFC -Davoidalloc -DNGXhalf \
# -DRPROMU_DGEMV -DRACCMU_DGEMV

CPP = $(CPP_) -DHOST=\"LinuxIFC_Opteron\" \
-Dkind8 -DNGXhalf -DCACHE_SIZE=5000 -DPGF90 -Davoidalloc
# -DRPROMU_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 -vec-report0
#FFLAGS = -FR -lowercase -assume byterecl -vec-report0

#-----------------------------------------------------------------------
# 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=-O3
OFLAG = -FR -O0 -g

OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =
OBJ_NOOPT =
DEBUG = -FR -O0 -g
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

# LAPACK, simplest use vasp.5.lib/lapack_double
#LAPACK= ../vasp.5.lib/lapack_double.o

# use the mkl Intel lapack
#LAPACK= -lmkl_lapack

# Intel MKL
MKL_PATH=/opt/intel/mkl/10.0.4.023/lib/em64t/
BLAS=-L${MKL_PATH} -lmkl_sequential -lmkl_core -lmkl_intel_lp64
LAPACK=-L${MKL_PATH} -lmkl_lapack

# use AMD core math libarary
#LAPACK=
#BLAS=-L/opt/acml4.0.1/pathscale64/lib/ -lacml -L/opt/pathscale/lib/3.1/ -lpathfortran


# use atlas optimized part of lapack
#BLAS=../../GotoBLAS_gnu/libgoto.a
#LAPACK= ../vasp.5.lib/lapack_atlas.o -llapack -lcblas

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

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

# Intel MKL fftw
#-I/opt/intel/mkl/10.0.5.025/include/fftw
FFT3D= fftw3d.o fft3dlib.o ${MKL_PATH}/libfftw3xf_intel.a

# FFTW3 (Pathscale)
#FFT3D = fftw3d.o fft3dlib.o /opt/fftw3_pathscale/lib/libfftw3.a /opt/pathscale/lib/3.1/libpathfortran.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=/usr/local/mpich-intel/bin/mpif90
#FC=/usr/local/mvapich-intel/bin/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 -DNGZhalf -DMPI_BLOCK=500

#-----------------------------------------------------------------------
# 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 /usr/lib64/libfftw3.a

# Intel mkl fftw
#FFT3D= fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o ${MKL_PATH}/libfftw3xf_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 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) -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 -O1 -xW -unroll0 -e95 -vec_report3 -c $*$(SUFFIX)

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

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

fft3d.o : fft3d.F
$(CPP)
$(FC) -FR -lowercase -O0 -c $*$(SUFFIX)

fft3dlib.o : fft3dlib.F
$(CPP)
$(FC) -FR -lowercase -O0 -c $*$(SUFFIX)

hamil.o : hamil.F
$(CPP)
$(FC) -FR -lowercase -O0 -g -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)

VASP 5.2.2 Seg Faults on some problems

Posted: Thu Jun 11, 2009 7:13 pm
by d-farrell2
Any thoughts on why this is happening and how to get around it?

A member of my group was able to compile and run the Mg-Al system without a problem in VASP 5.2.2 on a Xeon sytem with the following:

* intel/11/11.0.083 (ifort/mpif90)
* mkl/10.1.2.024

We haven't been able to try updating to the same compilers and libraries yet though.