[QE-users] Error in phonon calculation "forrtl: severe (174): SIGSEGV, segmentation fault occurred" with version 6.3

黄志硕 zhishuohuang at gmail.com
Thu Oct 11 16:02:33 CEST 2018


Dear QE users,

I am using Quantum espresso 6.3 to do phonon calculations. In the scf calculation, it works well, but it run into crash in the phonon calculations with the message:
###############################################################################
     Alpha used in Ewald sum =   0.3000
     PHONON       :    16.19s CPU        17.35s WALL



     Representation #  1 mode #   1

     Self-consistent Calculation
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
ph.x               00000000035BB38D  Unknown               Unknown  Unknown
libpthread-2.12.s  00000036BE60F710  Unknown               Unknown  Unknown
libmkl_avx.so      00007FC2CA1DDC12  mkl_blas_avx_xzdo     Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
ph.x               00000000035BB38D  Unknown               Unknown  Unknown
libpthread-2.12.s  00000036BE60F710  Unknown               Unknown  Unknown
libmkl_avx.so      00007F9460F8AC12  mkl_blas_avx_xzdo     Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
ph.x               00000000035BB38D  Unknown               Unknown  Unknown
libpthread-2.12.s  00000036BE60F710  Unknown               Unknown  Unknown
libmkl_avx.so      00007F88220F7C12  mkl_blas_avx_xzdo     Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
ph.x               00000000035BB38D  Unknown               Unknown  Unknown
libpthread-2.12.s  00000036BE60F710  Unknown               Unknown  Unknown
libmkl_avx.so      00007FE42FDB9C12  mkl_blas_avx_xzdo     Unknown  Unknown
###############################################################################

It is compiled with intel compiler of 2018. The configuration is like:
###############################################################################
#!/bin/bash
source switch_to_2018a
module load intel/2018a
export LAPACK_LIBS="${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a  ${MKLROOT}/lib/intel64/libmkl_sequential.a ${MKLROOT}/lib/intel64/libmkl_gf_lp64.a  ${MKLROOT}/lib/intel64/libmkl_core.a"
export FFT_LIBS="${MKLROOT}/lib/intel64/libmkl_cdft_core.a ${MKLROOT}/lib/intel64/libfftw3xc_intel.a  ${MKLROOT}/lib/intel64/libfftw3xf_intel.a   ${MKLROOT}/lib/intel64/libfftw3xc_intel_pic.a ${MKLROOT}/lib/intel64/libfftw3xf_intel_pic.a  ${MKLROOT}/lib/intel64/libmkl_gf_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a"
./configure LIBDIRS="/apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/" MPIF90=mpiifort F90=ifort CC=icc --enable-parallel --disable-openmp --with-scalapack=intel
###############################################################################

And the make.inc file generated by configure is:
###############################################################################
# make.inc.  Generated from make.inc.in by configure.
# compilation rules
.SUFFIXES :
.SUFFIXES : .o .c .f .f90
# most fortran compilers can directly preprocess c-like directives: use
#       $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
#       $(CPP) $(CPPFLAGS) $< -o $*.F90
#       $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!
.f90.o:
        $(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
        $(F77) $(FFLAGS) -c $<

.c.o:
        $(CC) $(CFLAGS)  -c $<

# Top QE directory, useful for locating libraries,  linking QE with plugins
# The following syntax should always point to TOPDIR:
TOPDIR = $(dir $(abspath $(filter %make.inc,$(MAKEFILE_LIST))))
# if it doesn't work, uncomment the following line (edit if needed):
# TOPDIR = /data/leuven/319/vsc31903/Soft/QE_6.3/QE_6.3_mpiifort
# DFLAGS  = precompilation options (possible arguments to -D and -U)
#           used by the C compiler and preprocessor
# To use libxc (v>=3.0.1), add -D__LIBXC to DFLAGS
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas
# MANUAL_DFLAGS  = additional precompilation option(s), if desired
#                  BEWARE: it does not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS  =
DFLAGS         =  -D__DFTI -D__MPI -D__SCALAPACK
FDFLAGS        = $(DFLAGS) $(MANUAL_DFLAGS)
# IFLAGS = how to locate directories with *.h or *.f90 file to be included
#          typically -I$(TOPDIR)/include -I/some/other/directory/
#          the latter contains .e.g. files needed by FFT libraries
# for libxc add -I/path/to/libxc/include/
IFLAGS         = -I$(TOPDIR)/include -I$(TOPDIR)/FoX/finclude -I$(TOPDIR)/S3DE/iotk/include/ -I/apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/include

# MOD_FLAG = flag used by f90 compiler to locate modules

MOD_FLAG      = -I
# BASEMOD_FLAGS points to directories containing basic modules,
# while BASEMODS points to the corresponding module libraries
# Each Makefile can add directories to MODFLAGS and libraries to QEMODS

BASEMOD_FLAGS= $(MOD_FLAG)$(TOPDIR)/iotk/src \
               $(MOD_FLAG)$(TOPDIR)/Modules \
               $(MOD_FLAG)$(TOPDIR)/FFTXlib \
               $(MOD_FLAG)$(TOPDIR)/LAXlib \
               $(MOD_FLAG)$(TOPDIR)/UtilXlib \
               $(MOD_FLAG)$(TOPDIR)/FoX/finclude

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90         = mpiifort
F90           = ifort
CC             = icc
F77            = ifort

# GPU architecture (Kepler: 35, Pascal: 60, Volta: 70 )
GPU_ARCH=
# CUDA runtime (Pascal: 8.0, Volta: 9.0)
CUDA_RUNTIME=
# CUDA F90 Flags
CUDA_F90FLAGS=
# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS
CPP            = cpp
CPPFLAGS       = -P -traditional $(DFLAGS) $(IFLAGS)
# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax
CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(CUDA_F90FLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -assume byterecl -g -traceback
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT   = -O0 -assume byterecl -g -traceback
# compiler flag needed by some compilers when the main program is not fortran
# Currently used for Yambo
FFLAGS_NOMAIN   = -nofor_main

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
# for libxc, set LD_LIBS=-L/path/to/libxc/lib/ -lxcf90 -lxc

LD             = mpiifort
LDFLAGS        = -static-intel
LD_LIBS        =

# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy via "--with-netlib" :
# BLAS_LIBS = /your/path/to/espresso/LAPACK/blas.a
# BLAS_LIBS_SWITCH = internal

BLAS_LIBS      =   -lmkl_intel_lp64  -lmkl_sequential -lmkl_core
BLAS_LIBS_SWITCH = external

# If you have nothing better, use the local copy via "--with-netlib" :
# LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS    = /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_lapack95_lp64.a  /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_sequential.a /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_gf_lp64.a  /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_core.a
LAPACK_LIBS_SWITCH = external
SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)

FFT_LIBS       = /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_cdft_core.a /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libfftw3xc_intel.a  /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libfftw3xf_intel.a   /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libfftw3xc_intel_pic.a /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libfftw3xf_intel_pic.a  /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_gf_lp64.a /apps/leuven/thinking/2018a/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64/libmkl_core.a

# HDF5
HDF5_LIB =
FOX_LIB  = -L$(TOPDIR)/FoX/lib  -lFoX_dom -lFoX_sax -lFoX_wxml -lFoX_common\
            -lFoX_utils -lFoX_fsys
FOX_FLAGS =
# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS       =
# IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS
MASS_LIBS      =
# CUDA libraries
CUDA_LIBS=
CUDA_EXTLIBS =
# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv
AR             = ar
ARFLAGS        = ruv
# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo
RANLIB         = ranlib
# all internal and external libraries - do not modify
FLIB_TARGETS   = all
LIBOBJS        = $(TOPDIR)/clib/clib.a  $(TOPDIR)/iotk/src/libiotk.a
LIBS           = $(CUDA_LIBS) $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FOX_LIB) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(HDF5_LIB) $(LD_LIBS)
# wget or curl - useful to download from network
WGET = wget -O
# Install directory - not currently used
PREFIX = /usr/local
###############################################################################

Could anyone please give me some clues about it? I will appreciate it for that.

Best regards
Zhishuo Huang

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