[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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20181011/1be43e1e/attachment.html>
More information about the users
mailing list