[QE-users] Error while running Quantum Espresso with Intel MPI
DAVID BARCENE
david.barcene at utp.ac.pa
Thu Feb 14 21:25:27 CET 2019
Dear Will and Nicola thank you for your fast reply.
I recently compiled with openmpi, following Will's advice, there were some warnings about missing include directories for FoX and iotk, I believe, but I just ignored them. Then run the example again and this is the output:
******************************************************************************************************************************************************************
[dbarcene at NGC2501 example01]$ ./run_example
/home/dbarcene/qe-6.3/PW/examples/example01 : starting
This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.
executables directory: /home/dbarcene/qe-6.3/bin
pseudo directory: /home/dbarcene/qe-6.3/pseudo
temporary directory: /home/dbarcene/qe-6.3/tempdir
checking that needed directories and files exist...
Downloading Si.pz-vbc.UPF to /home/dbarcene/qe-6.3/pseudo...
Downloading Al.pz-vbc.UPF to /home/dbarcene/qe-6.3/pseudo...
Downloading Cu.pz-d-rrkjus.UPF to /home/dbarcene/qe-6.3/pseudo...
Downloading Ni.pz-nd-rrkjus.UPF to /home/dbarcene/qe-6.3/pseudo... done
running pw.x as: mpirun -np 4 /home/dbarcene/qe-6.3/bin/pw.x -nk 1 -nd 1 -nb 1 -nt 1
running the scf calculation for Si... done
running the band-structure calculation for Si... done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Al... done
running the band-structure calculation for Al... done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Cu... done
running the band-structure calculation for Cu... done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Ni... done
running the band-structure calculation for Ni... done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Si... done
running the band-structure calculation for Si...Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Al... done
running the band-structure calculation for Al...Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Cu... done
running the band-structure calculation for Cu...Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
done
cleaning /home/dbarcene/qe-6.3/tempdir... done
running the scf calculation for Ni... done
running the band-structure calculation for Ni...Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
done
cleaning /home/dbarcene/qe-6.3/tempdir... done
/home/dbarcene/qe-6.3/PW/examples/example01 : done
**************************************************************************************************************************************
Comparing the results for Si.cg.out with the reference there were no difference aside for the use of RAM. I can work with this build as long as it remains without bugs (I hope so). I also downloaded the virtual machine provided by Nicola to take a look at it.
Finally, I'll let you with the make.inc file I used for the first build with Intel MPI, as I'm a novice I might have done something wrong there that you could point out and discard any bugs related to software by doing so. Thanks again.
*************************************************************************************************************************
# 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 = /home/dbarcene/qe-6.3
# 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__LIBXC -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/opt/intel/mkl/include -I/opt/libxc/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 = mpiicc
F77 = mpiifort
# 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 = icc -E
CPPFLAGS = $(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 -g -axAVX -mkl $(DFLAGS) $(IFLAGS)
F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(CUDA_F90FLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -O3 -g -axAVX -mkl -I/opt/intel/mkl/include/fftw
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback
# compiler flag needed by some compilers when the main program is not fortran
# Currently used for Yambo
FFLAGS_NOMAIN =
# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty
# for libxc, set LD_LIBS=-L/path/to/libxc/lib/ -lxcf90 -lxc
LD = mpiifort
LDFLAGS =
LD_LIBS = -L/opt/libxc/lib/ -lxcf90 -lxc
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy via "--with-netlib" :
# BLAS_LIBS = /your/path/to/espresso/LAPACK/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS = -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_tbb_thread -lmkl_core -lpthread -ltbb -lstdc++ -lm -ldl
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy via "--with-netlib" :
# LAPACK_LIBS = /your/path/to/espresso/LAPACK/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order
LAPACK_LIBS = -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_tbb_thread -lmkl_core -lpthread -ltbb -lstdc++ -lm -ldl
LAPACK_LIBS_SWITCH = external
SCALAPACK_LIBS = -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_tbb_thread -lmkl_core -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lpthread -ltbb -lstdc++ -lm -ldl
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS = -L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_tbb_thread -lmkl_core -lpthread -ltbb -lstdc++ -lm -ldl
# HDF5
HDF5_LIB =
FOX_LIB = -L$(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 = -L/opt/intel/impi/2019.1.144/intel64/lib -lmpi
# 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) $(LD_LIBS)
# wget or curl - useful to download from network
WGET = wget -O
# Install directory - not currently used
PREFIX = /usr/local
________________________________
De: users <users-bounces at lists.quantum-espresso.org> en nombre de Will DeBenedetti <wjd74 at cornell.edu>
Enviado: miércoles, 13 de febrero de 2019 17:16
Para: Quantum Espresso users Forum
Asunto: Re: [QE-users] Error while running Quantum Espresso with Intel MPI
HI David,
Have you attempted to compile with MPICH or OpenMPI? If so, can you provide the output files after running an example calculation?
Thanks,
On Feb 13, 2019, at 5:11 PM, DAVID BARCENE <david.barcene at utp.ac.pa<mailto:david.barcene at utp.ac.pa>> wrote:
Hello, I'm new to quantum espresso and I'm having some issues while running the examples. I installed QE in my laptop (Lenovo Thinkpad E480, i7-8550U running Fedora 29) using intel mpi to take advantage of the quad core cpu. I have compiled QE using the intel fortran compiler and intel C compiler including the MKL provided by the Intel Paralell Studio XE 2019 update 1 cluster edition. No warnings or errors were shown during the compilation but when I run the example ~/qe-6.3/PW/examples/example01 it just aborts. A forum suggested to set FI_LOG_LEVEL= debug to collect logs and this is the output I get:
********************************************************************************************************************************************
[dbarcene at NGC2501 example01]$ ./run_example
/home/dbarcene/qe-6.3/PW/examples/example01 : starting
This example shows how to use pw.x to calculate the total energy and
the band structure of four simple systems: Si, Al, Cu, Ni.
executables directory: /home/dbarcene/qe-6.3/bin
pseudo directory: /home/dbarcene/qe-6.3/pseudo
temporary directory: /home/dbarcene/qe-6.3/tempdir
checking that needed directories and files exist... done
running pw.x as: mpirun -np 4 /home/dbarcene/qe-6.3/bin/pw.x -nk 1 -nd 1 -nb 1 -nt 1
running the scf calculation for Si...Abort(1094543) on node 1 (rank 1 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(639)......:
MPID_Init(860).............:
MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
Abort(1094543) on node 2 (rank 2 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(639)......:
MPID_Init(860).............:
MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
Abort(1094543) on node 3 (rank 3 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(639)......:
MPID_Init(860).............:
MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
Abort(1094543) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(639)......:
MPID_Init(860).............:
MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
[cli_1]: readline failed
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
pw.x 0000000001A5EAC4 Unknown Unknown Unknown
libpthread-2.28.s 00007FE6FEB3B030 Unknown Unknown Unknown
pw.x 00000000011BF2F0 Unknown Unknown Unknown
pw.x 0000000000CBA309 Unknown Unknown Unknown
pw.x 0000000000CB9D37 Unknown Unknown Unknown
pw.x 0000000000407286 Unknown Unknown Unknown
pw.x 0000000000407222 Unknown Unknown Unknown
libc-2.28.so 00007FE6FADC0413 __libc_start_main Unknown Unknown
pw.x 000000000040712E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
pw.x 0000000001A5EAC4 Unknown Unknown Unknown
libpthread-2.28.s 00007F05A7AEF030 Unknown Unknown Unknown
libpthread-2.28.s 00007F05A7AEDDC0 __read Unknown Unknown
libmpi.so.12.0.0 00007F05A65D399F Unknown Unknown Unknown
libmpi.so.12.0.0 00007F05A65D2D32 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F05A4C158D0 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F05A4CC6613 MPIR_Err_return_c Unknown Unknown
libmpi.so.12.0.0 00007F05A58AA299 MPI_Init Unknown Unknown
libmpifort.so.12. 00007F05A40114EB MPI_INIT Unknown Unknown
pw.x 0000000000CBA2F8 Unknown Unknown Unknown
pw.x 0000000000CB9D37 Unknown Unknown Unknown
pw.x 0000000000407286 Unknown Unknown Unknown
pw.x 0000000000407222 Unknown Unknown Unknown
libc-2.28.so 00007F05A3D74413 __libc_start_main Unknown Unknown
pw.x 000000000040712E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
pw.x 0000000001A5EAC4 Unknown Unknown Unknown
libpthread-2.28.s 00007F73A282A030 Unknown Unknown Unknown
libpthread-2.28.s 00007F73A2828DC0 __read Unknown Unknown
libmpi.so.12.0.0 00007F73A130E99F Unknown Unknown Unknown
libmpi.so.12.0.0 00007F73A130DD32 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F739F9508D0 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F739FA01613 MPIR_Err_return_c Unknown Unknown
libmpi.so.12.0.0 00007F73A05E5299 MPI_Init Unknown Unknown
libmpifort.so.12. 00007F739ED4C4EB MPI_INIT Unknown Unknown
pw.x 0000000000CBA2F8 Unknown Unknown Unknown
pw.x 0000000000CB9D37 Unknown Unknown Unknown
pw.x 0000000000407286 Unknown Unknown Unknown
pw.x 0000000000407222 Unknown Unknown Unknown
libc-2.28.so 00007F739EAAF413 __libc_start_main Unknown Unknown
pw.x 000000000040712E Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
pw.x 0000000001A5EAC4 Unknown Unknown Unknown
libpthread-2.28.s 00007F114000F030 Unknown Unknown Unknown
libpthread-2.28.s 00007F114000DDC0 __read Unknown Unknown
libmpi.so.12.0.0 00007F113EAF399F Unknown Unknown Unknown
libmpi.so.12.0.0 00007F113EAF2D32 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F113D1358D0 Unknown Unknown Unknown
libmpi.so.12.0.0 00007F113D1E6613 MPIR_Err_return_c Unknown Unknown
libmpi.so.12.0.0 00007F113DDCA299 MPI_Init Unknown Unknown
libmpifort.so.12. 00007F113C5314EB MPI_INIT Unknown Unknown
pw.x 0000000000CBA2F8 Unknown Unknown Unknown
pw.x 0000000000CB9D37 Unknown Unknown Unknown
pw.x 0000000000407286 Unknown Unknown Unknown
pw.x 0000000000407222 Unknown Unknown Unknown
libc-2.28.so 00007F113C294413 __libc_start_main Unknown Unknown
pw.x 000000000040712E Unknown Unknown Unknown
Error condition encountered during test: exit status = 179
Aborting
***************************************************************************************************************************************
Thanks in advance for any help you may provide.
All the best
David Barcene
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William DeBenedetti
Cornell University
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***************Este mensaje (y sus adjuntos), en adelante "mensaje", ha sido enviado exclusivamente a su(s) destinatario(s) y es confidencial. Si usted recibe este mensaje por error, por favor bórrelo y comunique inmediatamente al remitente. Toda utilización o publicación, total o parcial, queda prohibida salvo autorización expresa. La UTP no podrá ser considerada responsable si el mensaje ha sido modificado y/o utilizado sin autorización. This message (and any attachments), are confidential intended solely for the people whose addresses appear. If you have received this message by error, please delete it and immediately notify the sender. Any use, dissemination or disclosure, either whole or partial, without formal approval is prohibited. The UTP will not therefore be liable for the message if modified and/or used without approval.**************
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