[Pw_forum] Error in Execution while linked with Intel MKL - 11.0 64-bit : QE-5.0.2
Nisha Agrawal
itlinkstonisha at gmail.com
Wed Mar 6 06:48:11 CET 2013
Hi
I am using the below configuration while installing the Parallel
version of Quantum Espresso-5.0.2
1. Intel MPI
2. Intel compose xe_2013 ( Intel MKL-11.0, ifort 13.0, Intel MKL LAPACK & FFTW3)
I) Below are the steps I am using to configure and install quantum
espresso-5.0.2 ( attached make.sys file)
Step 1: below is the configure command
./configure --prefix=~/espresso_5.0.2 MPIF90=mpiifort FC=ifort
F77=ifort F90=ifort CXX=icpc CC=icc
BLAS_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64
-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm"
LAPACK_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/"
FFT_LIBS="/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libfftw3x_cdft_ilp64.a"
SCALAPACK_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/
-lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"
Step 2: make all
II) Command for execution
mpirun -np 2 ./bin/pw.x -in BN.in
III) While running I am getting the following error message (
attached input file)
---------------------------------------------------------------------------------------------------
Program PWSCF v.5.0.2 (svn rev. 9392) starts on 4Mar2013 at 16:50:15
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote.php
Parallel version (MPI), running on 2 processors
R & G space division: proc/nbgrp/npool/nimage = 2
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 3
Reading input from ./only-BN.in
Warning: card &IONS ignored
Warning: card / ignored
[eval_infix.c] A parsing error occurred
helper string:
-
error code:
Error: missing operand
[eval_infix.c] A parsing error occurred
helper string:
-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine card_atomic_positions (1):
Error while parsing atomic position card.
error code:
Error: missing operand
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine card_atomic_positions (1):
Error while parsing atomic position card.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
------------------------------------------------------------------------------------------------------------
Kindly help to resolve this issue.
With Thanks & Regards
Nis
"Apologizing does not mean that you are wrong and the other one is right...
It simply means that you value the relationship much more than your ego.."
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# make.sys. Generated from make.sys.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 $<
# DFLAGS = precompilation options (possible arguments to -D and -U)
# used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# 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 =
DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS)
FDFLAGS = $(DFLAGS)
# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include
IFLAGS = -I../include
# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS
MOD_FLAG = -I
# 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
# 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 = -DMKL_ILP64 -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS = -i8 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0
# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack
FFLAGS_NOOPT = -i8 -O0 -assume byterecl -g -traceback
# compiler flag needed by some compilers when the main 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
LD = mpiifort
LDFLAGS = -ilp64
LD_LIBS =
# External Libraries (if any) : blas, lapack, fft, MPI
# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal
BLAS_LIBS = -L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_sequential-lmkl_core -lpthread -lm
BLAS_LIBS_SWITCH = external
# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/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 =
LAPACK_LIBS_SWITCH = external
ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS = -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64
# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)
FFT_LIBS = /opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libfftw3x_cdft_ilp64.a
# 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 =
# 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 = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
LIBS = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS)
# wget or curl - useful to download from network
WGET = wget -O
# topdir for linking espresso libs with plugins
TOPDIR = /home/internal/sysadmin/anisha/software/Test-espresso/espresso-5.0.2
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