[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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