Elio,
usually, /opt is a local filesystem, so it is possible /opt/intel is
only available on your login nodes.
your best option is to ask your sysadmin where the mkl libs are on the
compute nodes, and/or how to use mkl in your jobs.
feel free to submit a dumb pbs script
ls -l /opt
ls -l /opt/intel
ls -l /opt/intel/mkl
so you can hopefully find that by yourself.
an other option is to use the static mkl libs if they are available
for example, your LIB line could be
LIB = -static -L/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
-lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core
-lmkl_sequential -dynamic
Cheers,
Gilles
On 3/24/2016 12:43 PM, Elio Physics wrote:
Dear Gilles,
thanks for your reply and your options. I have tried the first option,
hich for me basically is the easiest. I have compiled using "make.inc"
but now setting LIB = -L/opt/intel/mkl/lib/intel64 -lmkl_blas95_lp64
-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential
Every went well. Then I tried the PBS script wjere I have added these
two lines:
source /opt/intel/mkl/bin/mklvars.sh
export LD_LIBRARY_PATH=/opt/intel/mkl/bin/mklvars.sh
But i still get the same error:
/opt/intel/mkl/bin/mklvars.sh: No such file or directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
I just cannot understand why is it giving the same error and why it
could not find the file : /opt/intel/mkl/bin/mklvars.sh although the
link is true!
Any advice please?
Thanks
------------------------------------------------------------------------
*From:* users <users-boun...@open-mpi.org> on behalf of Gilles
Gouaillardet <gil...@rist.or.jp>
*Sent:* Thursday, March 24, 2016 12:22 AM
*To:* Open MPI Users
*Subject:* Re: [OMPI users] Problems in compiling a code with dynamic
linking
Elio,
it seems /opt/intel/composer_xe_2013_sp1/bin/compilervars.sh is only
available on your login/frontend nodes,
but not on your compute nodes.
you might be luckier with
/opt/intel/mkl/bin/mklvars.sh
an other option is to
ldd /home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI
on your login node, and explicitly set the LD_LIBRARY_PATH in your PBS
script
if /opt/intel/composer_xe_2013_sp1/mkl/lib/intel64 is available on
your compute nodes, you might want to append
-Wl,-rpath,/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
to LIB
/* if you do that, keep in mind you might not automatically use the
most up to date mkl lib when they get upgraded by your sysadmin */
Cheers,
Gilles
On 3/24/2016 11:03 AM, Elio Physics wrote:
Dear all,
I have been trying ,for the last week, compiling a code (SPRKKR). the
compilation went through ok. however, there are problems with the
executable (kkrscf6.3MPI) not finding the MKL library links. i could
not fix the problem..I have tried several things but in vain..I will
post both the "make" file and the "PBS" script file. Please can
anyone help me in this? the error I am getting is:
/opt/intel/composer_xe_2013_sp1/bin/compilervars.sh: No such file or
directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
_make file :_
_
_
###############################################################################
# Here the common makefile starts which does depend on the
OS ####
###############################################################################
#
# FC: compiler name and common options e.g. f77 -c
# LINK: linker name and common options e.g. g77 -shared
# FFLAGS: optimization e.g. -O3
# OP0: force nooptimisation for some routiens e.g. -O0
# VERSION: additional string for executable e.g. 6.3.0
# LIB: library names e.g. -L/usr/lib -latlas -lblas -llapack
# (lapack and blas libraries are needed)
# BUILD_TYPE: string "debug" switches on debugging options
# (NOTE: you may call, e.g. "make scf BUILD_TYPE=debug"
# to produce executable with debugging flags from
command line)
# BIN: directory for executables
# INCLUDE: directory for include files
# (NOTE: directory with mpi include files has to be
properly set
# even for sequential executable)
###############################################################################
BUILD_TYPE ?=
#BUILD_TYPE := debug
VERSION = 6.3
ifeq ($(BUILD_TYPE), debug)
VERSION := $(VERSION)$(BUILD_TYPE)
endif
BIN =~/Elie/SPRKKR/bin
#BIN=~/bin
#BIN=/tmp/$(USER)
LIB = -L/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
-lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core
-lmkl_sequential
# Include mpif.h
INCLUDE =-I/usr/include/openmpi-x86_64
#FFLAGS
FFLAGS = -O2
FC = mpif90 -c $(FFLAGS) $(INCLUDE)
LINK = mpif90 $(FFLAGS) $(INCLUDE)
MPI=MPI
_PBS script:_
_
_
BIN =~/Elie/SPRKKR/bin
#BIN=~/bin
#BIN=/tmp/$(USER)
LIB = -L/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
-lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core
-lmkl_sequential
# Include mpif.h
INCLUDE =-I/usr/include/openmpi-x86_64
#FFLAGS
FFLAGS = -O2
FC = mpif90 -c $(FFLAGS) $(INCLUDE)
LINK = mpif90 $(FFLAGS) $(INCLUDE)
MPI=MPI
[emoujaes@jlborges SPRKKR]$ cd Fe
[emoujaes@jlborges Fe]$ ls
Fe.inp Fe.pbs Fescf.e50505 Fescf.o50505
scf-50505.jlborges.fisica.ufmg.br.out
[emoujaes@jlborges Fe]$ more Fe.pbs
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=8
#PBS -l walltime=70:00:00
#PBS -N Fescf
# procura o nome o input baseado no nome do job (linha #PBS -N xxx
acima).
INP=Fe.inp
OUT=scf-$PBS_JOBID.out
## Configura o no de calculo
source /opt/intel/composer_xe_2013_sp1/bin/compilervars.sh
module load libraries/openmpi-1.5.4/gnu-4.4
#ormacoes do job no arquivo de saida
qstat -an -u $USER
cat $PBS_NODEFILE
########################################
#------- Inicio do trabalho ----- #
########################################
## executa o programa
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
mpirun ~/Elie/SPRKKR/bin/kkrscf6.3MPI $INP > $OUT
_______________________________________________
users mailing list
us...@open-mpi.org
Subscription:http://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this
post:http://www.open-mpi.org/community/lists/users/2016/03/28812.php
_______________________________________________
users mailing list
us...@open-mpi.org
Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post:
http://www.open-mpi.org/community/lists/users/2016/03/28814.php
