[GE users] run time intel compiler library libsvml not found

SLIM H.A. h.a.slim at durham.ac.uk
Fri Dec 21 12:04:08 GMT 2007


Maybe it clarifies if I show the script:

#!/bin/csh
... some standard sge options here
#$ -cwd
setenv MPICH_PROCESS_GROUP no
# request submission to a queue for parallel jobs
#$ -q par.q
##$ -S /bin/csh
#   ^^ no effect
# set up the mpich version to use
# load the modules
module purge
module load intel/fce/9.0.032 mpich/ge/intel/64/1.2.7 sge/6.0u7_1
ldd ./monte
echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH
# $ -v LD_LIBRARY_PATH=$LD_LIBRARY_PATH
#   ^^ no effect
#$ -V
#   ^^ only works if the session shell has the module loaded as well
# execute command
mpirun -np $NSLOTS -machinefile $TMPDIR/machines ./monte

I built monte with

module purge
module load intel/fce/9.0.032 mpich/ge/intel/64/1.2.7
mpif90 monte.f90 -o monte 

These are snippets from the output file
...
        libsvml.so =>
/usr/local/Cluster-Apps/intel/fce/9.0//lib/libsvml.so
(0x00002b21417de000)
...
LD_LIBRARY_PATH=/usr/local/lib:/usr/X11R6/lib:/usr/local/Cluster-Apps/in
tel/fce/9.0//lib:/usr/local/Cluster-App
s/mpich/ge/intel/64/1.2.7/lib/shared:/usr/local/Cluster-Apps/sge/lib/lx2
6-amd64
/usr/local/Cluster-Apps/sge/bin/lx24-amd64/qrsh -inherit -nostdin
node231 /data/hamilton/drk1has/hamilton_monte
pi/amd64_lnx_ifort/./monte node231 50375 \-p4amslave \-p4yourname
node231 \-p4rmrank 1
/data/hamilton/drk1has/hamilton_montepi/amd64_lnx_ifort/./monte: error
while loading shared libraries: libsvml.
so: cannot open shared object file: No such file or directory
...

I made sure only the libraries for ifort were used and loaded. I wonder
if there is a problem with the Intel compiler...

Henk

> -----Original Message-----
> From: Reuti [mailto:reuti at staff.uni-marburg.de] 
> Sent: 19 December 2007 20:15
> To: users at gridengine.sunsource.net
> Subject: Re: [GE users] run time intel compiler library 
> libsvml not found
> 
> Am 19.12.2007 um 19:08 schrieb SLIM H.A.:
> 
> > Reuti
> >
> >> what about having a:
> >>
> >> echo $PATH
> >> echo $LD_LIBRARY_PATH
> >> ldd <myexe>
> >>
> >> in the jobscript to see what it has at execution time.
> >
> > The first and second suggestion are what I had done in the 
> jobscript 
> > as # 1 and 2, the libray could be resolved and the env 
> variable was up 
> > to date.
> 
> Sorry, I got it wrong.
> 
> > 1) ldd on the exe => ok, all libraries are resolved
> > 2) print value of LD_LIBRARY_PATH => ok, includes the 
> directory to the 
> > intel lib path
> > 3) added #$ -V => no effect
> > 4) added #$ -S /bin/tcsh as this is the shell the script is 
> run from.
> >
> > I also had tried already
> > 5) login to an execution host and check ldd and env 
> variable there and 
> > they were ok
> 
> An interactive login is different from executing a 
> non-interactive jobscript. I.e. a batch job starts nearly 
> naked, only with the necessary set environment varibles by SGE.
> 
> > The strange thing is that it also depends on whether the 
> Intel library 
> > path is set in LD_LIBRARY_PATH, in the tcsh shell from 
> which qsub is 
> > called. If it is set it works but if not, the job fails.
> 
> Sounds okay with the -V switch, as then the variable is also 
> defined during jobtime (or not); it's inherited this way from 
> the shell session. Best would be to:
> 
> a) define the LD_LIBRARY_PATH in the job script
> 
> b) add -v LD_LIBRARY_PATH=<path_to_libs> as default request
> 
> > (We use the
> > module setup but that should not make a difference?) Is there some 
> > inheritance problem here?
> 
> -- Reuti
> 
> 
> > I'll try the rpath setup again that Rayson mentioned.
> >
> > Henk
> >
> >
> >> -----Original Message-----
> >> From: Reuti [mailto:reuti at staff.uni-marburg.de]
> >> Sent: 19 December 2007 16:15
> >> To: users at gridengine.sunsource.net
> >> Subject: Re: [GE users] run time intel compiler library 
> libsvml not 
> >> found
> >>
> >> Hi,
> >>
> >> Am 19.12.2007 um 16:24 schrieb SLIM H.A.:
> >>
> >>> We have a problem with submitting jobs that start an executable 
> >>> compiled with the Intel fortan compiler.
> >>>
> >>> The error message at run time is this:
> >>>
> >>> "error while loading shared libraries: libsvml.so: cannot
> >> open shared
> >>> object file: No such file or directory"
> >>>
> >>> In attempts to solve this I tried the following in the job script:
> >>>
> >>> 1) ldd on the exe => ok, all libraries are resolved
> >>> 2) print value of LD_LIBRARY_PATH => ok, includes the
> >> directory to the
> >>> intel lib path
> >>> 3) added #$ -V => no effect
> >>> 4) added #$ -S /bin/tcsh as this is the shell the script is
> >> run from.
> >>
> >> what about having a:
> >>
> >> echo $PATH
> >> echo $LD_LIBRARY_PATH
> >> ldd <myexe>
> >>
> >> in the jobscript to see what it has at execution time.
> >>
> >> -- Reuti
> >>
> >>
> >>> A final possibility might be to link with -rpath, but first
> >> impression
> >>> is that does not work either.
> >>>
> >>> Is anyone familiar with this problem and, hopefully, knows
> >> a solution?
> >>>
> >>> Thanks in advance
> >>>
> >>> Henk
> >>>
> >>>
> >> 
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> >>
> >
> > 
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