[Nek5000-users] Submitting Job Nek Enabled Moab

[nek5000-users at lists.mcs.anl.gov]

Friedrich,

If you are not sure about how to compile/link/run with shared
libraries, it is in general advisable to use static libraries
everywhere with position-independent-code (--with-pic or CFLAGS,
FCFLAGS="-fPIC"). This would remove any headaches about symbols not
getting resolved during runtime.

Alternately, if you do want to use shared libraries, then make sure
LD_LIBRARY_PATH has all the relevant paths to the libraries so that
the runtime loader can resolve the symbols correctly. To check, try

ldd ./nek5000 | grep "not found"

If all the libraries are resolved (no output from above command), then
please send us the architecture, compiler info (intel ?), HDF5
config.log, MOAB config.log so that we can find out the cause of the
issues.

> ./nek5000: error while loading shared libraries: libintlc.so.5: failed to
> map segment from shared object: Cannot allocate memory

This is indicative of hitting shared memory limit -- and I can't
really place whether this is due to your job submission system or
system configuration. Can you try running interactively and see if you
are still getting the errors below ?

Vijay

On Wed, Oct 29, 2014 at 10:37 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> Hi Again,
>
>
> I just wanted to update that although I have added the szip library to the
> LD_LIBRARY_PATH I still receive the same error:
>
>
> mv: cannot stat `pipe.log.12': No such file or directory
> mv: cannot stat `pipe.sch': No such file or directory
> ./nek5000: error while loading shared libraries: libintlc.so.5: failed to
> map segment from shared object: Cannot allocate memory
> ./nek5000: error while loading shared libraries: libintlc.so.5: failed to
> map segment from shared object: Cannot allocate memory
> ./nek5000: error while loading shared libraries: libintlc.so.5: failed to
> map segment from shared object: Cannot allocate memory
> ./nek5000: error while loading shared libraries: libintlc.so.5: failed to
> map segment from shared object: Cannot allocate memory
>
>
> Should I consider loading zlib etc in the same way or is this something
> else?
>
>
> Regards, Friedrich.
>
>
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