Hi Syed Ahsan Ali
On 02/27/2015 12:46 PM, Syed Ahsan Ali wrote:
Oh sorry. That is related to application. I need to recompile
application too I guess.
You surely do.
Also, make sure the environment, in particular PATH and LD_LIBRARY_PATH
is propagated to the compute nodes.
Not doing that is a common cause of trouble.
OpenMPI needs PATH and LD_LIBRARY_PATH at runtime also.
I hope this helps,
Gus Correa
On Fri, Feb 27, 2015 at 10:44 PM, Syed Ahsan Ali <ahsansha...@gmail.com> wrote:
Dear Gus
Thanks once again for suggestion. Yes I did that before installation
to new path. I am getting error now about some library
tstint2lm: error while loading shared libraries:
libmpi_usempif08.so.0: cannot open shared object file: No such file or
directory
While library is present
[pmdtest@hpc bin]$ locate libmpi_usempif08.so.0
/state/partition1/apps/openmpi-1.8.4_gcc-4.9.2/lib/libmpi_usempif08.so.0
/state/partition1/apps/openmpi-1.8.4_gcc-4.9.2/lib/libmpi_usempif08.so.0.6.0
in path as well
echo $LD_LIBRARY_PATH
/share/apps/openmpi-1.8.4_gcc-4.9.2/lib:/share/apps/libpng-1.6.16/lib:/share/apps/netcdf-fortran-4.4.1_gcc-4.9.2_wo_hdf5/lib:/share/apps/netcdf-4.3.2_gcc_wo_hdf5/lib:/share/apps/grib_api-1.11.0/lib:/share/apps/jasper-1.900.1/lib:/share/apps/zlib-1.2.8_gcc-4.9.2/lib:/share/apps/gcc-4.9.2/lib64:/share/apps/gcc-4.9.2/lib:/usr/lib64:/usr/share/Modules/lib:/opt/python/lib
[pmdtest@hpc bin]$
Ahsan
On Fri, Feb 27, 2015 at 10:17 PM, Gus Correa <g...@ldeo.columbia.edu> wrote:
Hi Syed Ahsan Ali
To avoid any leftovers and further confusion,
I suggest that you delete completely the old installation directory.
Then start fresh from the configure step with the prefix pointing to
--prefix=/share/apps/openmpi-1.8.4_gcc-4.9.2
I hope this helps,
Gus Correa
On 02/27/2015 12:11 PM, Syed Ahsan Ali wrote:
Hi Gus
Thanks for prompt response. Well judged, I compiled with /export/apps
prefix so that is most probably the reason. I'll check and update you.
Best wishes
Ahsan
On Fri, Feb 27, 2015 at 10:07 PM, Gus Correa <g...@ldeo.columbia.edu>
wrote:
Hi Syed
This really sounds as a problem specific to Rocks Clusters,
not an issue with Open MPI.
A confusion related to mount points, and soft links used by Rocks.
I haven't used Rocks Clusters in a while,
and I don't remember the details anymore, so please take my
suggestions with a grain of salt, and check them out
before committing to them
Which --prefix did you use when you configured Open MPI?
My suggestion is that you don't use "/export/apps" as a prefix
(and this goes to any application that you install).
but instead use a /share/apps subdirectory, something like:
--prefix=/share/apps/openmpi-1.8.4_gcc-4.9.2
This is because /export/apps is just a mount point on the
frontend/head node, whereas /share/apps is a mount point
across all nodes in the cluster (and, IIRR, a soft link on the
head node).
My recollection is that the Rocks documentation was obscure
about this, not making clear the difference between
/export/apps and /share/apps.
Issuing the Rocks commands:
"tentakel 'ls -d /export/apps'"
"tentakel 'ls -d /share/apps'"
may show something useful.
I hope this helps,
Gus Correa
On 02/27/2015 11:47 AM, Syed Ahsan Ali wrote:
I am trying to run openmpi application on my cluster. But the mpirun
fails, simple hostname command gives this error
[pmdtest@hpc bin]$ mpirun --host compute-0-0 hostname
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/export/apps/openmpi-1.8.4_gcc-4.9.2/share/openmpi/help-opal-runtime.txt:
No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/export/apps/openmpi-1.8.4_gcc-4.9.2/share/openmpi/help-orte-runtime:
No such file or directory. Sorry!
--------------------------------------------------------------------------
[compute-0-0.local:03410] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in
file orted/orted_main.c at line 369
--------------------------------------------------------------------------
ORTE was unable to reliably start one or more daemons.
I am using Environment modules to load OpenMPI 1.8.4 and PATH and
LD_LIBRARY_PATH points to same openmpi on nodes
[pmdtest@hpc bin]$ which mpirun
/share/apps/openmpi-1.8.4_gcc-4.9.2/bin/mpirun
[pmdtest@hpc bin]$ ssh compute-0-0
Last login: Sat Feb 28 02:15:50 2015 from hpc.local
Rocks Compute Node
Rocks 6.1.1 (Sand Boa)
Profile built 01:53 28-Feb-2015
Kickstarted 01:59 28-Feb-2015
[pmdtest@compute-0-0 ~]$ which mpirun
/share/apps/openmpi-1.8.4_gcc-4.9.2/bin/mpirun
The only this I notice important is that in the error it is referring to
/export/apps/openmpi-1.8.4_gcc-4.9.2/share/openmpi/help-opal-runtime.txt:
While it should have shown
/share/apps/openmpi-1.8.4_gcc-4.9.2/share/openmpi/help-opal-runtime.txt:
which is the path compute nodes see.
Please help!
Ahsan
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--
Syed Ahsan Ali Bokhari
Electronic Engineer (EE)
Research & Development Division
Pakistan Meteorological Department H-8/4, Islamabad.
Phone # off +92518358714
Cell # +923155145014
