Oh sorry. That is related to application. I need to recompile application too I guess.
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 >>>>> _______________________________________________ >>>>> 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/2015/02/26411.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/2015/02/26412.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/2015/02/26415.php > > > > -- > Syed Ahsan Ali Bokhari > Electronic Engineer (EE) > > Research & Development Division > Pakistan Meteorological Department H-8/4, Islamabad. > Phone # off +92518358714 > Cell # +923155145014 -- Syed Ahsan Ali Bokhari Electronic Engineer (EE) Research & Development Division Pakistan Meteorological Department H-8/4, Islamabad. Phone # off +92518358714 Cell # +923155145014
