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Subject: Re: [OMPI users] error while loading shared libraries: libhdf5.so.7:
From: Syed Ahsan Ali (ahsanshah01_at_[hidden])
Date: 2013-02-07 12:53:00


Dear John
Looking into output of ldd for master and compute nodes solved my problem.
Thanks for such a simple solution. :)

On Thu, Feb 7, 2013 at 9:37 PM, Syed Ahsan Ali <ahsanshah01_at_[hidden]>wrote:

> Dear John
> Thanks for the reply. I'll need help of you people to solve this problem.
> I am not expert in HPC and this would be my learning as well. Let me add
> that the cluster is based on Platform Cluster Manager (PCM) by IBM
> Computing. The compute nodes are NFS mounted with the installer node.
> Therefore the directory containing binary rca.x is also present in the
> compute nodes. Unfortunately I was trying to copy gfortran libraries from
> installer node to compute nodes using rsync but something went wrong and
> the model binary rca.x stopped working. I have recompiled the binary after
> reinstalling hdf as well as netcdf which model uses during compilation. All
> path are set in bashrc as well.
> Below is the output of ldd on master as well as compute nodes
>
>
>
> [pmdtest_at_pmd HadGEM]$ ldd rca.x
>
> libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6 (0x00002b6a9503c000)
>
> libnetcdff.so.5 => /usr/local/lib/libnetcdff.so.5 (0x00002b6a95344000)
>
> libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0x00002b6a95798000)
>
> libhdf5.so.7 => /usr/local/lib/libhdf5.so.7 (0x00002b6a95aa1000)
>
> libhdf5_hl.so.7 => /usr/local/lib/libhdf5_hl.so.7 (0x00002b6a95f5c000)
>
> libsz.so.2 => /usr/local/lib/libsz.so.2 (0x00002b6a9618b000)
>
> libz.so.1 => /usr/local/lib/libz.so.1 (0x00002b6a9639f000)
>
> libmpi_f90.so.0 => /home/openmpi/lib/libmpi_f90.so.0 (0x00002b6a965b4000)
>
> libmpi_f77.so.0 => /home/openmpi/lib/libmpi_f77.so.0 (0x00002b6a967b7000)
>
> libmpi.so.0 => /home/openmpi/lib/libmpi.so.0 (0x00002b6a969ee000)
>
> libopen-rte.so.0 => /home/openmpi/lib/libopen-rte.so.0 (0x00002b6a96cb6000)
>
> libopen-pal.so.0 => /home/openmpi/lib/libopen-pal.so.0 (0x00002b6a96f16000)
>
> libdl.so.2 => /lib64/libdl.so.2 (0x00000033e0e00000)
>
> libnsl.so.1 => /lib64/libnsl.so.1 (0x00000033e2200000)
>
> libutil.so.1 => /lib64/libutil.so.1 (0x00000033ee400000)
>
> libm.so.6 => /lib64/libm.so.6 (0x00000033e1200000)
>
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000033e1600000)
>
> libc.so.6 => /lib64/libc.so.6 (0x00000033e0a00000)
>
> libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1 (0x00002b6a971a0000)
>
> /lib64/ld-linux-x86-64.so.2 (0x00000033e0600000)
>
> librt.so.1 => /lib64/librt.so.1 (0x000000362ac00000)
>
> libifport.so.5 => /opt/intel/Compiler/11.1/064/lib/intel64/libifport.so.5
> (0x00002b6a973b5000)
>
> libifcore.so.5 => /opt/intel/Compiler/11.1/064/lib/intel64/libifcore.so.5
> (0x00002b6a974ef000)
>
> libimf.so =>
> /opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/libimf.so
> (0x00002b6a97765000)
>
> libsvml.so =>
> /opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/libsvml.so
> (0x00002b6a97c2f000)
>
> libintlc.so.5 =>
> /opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/libintlc.so.5
> (0x00002b6a984f5000)
>
> libifcoremt.so.5 =>
> /opt/intel/Compiler/11.1/064/lib/intel64/libifcoremt.so.5
> (0x00002b6a98743000)
>
> libirng.so =>
> /opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/libirng.so
> (0x00002b6a989e8000)
>
> [pmdtest_at_pmd HadGEM]$ ssh compute-01-18
>
> ssh: connect to host compute-01-18 port 22: No route to host
>
> [pmdtest_at_pmd HadGEM]$ ssh compute-01-13
>
> Last login: Mon Jan 28 07:48:08 2013 from pmd-eth0.private.dns.zone
>
> [pmdtest_at_compute-01-13 ~]$ ldd rca.x
>
> ldd: ./rca.x: No such file or directory
>
> [pmdtest_at_compute-01-13 ~]$ ls
> /home/pmdtest/RCA4_CORDEX/RCA4_CORDEX_SAsia/HadGEM/rca.x
> Regards
> Ahsan
>
>
> On Thu, Feb 7, 2013 at 7:40 PM, John Hearns <hearnsj_at_[hidden]>wrote:
>
>> ldd rca.x
>>
>> Try logging in to each node and run this command.
>> Even better use pdsh
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
>
>

-- 
Syed Ahsan Ali Bokhari
Electronic Engineer (EE)
Research & Development Division
Pakistan Meteorological Department H-8/4, Islamabad.
Phone # off  +92518358714
Cell # +923155145014