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Subject: Re: [OMPI users] OpenMPI 1.6.4 and Intel Composer_xe_2013.4.183: problem with remote runs, orted: error while loading shared libraries: libimf.so
From: Stefano Zaghi (stefano.zaghi_at_[hidden])
Date: 2013-06-21 04:35:59


Wow... I think you are right... I will am check after the job I have just
started will finish.

Thank you again.

See you soon

Stefano Zaghi
Ph.D. Aerospace Engineer,
Research Scientist, Dept. of Computational Hydrodynamics at
*CNR-INSEAN*<http://www.insean.cnr.it/en/content/cnr-insean>

The Italian Ship Model Basin
(+39) 06.50299297 (Office)
My codes:
*OFF* <https://github.com/szaghi/OFF>, Open source Finite volumes Fluid
dynamics code
*Lib_VTK_IO* <https://github.com/szaghi/Lib_VTK_IO>, a Fortran library to
write and read data conforming the VTK standard
*IR_Precision* <https://github.com/szaghi/IR_Precision>, a Fortran
(standard 2003) module to develop portable codes

2013/6/21 <thomas.forde_at_[hidden]>

> hi Stefano
>
> /home/stefano/opt/intel/2013.4.183/lib/intel64/ is also the wrong path, as
> the file is in ..183/lib/ and not ...183/lib/intel64/
>
> is that why?
> ./Thomas
>
>
> Den 21. juni 2013 kl. 10:26 skrev "Stefano Zaghi" <stefano.zaghi_at_[hidden]
> >:
>
> Dear Thomas,
> thank you again.
>
> Symlink in /usr/lib64 is not enough, I have symlinked also
> in /home/stefano/opt/mpi/openmpi/1.6.4/intel/lib and, as expected, not only
> libimf.so but also ibirng.so and libintlc.so.5 are necessary.
>
> Now also remote runs works, but this is only a workaround, I still not
> understand why mpirun do not find intel library even if LD_LIBRARY_PATH
> contains also /home/stefano/opt/intel/2013.4.183/lib/intel64. Can you try
> explain again?
>
> Thank you very much.
>
> Stefano Zaghi
> Ph.D. Aerospace Engineer,
> Research Scientist, Dept. of Computational Hydrodynamics at *CNR-INSEAN*<http://www.insean.cnr.it/en/content/cnr-insean>
>
> The Italian Ship Model Basin
> (+39) 06.50299297 (Office)
> My codes:
> *OFF* <https://github.com/szaghi/OFF>, Open source Finite volumes Fluid
> dynamics code
> *Lib_VTK_IO* <https://github.com/szaghi/Lib_VTK_IO>, a would Fortran
> library to write and read data conforming the VTK standard
> *IR_Precision* <https://github.com/szaghi/IR_Precision>, a Fortran
> (standard 2003) module to develop portable codes
>
>
> 2013/6/21 <thomas.forde_at_[hidden]>
>
>> your settings are as following:
>> export MPI=/home/stefano/opt/mpi/openmpi/1.6.4/intel
>> export PATH=${MPI}/bin:$PATH
>> export LD_LIBRARY_PATH=${MPI}/lib/openmpi:${MPI}/lib:$LD_LIBRARY_PATH
>> export LD_RUN_PATH=${MPI}/lib/openmpi:${MPI}/lib:$LD_RUN_PATH
>>
>> and your path to libimf.so file is
>> /home/stefano/opt/intel/2013.4.183/lib/libimf.so
>>
>> your export LD_LIbrary_PATH if i can decude it right would be because you
>> use the $MPI first.
>>
>> /home/stefano/opt/mpi/openmpi/1.64./intel/lib/openmpi and
>> /home/stefano/opt/mpi/openmpi/1.64./intel/lib
>>
>> as you can see it doesnt look for the files int he right place.
>>
>> the simplest thing i would try is to symlink the libimf.so file to
>> /usr/lib64 and should give you a workaround.
>>
>>
>>
>>
>>
>>
>> From: Stefano Zaghi <stefano.zaghi_at_[hidden]>
>> To: Open MPI Users <users_at_[hidden]>,
>> Date: 21.06.2013 09:45
>> Subject: Re: [OMPI users] OpenMPI 1.6.4 and Intel
>> Composer_xe_2013.4.183: problem with remote runs, orted: error while
>> loading shared libraries: libimf.so
>> Sent by: users-bounces_at_[hidden]
>> ------------------------------
>>
>>
>>
>> Dear Thomas,
>>
>> thank you very much for your very fast replay.
>>
>> Yes I have that library in the correct place:
>>
>> -rwxr-xr-x 1 stefano users 3.0M May 20 14:22
>> opt/intel/2013.4.183/lib/intel64/libimf.so
>>
>> Stefano Zaghi
>> Ph.D. Aerospace Engineer,
>> Research Scientist, Dept. of Computational Hydrodynamics at *CNR-INSEAN*<http://www.insean.cnr.it/en/content/cnr-insean>
>>
>> The Italian Ship Model Basin
>> (+39) 06.50299297 (Office)
>> My codes:
>> *OFF* <https://github.com/szaghi/OFF>, Open source Finite volumes Fluid
>> dynamics code
>> *Lib_VTK_IO* <https://github.com/szaghi/Lib_VTK_IO>, a Fortran library
>> to write and read data conforming the VTK standard
>> *IR_Precision* <https://github.com/szaghi/IR_Precision>, a Fortran
>> (standard 2003) module to develop portable codes
>>
>>
>> 2013/6/21 <*thomas.forde_at_[hidden]* <thomas.forde_at_[hidden]>>
>> hi Stefano
>>
>> your error message show that you are missing a shared library, not
>> necessary that library path is wrong.
>>
>> do you actually have libimf.so, can you find the file on your system.
>>
>> ./Thomas
>>
>>
>>
>>
>> From: Stefano Zaghi <*stefano.zaghi_at_[hidden]*<stefano.zaghi_at_[hidden]>
>> >
>> To: *users_at_[hidden]* <users_at_[hidden]>,
>> Date: 21.06.2013 09:27
>> Subject: [OMPI users] OpenMPI 1.6.4 and Intel
>> Composer_xe_2013.4.183: problem with remote runs, orted: error while
>> loading shared libraries: libimf.so
>> Sent by: *users-bounces_at_[hidden]* <users-bounces_at_[hidden]>
>> ------------------------------
>>
>>
>>
>>
>> Dear All,
>> I have compiled OpenMPI 1.6.4 with Intel Composer_xe_2013.4.183.
>>
>> My configure is:
>>
>> ./configure --prefix=/home/stefano/opt/mpi/openmpi/1.6.4/intel CC=icc
>> CXX=icpc F77=ifort FC=ifort
>>
>> Intel Composer has been installed in:
>>
>> /home/stefano/opt/intel/2013.4.183/composer_xe_2013.4.183
>>
>> Into the .bashrc and .profile in all nodes there is:
>>
>> source /home/stefano/opt/intel/2013.4.183/bin/compilervars.sh intel64
>> export MPI=/home/stefano/opt/mpi/openmpi/1.6.4/intel
>> export PATH=${MPI}/bin:$PATH
>> export LD_LIBRARY_PATH=${MPI}/lib/openmpi:${MPI}/lib:$LD_LIBRARY_PATH
>> export LD_RUN_PATH=${MPI}/lib/openmpi:${MPI}/lib:$LD_RUN_PATH
>>
>> If I run parallel job into each single node (e.g. mpirun -np 8 myprog)
>> all works well. However, when I tried to run parallel job in more nodes of
>> the cluster (remote runs) like the following:
>>
>> mpirun -np 16 --bynode --machinefile nodi.txt -x LD_LIBRARY_PATH -x
>> LD_RUN_PATH myprog
>>
>> I got the following error:
>>
>> /home/stefano/opt/mpi/openmpi/1.6.4/intel/bin/orted: error while loading
>> shared libraries: libimf.so: cannot open shared object file: No such file
>> or directory
>>
>> I have read many FAQs and online resources, all indicating
>> LD_LIBRARY_PATH as the possible problem (wrong setting). However I am not
>> able to figure out what is going wrong, the LD_LIBRARY_PATH seems to set
>> right in all nodes.
>>
>> It is worth noting that in the same cluster I have successful installed
>> OpenMPI 1.4.3 with Intel Composer_xe_2011_sp1.6.233 following exactly the
>> same procedure.
>>
>> Thank you in advance for all suggestion,
>> sincerely
>>
>> Stefano Zaghi
>> Ph.D. Aerospace Engineer,
>> Research Scientist, Dept. of Computational Hydrodynamics at *CNR-INSEAN*<http://www.insean.cnr.it/en/content/cnr-insean>
>>
>> The Italian Ship Model Basin
>> (+39) 06.50299297 (Office)
>> My codes: *
>> **OFF* <https://github.com/szaghi/OFF>, Open source Finite volumes Fluid
>> dynamics code *
>> **Lib_VTK_IO* <https://github.com/szaghi/Lib_VTK_IO>, a Fortran library
>> to write and read data conforming the VTK standard
>> *IR_Precision* <https://github.com/szaghi/IR_Precision>, a Fortran
>> (standard 2003) module to develop portable codes
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