[Trilinos-Users] [Pytrilinos-users] Some Days the Fun Never Stops

Daniel Wheeler daniel.wheeler2 at gmail.com
Mon Mar 16 10:34:23 MDT 2009


Hi,

I have recently built trilinos on the following architecture,

          Linux Something 2.6.16.60-0.23.PTF.403865.0-default #1 SMP
Thu May 15 06:38:31 UTC 2008 ia64 ia64 ia64 GNU/Linux

I used the following configure command to do this,

         $ ../configure CC=icc CXX=icc F77=ifort CFLAGS="-O3 -fPIC"
CXXFLAGS="-O3 -fPIC -LANG:std -LANG:ansi -DMPI_NO_CPPBIND" FFLAGS="-O3
-fPIC" --prefix=${USR} --with-install=/usr/bin/install -p
--with-blas="-L/opt/intel/Compiler/11.0/074/mkl/lib/ 64
-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_lapack -lmkl_core -liomp5
-lpthread" --with-lapack="-L/opt/intel/Compiler/11.0/074/mkl/lib/64
-lmkl _intel_lp64 -lmkl_intel_thread -lmkl_lapack -lmkl_core -liomp5
-lpthread" --enable-mpi --enable-amesos --enable-ifpack
--enable-shared --enable -aztecoo --enable-epetra --enable-epetraext
--enable-external --enable-ml --enable-threadpool --enable-thyra
--enable-stratimikos --enable-triu tils --enable-galeri
--cache-file=config.cache &&make && make install

Everything seems cool with the build.

Currently when I try to run without mpi I get the following:

       $ ./input.py
       Traceback (most recent call last):
       File "./input.py", line 321, in ?
       from PyTrilinos import Epetra
       File "/users/wd15/usr/ia64/2.6.16.60-0.23.PTF.403865.0-default//lib/python2.4/site-packages/PyTrilinos/Epetra.py",
line 59, in ?
       import _Epetra
       ImportError:
/users/wd15/usr/ia64/2.6.16.60-0.23.PTF.403865.0-default//lib/libteuchos.so:
undefined symbol:    _ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb

If I try to run with mpi I get the following:

    $mpirun -np 1 ./input.py
    MPI: could not run executable (case #3)
    MPI: No details available, no log files found
    Killed

Any bright ideas?

Regarding Matt's problem with the undefined symbol. Did the problem go
away when running under mpi as Bill suggested?

Thanks

On Sat, Mar 7, 2009 at 5:05 PM, Bill Spotz <wfspotz at sandia.gov> wrote:
> No, this is an improvement.  But shared libraries can be a little more
> touchy to use.  This message is saying that the libraries are found
> but that an (actually all) MPI symbol(s) is (are) undefined.
>
> Different systems and MPI versions behave differently, but you appear
> to need to run PyTrilinos scripts under mpirun or mpiexec, etc.
>
> On Mar 7, 2009, at 3:53 PM, Matt G wrote:
>
>> I came up with a new interesting glitch:
>>
>> Originally my installation (prefixed to my home directory on the HPC
>> here)  could not find "libteuchos.so" located in my local lib
>> directory, but after doing:
>>
>> export LD_LIBRARY_PATH=/home/u27/mgoodman/lib
>>
>> I get a new and not very meaningful error message:
>>
>> In [1]: from PyTrilinos import *
>> ---------------------------------------------------------------------------
>> ImportError                               Traceback (most recent
>> call last)
>>
>> /homeB/home4/u24/agh/<ipython console> in <module>()
>>
>> /home/u27/mgoodman/lib/python2.6/site-packages/PyTrilinos/Teuchos.py
>> in <module>()
>>      43 """
>>      44
>> ---> 45 import _Teuchos
>>      46 import new
>>      47 new_instancemethod = new.instancemethod
>>
>> ImportError: /home/u27/mgoodman/lib/libepetra.so: undefined symbol:
>> _ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb
>>
>> Which looks much uglier, frankly.  Are my libraries landing in the
>> wrong directories somehow?
>>
>> Any thoughts?
>> -Matt
>> <ATT00001.txt>
>
> ** Bill Spotz                                              **
> ** Sandia National Laboratories  Voice: (505)845-0170      **
> ** P.O. Box 5800                 Fax:   (505)284-0154      **
> ** Albuquerque, NM 87185-0370    Email: wfspotz at sandia.gov **
>
>
>
>
>
> _______________________________________________
> Pytrilinos-users mailing list
> Pytrilinos-users at software.sandia.gov
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>



-- 
Daniel Wheeler



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