[Bioclusters] mpi library problem

[landman]

Err... I forgot to indicate that it is likely to be at minimum a command line
option problem, to specify the appropriate gcc enabling linkage.  There are
other mitigating factors I indicated in the previous message.  You will likely
prefer to compile everything using the ifc and icc compilers rather than
trying to mix gcc, g77, ifc.

Joe

On Wed, 25 Jun 2003 14:04:34 +0100, andy law (RI) wrote
> All,
> 
> The answer is probably out there, but pointers to the answer will 
> save me time.
> 
> We are setting up a test cluster (of 2 machines) as a pilot to more 
> extensive work on our 30 CPU cluster. The software to be 
> compiled/tested requires mpi and pgapack. We are running on Red Hat 7.x.
> 
> One of my troops compiled and installed mpich 1.2.5 (he is off on 
> leave for a couple of weeks and I don't have immediate access to his 
> notes). I know (because we spoke about it efore he went off) that we 
> had problems with the test suite initially, but once we worked out 
> that we could circumvent the race condition inherent in the test 
> suite by installing on an NFS mount then everything went fine. Thus, 
> we have mpich in /local/Mpich/current (softlink to 
> /local/Mpich/mpich-1.2.5) on the two nodes and 'make test' is as 
> happy as it could be.
> 
> I installed pgapack. I gave it the path to libmpich.a that it was 
> looking for, and the path to the includes directory. It was happy 
> with 'make' and 'make test'. However, the end bit of 'make' 
> suggested running a script called 'instverf' (installation 
> verification) and although that seemed to run OK, it did mention 
> that there were errors in each of the tests (although it reported 
> them in a 'by the way there were some errors' rather than a 
> 'STOP!!!!! THRERE ARE ERRORS' kind of way).
> 
> Now we are trying to compile the *real* code, we are getting a 
> failure at the link stage, with reference to a whole load of mpi_* 
> routines (amongst others). We have the necessary 
> -L/local/Mpich/current/lib and -lmpich flags set, but nothing seems 
> to work. objdump on the library suggests that at least some of them 
> are in there (although I am no expert at decoding the output of 
> objdump - it could be that there is a problem in there).
> 
> Are there any obvious things that we might have done wrong, or ways 
> that we can track it down further?
> 
> Thanks in advance,
> 
> Later,
> 
> Andy
> 
> -------------
> Dr. Andy Law
> --------------------
> Head of Bioinformatics - Roslin Institute
> 
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--
Joseph Landman, Ph.D
Scalable Informatics LLC,
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