[mpich-discuss] MPICH2 problem

[Dave Goodell]

It looks more like a linking problem to me.  Make sure you are using the mpicc/mpicxx/mpif77/mpif90 wrappers to compile your program, they should include a "-lpthread" on the link line.  If that's not working, try inserting "-lpthread" manually on the link line.

-Dave

On Jul 28, 2010, at 12:46 PM CDT, Ivan Pulido wrote:

> 
> 
> On Wed, Jul 28, 2010 at 12:19 PM, Grzegorz Dwornicki <gd1100 at gmail.com> wrote:
> Ive reinstaled the distribution to clean debian squeeze. Now when im compiling im getting:
> 
> /usr/lib/libmpich.a(info_getnth.o): In function `MPI_Info_get_nthkey':
> (.text+0x2f9): undefined reference to `pthread_getspecific'
> /usr/lib/libmpich.a(info_getnth.o): In function `MPI_Info_get_nthkey':
> (.text+0x32a): undefined reference to `pthread_setspecific'
> /usr/lib/libmpich.a(info_getvallen.o): In function `MPI_Info_get_valuelen':
> (.text+0x2e): undefined reference to `pthread_getspecific'
> /usr/lib/libmpich.a(info_getvallen.o): In function `MPI_Info_get_valuelen':
> (.text+0x368): undefined reference to `pthread_setspecific'
> /usr/lib/libmpich.a(info_getvallen.o): In function `MPI_Info_get_valuelen':
> (.text+0x381): undefined reference to `pthread_getspecific'
> /usr/lib/libmpich.a(info_getvallen.o): In function `MPI_Info_get_valuelen':
> (.text+0x3b2): undefined reference to `pthread_setspecific'
> 
> 
> Ive made a symlink from /usr/bin/gfortran to /ust/bin/g77. It worked before but not it doesn work. Any ideas? This errors are slim part of full output but they are are nearly the same (same kind but diferent sections).  I have only 1 idea but it might blow everything up. The idea is to try using gfortran from lenny. But it wil require to change a lot of libs and some programs including gcc it self.
> 
> 
> Not sure if this is the problem, forgive me if it isn't. But those pthread functions are declared in pthread.h (make sure you have it, usually it's in /usr/include/pthread.h). On Debian you should accomplish this by installing "libc6-dev" package. Hope this helps.
>  
> Gregory
> 
> 2010/7/21 Grzegorz Dwornicki <gd1100 at gmail.com>
> yea ive typed apt-get remove mpich-bin. And then ive used "make clean" and "make arch=Linux_PII_CBLAS". Hmm i can doo even more - If some liblaries are messing things up I will reinstall distribution to be sure. I'll update this topic on monday :)
> 
> Gregory.
> 
> 2010/7/21 Pavan Balaji <balaji at mcs.anl.gov>
> 
> 
> > [0]  Aborting program !
> > [0] Aborting program!
> > p0_3435:  p4_error: : 9039
> 
> Well, P4 is used in MPICH-1, not MPICH-2. So, you cannot get the same error if you are not using MPICH-1 :-).
> 
> Did you recompile with MPICH2?
> 
>  -- Pavan
> 
> 
> On 07/21/2010 11:16 AM, Grzegorz Dwornicki wrote:
> Ive remove mpich-bin package and recompiled the hpl linpack. But im geting the same error :(
> 
> 2010/7/19 Grzegorz Dwornicki <gd1100 at gmail.com <mailto:gd1100 at gmail.com>>
> 
> 
>    Thx you both for such fast reply. Ill try your advices on wednesday
>    and report results.
>    Gregory.
> 
>    2010/7/19 Dave Goodell <goodell at mcs.anl.gov
>    <mailto:goodell at mcs.anl.gov>>
> 
> 
>        On Jul 19, 2010, at 11:51 AM CDT, Grzegorz Dwornicki wrote:
> 
>         > If im writing double message on list pls let me know.
>         >
>         > Im writing a graduating paper on my university about MPICH
>        and im having some trouble launching programs. For example I
>        need to run perfomance tests on cluster, to determine it max.
>        potencial. To do this Im using hpl linpack from
>        http://www.netlib.org/benchmark/hpl/. Compilation goes without
>        any errors but when I type f.e:
>         >
>         > mpirun -np 4 ./xhpl
>         >
>         > Im getting output like this:
>         > 0 - <NO ERROR MESSAGE> : Could not convert index 1140850688
>        into a pointer
>         > The index may be an incorrect argument.
> 
>        You have somehow mixed MPICH2's mpi.h or mpif.h headers  with
>        the library from MPICH:
> 
>        % perl -e 'printf("%#x\n",1140850688);'
>        0x44000000
>        % grep 0x44000000 mpi.h
>        #define MPI_COMM_WORLD ((MPI_Comm)0x44000000)
> 
>        As Pavan suggested, uninstall MPICH and make sure that MPICH2 is
>        fully installed.  Also, make sure that you recompile your
>        application once the MPICH installation is removed.  Make sure
>        to use the compiler wrappers provided by MPICH2 (mpicc, mpif90,
>        etc) when building your application.
> 
>        -Dave
> 
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> -- 
> Pavan Balaji
> http://www.mcs.anl.gov/~balaji
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> 
> -- 
> Ivan Pulido
> Estudiante de Física
> Universidad Nacional de Colombia
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