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Subject: Re: [OMPI users] Segmentation Fault--libc.so.6(__libc_start_main...
From: Shafagh Jafer (barfy27_at_[hidden])
Date: 2008-09-21 15:46:24


Yes I am using openmpi mpicc and mpic++ to compile my code, and I only have openmpi's lib directory in my LD_LIBRARY_PATH. to make sure that I am including the mpi.h of openmpi, i added this line to my source code
#include "/opt/openmpi/1.2.7/include/mpi.h"instead of only saying
#include "mpi.h"
but now i get the following errors, which show that the wrapper compiler is not adding "
-I${prefix}/include/openmpi" infron of the included files from cxx folder.
 
In file included from /opt/openmpi/1.2.7/include/mpi.h:1795,
                 from CommPhyMPI.cc:36:
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:167: CommMgrInterface.cc -o /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/warped/TimeWarp/src/obj/CommMgrInterface.o
openmpi/ompi/mpi/cxx/constants.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:168: openmpi/ompi/mpi/cxx/functions.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:169: openmpi/ompi/mpi/cxx/datatype.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:193: openmpi/ompi/mpi/cxx/exception.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:194: openmpi/ompi/mpi/cxx/op.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:195: openmpi/ompi/mpi/cxx/status.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:196: openmpi/ompi/mpi/cxx/request.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:197: openmpi/ompi/mpi/cxx/group.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:198: openmpi/ompi/mpi/cxx/comm.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:199: openmpi/ompi/mpi/cxx/win.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:200: openmpi/ompi/mpi/cxx/file.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:201: openmpi/ompi/mpi/cxx/errhandler.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:202: openmpi/ompi/mpi/cxx/intracomm.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:203: openmpi/ompi/mpi/cxx/topology.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:204: openmpi/ompi/mpi/cxx/intercomm.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:205: openmpi/ompi/mpi/cxx/info.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:244: openmpi/ompi/mpi/cxx/datatype_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:245: openmpi/ompi/mpi/cxx/functions_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:246: openmpi/ompi/mpi/cxx/request_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:247: openmpi/ompi/mpi/cxx/comm_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:248: openmpi/ompi/mpi/cxx/intracomm_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:249: openmpi/ompi/mpi/cxx/topology_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:250: openmpi/ompi/mpi/cxx/intercomm_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:251: openmpi/ompi/mpi/cxx/group_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:252: openmpi/ompi/mpi/cxx/op_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:253: openmpi/ompi/mpi/cxx/errhandler_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:254: openmpi/ompi/mpi/cxx/status_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:255: openmpi/ompi/mpi/cxx/info_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:256: openmpi/ompi/mpi/cxx/win_inln.h: No such file or directory
/opt/openmpi/1.2.7/include/openmpi/ompi/mpi/cxx/mpicxx.h:257: openmpi/ompi/mpi/cxx/file_inln.h: No such file or directory
make[1]: *** [/nfs/sjafer/phd/openMPI/latest_cd++_timewarp/warped/TimeWarp/src/obj/CommPhyMPI.o] Error 1

--- On Sun, 9/21/08, Aurélien Bouteiller <bouteill_at_[hidden]> wrote:

From: Aurélien Bouteiller <bouteill_at_[hidden]>
Subject: Re: [OMPI users] Segmentation Fault--libc.so.6(__libc_start_main...
To: "Open MPI Users" <users_at_[hidden]>
Date: Sunday, September 21, 2008, 9:35 AM

Are you sure that you have matching versions of the MPI library and
mpi.h file ? Open MPI and MPICH have different internal types for the
opaque MPI objects (such as MPI_Comm). If you have mismatching mpi.h
and mpi library, you'll transmit those as integer to the library while
it is expecting pointers. This will obviously segfault very badly.
Please make sure that you actually use the mpi.h from open MPI (by
using Open MPI's mpicc) to compile your program when using Open MPI.
Also make sure that you don't have another version of libmpi in your
LD_LIBRARY_PATH that could be used instead of the one you used to
compile.

Aurelien

Le 21 sept. 08 à 04:38, Shafagh Jafer a écrit :

>
> Ok. I noticed that whenever in my code, i use an MPI fucntion that has
> "OMPI_DECLSPEC" in front of it in mpi.h , I get this segfault
> error. Could some one please tell me what is "OMPI_DECLSPEC"??
is it
> a macro that I need to enable ?!?
> forexample, in MPICH the function getsize in mpi.h looks like the
> following:
>
> int MPI_Comm_size(MPI_Comm, int *);
>
> but the same function in OMPI apears as follows:
> OMPI_DECLSPEC int MPI_Comm_size(MPI_Comm comm, int *size);
>
> --- On Sat, 9/20/08, Shafagh Jafer <barfy27_at_[hidden]> wrote:
> From: Shafagh Jafer <barfy27_at_[hidden]>
> Subject: Re: [OMPI users] Segmentation Fault--libc.so.
> 6(__libc_start_main...
> To: "Open MPI Users" <users_at_[hidden]>
> Date: Saturday, September 20, 2008, 9:50 PM
>
> My code was working perfect when I had it with MPICH now I have
> replaced that with OMPI. Could that be the problem?? Do I need to
> change any part of my source code if I migrate from MPICH-1.2.6 to
> OpenMPI-1.2.7?? Please let me know.
>
> --- On Sat, 9/20/08, Aurélien Bouteiller <bouteill_at_[hidden]>
> wrote:
> From: Aurélien Bouteiller <bouteill_at_[hidden]>
> Subject: Re: [OMPI users] Segmentation Fault--libc.so.
> 6(__libc_start_main...
> To: "Open MPI Users" <users_at_[hidden]>
> Date: Saturday, September 20, 2008, 6:54 AM
>
> Shafagh,
>
> You have a segfault in your own code. Because Open MPI detects it, it
> forwards the error to you and pretty print it but Open MPI is not the
> source of the bug. From the stack trace, I suggest you gdb debug the
> PhysicalGetID function.
>
> Aurelien
>
> Le 19 sept. 08 à 22:22, Shafagh Jafer a écrit :
>
> > Hi every one,
> > I need urgent help plz :-(
> > I am getting the following error when i run my program. OpenMPI
> > compilation was all fine and went well, but now i dont understand
> > the source of this error:
> > ============================================
> > [node01:29264] *** Process received signal ***
> > [node01:29264] Signal: Segmentation fault (11)
> > [node01:29264] Signal code: Address not mapped (1)
> > [node01:29264] Failing at address: 0xcf
> > [node01:29264] [ 0] /lib/tls/libpthread.so.0 [0x7ccf80]
> > [node01:29264] [ 1] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (physicalGetId__C10CommPhyMPI+0x14) [0x8305880]
> > [node01:29264] [ 2] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (physicalCommGetId__Fv+0x43) [0x82ff81b]
> > [node01:29264] [ 3] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (openComm__16StandAloneLoader+0x1f) [0x80fdf43]
> > [node01:29264] [ 4] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (run__21ParallelMainSimulator+0x1640) [0x81ea53c]
> > [node01:29264] [ 5] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (main+0xde) [0x80a58ce]
> > [node01:29264] [ 6] /lib/tls/libc.so.6(__libc_start_main+0xda)
> > [0xe3d79a]
> > [node01:29264] [ 7] /nfs/sjafer/phd/openMPI/latest_cd++_timewarp/cd
> ++
> > (sinh+0x4d) [0x80a2221]
> > [node01:29264] *** End of error message ***
> > mpirun noticed that job rank 0 with PID 29264 on node node01 exited
> > on signal 11 (Segmentation fault).
> > ===========================================
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
>
> --
> * Dr. Aurélien Bouteiller
> * Sr. Research Associate at Innovative Computing Laboratory
> * University of Tennessee
> * 1122 Volunteer Boulevard, suite 350
> * Knoxville, TN 37996
> * 865 974 6321
>
>
>
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
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