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Subject: Re: [OMPI users] conflict among differenv MPIs
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2008-09-22 15:31:34


On Sep 22, 2008, at 2:48 PM, Shafagh Jafer wrote:

> I am not using any of the files that exist in /usr/local/include,
> this doesn't even show on my PATH and my mpicc -show tells that the
> openmpi path is correct.

/usr/local/include is likely a default include path from the
compiler. So even if you don't reference it directly, the compiler
may still be using files from there. It *shouldn't*, if the same file
exists in /opt/openmpi*/include and /usr/local/include/*, but there
seems to be some confusion on your machine.

Note that include directories have nothing to do with your PATH.

> I dont know what to do, I have contacted the technician to hide or
> delete /usr/local/include...Millions of thanks for ur replies and
> patience. I'll keep you updated!

Don't just move or hide /usr/local/include -- that will likely break
things. Just uninstall MPICH from /usr/local and re-install it
somewhere else.

Good luck.

>
> --- On Mon, 9/22/08, Jeff Squyres <jsquyres_at_[hidden]> wrote:
> From: Jeff Squyres <jsquyres_at_[hidden]>
> Subject: Re: [OMPI users] conflict among differenv MPIs
> To: "Open MPI Users" <users_at_[hidden]>
> Date: Monday, September 22, 2008, 11:28 AM
>
> On Sep 22, 2008, at 2:12 PM, Shafagh Jafer wrote:
>
> > I am gonna kill myself :( i dont know what the problem is... I 'm
> > gonna explain the details again, please bare me and help me :(
> >
> > Ok yes I used mpic++. Actually I checked mpicxx -show and the path
> > were correct. let me describe my problem again.
> > When I run my code (after making sure that openmpi is installed
> > correctly and all the env varibles are set properly), i get the
> > following error which is when I make a call to the following
> function:
> > ----------------------------------------------
> > int CommPhyMPI:: physicalGetSize() const {
> > int size ;
> > MPI_Comm_size(MPI_COMM_WORLD,&size);
> > return size ;
> > }
> > -------------------------------------------
> > The errors i get are the follwoing:
> > =====================
> > [DeepThought:31144] *** Process received signal ***
> > [DeepThought:31144] Signal: Segmentation fault (11)
> > [DeepThought:31144] Signal code: Address not mapped (1)
> > [DeepThought:31144] Failing at address: 0xcf
> > [DeepThought:31144] [ 0] /lib/tls/libpthread.so.0 [0xc16f80]
> > [DeepThought:31144] [ 1] /nfs/sjafer/phd/openMPI/latest_cd+
> > +_timewarp/cd++(physicalGetId__C10CommPhyMPI+0x14) [0x8305880]
>
> This *likely* indicates that you are mixing MPI implementations.
>
> > So I thought that maybe my problem is that when I include
> "mpi.h" in
> > my source code, it picks the wrong one. So in my source code instead
> > of just saying include "mpi.h" I put the path too, so it looks
> like
> > => "include /opt/openmpi/1.2.7/include/mpi.h", and now when I
> run my
> > code aftre this change, aside from errors which I will paste below,
> > i get a warning that shows mpi.h in mpicxx.h is the wrong one from
> > usr/local/include and not from /opt/openmpi/...
> > ------------------
> > In file included from /usr/local/include/mpidefs.h:49,
>
> What is /usr/local/include/mpidefs.h? Is that part of your
> application?
>
> > from /usr/local/include/mpi.h:230,
>
> This definitely indicates that you're including the wrong file.
>
> I don't know what the exact cause of your problem is, but it seems
> like you are somehow mixing multiple mpi.h files together. This can
> definitely lead to segv's at run time.
>
> As I think I indicated before, I think your best solution is likely to
> uninstall MPICH from /usr/local and install it somewhere else (e.g., /
> opt/mpich). Then the compiler won't automatically pick up header
> files from MPICH (it shouldn't do that anyway, but there seems to be
> some confusion on your system, so who knows?).
>
> You should probably get your local system administrator involved; they
> can actually see exactly what is happening on your system, diagnose
> the default compiler include paths, etc. But I'd try moving the MPICH
> install first.
>
> --
> Jeff Squyres
> Cisco Systems
>
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-- 
Jeff Squyres
Cisco Systems