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Subject: Re: [OMPI users] Prototypes for Fortran MPI_ commands using 64-bit indexing
From: Jim Parker (jimparker96313_at_[hidden])
Date: 2013-11-01 16:51:54


@Jeff,

 Well, it may have been "just for giggles", but it Worked!! My helloWorld
program ran as expected. My original code ran through the initialization
parts without overwriting data. It will take a few days to finish
computation and analysis to ensure it ran as expected. I'll report back
when I get done.

It looks like a good Friday!

Cheers,
--Jim

On Thu, Oct 31, 2013 at 4:06 PM, Jeff Squyres (jsquyres) <jsquyres_at_[hidden]
> wrote:

> For giggles, try using MPI_STATUS_IGNORE (assuming you don't need to look
> at the status at all). See if that works for you.
>
> Meaning: I wonder if we're computing the status size for Fortran
> incorrectly in the -i8 case...
>
>
> On Oct 31, 2013, at 1:58 PM, Jim Parker <jimparker96313_at_[hidden]> wrote:
>
> > Some additional info that may jog some solutions. Calls to MPI_SEND do
> not cause memory corruption. Only calls to MPI_RECV. Since the main
> difference is the fact that MPI_RECV needs a "status" array and SEND does
> not, seems to indicate to me that something is wrong with status.
> >
> > Also, I can run a C version of the helloWorld program with no errors.
> However, int types are only 4-byte. To send 8byte integers, I define
> tempInt as long int and pass MPI_LONG as a type.
> >
> > @Jeff,
> > I got a copy of the openmpi conf.log. See attached.
> >
> > Cheers,
> > --Jim
> >
> > On Wed, Oct 30, 2013 at 10:55 PM, Jim Parker <jimparker96313_at_[hidden]>
> wrote:
> > Ok, all, where to begin...
> >
> > Perhaps I should start with the most pressing issue for me. I need
> 64-bit indexing
> >
> > @Martin,
> > you indicated that even if I get this up and running, the MPI library
> still uses signed 32-bit ints to count (your term), or index (my term) the
> recvbuffer lengths. More concretely,
> > in a call to MPI_Allgatherv( buffer, count, MPI_Integer, recvbuf,
> recv-count, displ, MPI_integer, MPI_COMM_WORLD, status, mpierr): count,
> recvcounts, and displs must be 32-bit integers, not 64-bit. Actually, all
> I need is displs to hold 64-bit values...
> > If this is true, then compiling OpenMPI this way is not a solution.
> I'll have to restructure my code to collect 31-bit chunks...
> > Not that it matters, but I'm not using DIRAC, but a custom code to
> compute circuit analyses.
> >
> > @Jeff,
> > Interesting, your runtime behavior has a different error than mine.
> You have problems with the passed variable tempInt, which would make sense
> for the reasons you gave. However, my problem involves the fact that the
> local variable "rank" gets overwritten by a memory corruption after
> MPI_RECV is called.
> >
> > Re: config.log. I will try to have the admin guy recompile tomorrow and
> see if I can get the log for you.
> >
> > BTW, I'm using the gcc 4.7.2 compiler suite on a Rocks 5.4 HPC cluster.
> I use the options -m64 and -fdefault-integer-8
> >
> > Cheers,
> > --Jim
> >
> >
> >
> > On Wed, Oct 30, 2013 at 7:36 PM, Martin Siegert <siegert_at_[hidden]> wrote:
> > Hi Jim,
> >
> > I have quite a bit experience with compiling openmpi for dirac.
> > Here is what I use to configure openmpi:
> >
> > ./configure --prefix=$instdir \
> > --disable-silent-rules \
> > --enable-mpirun-prefix-by-default \
> > --with-threads=posix \
> > --enable-cxx-exceptions \
> > --with-tm=$torquedir \
> > --with-wrapper-ldflags="-Wl,-rpath,${instdir}/lib" \
> > --with-openib \
> > --with-hwloc=$hwlocdir \
> > CC=gcc \
> > CXX=g++ \
> > FC="$FC" \
> > F77="$FC" \
> > CFLAGS="-O3" \
> > CXXFLAGS="-O3" \
> > FFLAGS="-O3 $I8FLAG" \
> > FCFLAGS="-O3 $I8FLAG"
> >
> > You need to set FC to either ifort or gfortran (those are the two
> compilers
> > that I have used) and set I8FLAG to -fdefault-integer-8 for gfortran or
> > -i8 for ifort.
> > Set torquedir to the directory where torque is installed ($torquedir/lib
> > must contain libtorque.so), if you are running jobs under torque;
> otherwise
> > remove the --with-tm=... line.
> > Set hwlocdir to the directory where you have hwloc installed. You many
> not
> > need the -with-hwloc=... option because openmpi comes with a hwloc
> version
> > (I don't have experience with that because we install hwloc
> independently).
> > Set instdir to the directory where you what to install openmpi.
> > You may or may not need the --with-openib option depending on whether
> > you have an Infiniband interconnect.
> >
> > After configure/make/make install this so compiled version can be used
> > with dirac without changing the dirac source code.
> > (there is one caveat: you should make sure that all "count" variables
> > in MPI calls in dirac are smaller than 2^31-1. I have run into a few
> cases
> > when that is not the case; this problem can be overcome by replacing
> > MPI_Allreduce calls in dirac with a wrapper that calls MPI_Allreduce
> > repeatedly). This is what I use to setup dirac:
> >
> > export PATH=$instdir/bin
> > ./setup --prefix=$diracinstdir \
> > --fc=mpif90 \
> > --cc=mpicc \
> > --int64 \
> > --explicit-libs="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core"
> >
> > where $instdir is the directory where you installed openmpi from above.
> >
> > I would never use the so-compiled openmpi version for anything other
> > than dirac though. I am not saying that it cannot work (at a minimum
> > you need to compile Fortran programs with the appropriate I8FLAG),
> > but it is an unnecessary complication: I have not encountered a piece
> > of software other than dirac that requires this.
> >
> > Cheers,
> > Martin
> >
> > --
> > Martin Siegert
> > Head, Research Computing
> > WestGrid/ComputeCanada Site Lead
> > Simon Fraser University
> > Burnaby, British Columbia
> > Canada
> >
> > On Wed, Oct 30, 2013 at 06:00:56PM -0500, Jim Parker wrote:
> > >
> > > Jeff,
> > > Here's what I know:
> > > 1. Checked FAQs. Done
> > > 2. Version 1.6.5
> > > 3. config.log file has been removed by the sysadmin...
> > > 4. ompi_info -a from head node is in attached as headnode.out
> > > 5. N/A
> > > 6. compute node info in attached as compute-x-yy.out
> > > 7. As discussed, local variables are being overwritten after calls
> to
> > > MPI_RECV from Fortran code
> > > 8. ifconfig output from head node and computes listed as
> *-ifconfig.out
> > > Cheers,
> > > --Jim
> > >
> > > On Wed, Oct 30, 2013 at 5:29 PM, Jeff Squyres (jsquyres)
> > > <[1]jsquyres_at_[hidden]> wrote:
> > >
> > > Can you send the information listed here:
> > > [2]http://www.open-mpi.org/community/help/
> > >
> > > On Oct 30, 2013, at 6:22 PM, Jim Parker <[3]
> jimparker96313_at_[hidden]>
> > > wrote:
> > > > Jeff and Ralph,
> > > > Ok, I downshifted to a helloWorld example (attached), bottom
> line
> > > after I hit the MPI_Recv call, my local variable (rank) gets borked.
> > > >
> > > > I have compiled with -m64 -fdefault-integer-8 and even have
> assigned
> > > kind=8 to the integers (which would be the preferred method in my
> case)
> > > >
> > > > Your help is appreciated.
> > > >
> > > > Cheers,
> > > > --Jim
> > > >
> > > >
> > > >
> > > > On Wed, Oct 30, 2013 at 4:49 PM, Jeff Squyres (jsquyres)
> > > <[4]jsquyres_at_[hidden]> wrote:
> > > > On Oct 30, 2013, at 4:35 PM, Jim Parker <[5]
> jimparker96313_at_[hidden]>
> > > wrote:
> > > >
> > > > > I have recently built a cluster that uses the 64-bit indexing
> > > feature of OpenMPI following the directions at
> > > > >
> > > [6]
> http://wiki.chem.vu.nl/dirac/index.php/How_to_build_MPI_libraries_fo
> > > r_64-bit_integers
> > > >
> > > > That should be correct (i.e., passing -i8 in FFLAGS and FCFLAGS
> for
> > > OMPI 1.6.x).
> > > >
> > > > > My question is what are the new prototypes for the MPI calls ?
> > > > > specifically
> > > > > MPI_RECV
> > > > > MPI_Allgathterv
> > > >
> > > > They're the same as they've always been.
> > > >
> > > > The magic is that the -i8 flag tells the compiler "make all
> Fortran
> > > INTEGERs be 8 bytes, not (the default) 4." So Ralph's answer was
> > > correct in that all the MPI parameters are INTEGERs -- but you can
> tell
> > > the compiler that all INTEGERs are 8 bytes, not 4, and therefore get
> > > "large" integers.
> > > >
> > > > Note that this means that you need to compile your application
> with
> > > -i8, too. That will make *your* INTEGERs also be 8 bytes, and then
> > > you'll match what Open MPI is doing.
> > > >
> > > > > I'm curious because some off my local variables get killed (set
> to
> > > null) upon my first call to MPI_RECV. Typically, this is due (in
> > > Fortran) to someone not setting the 'status' variable to an
> appropriate
> > > array size.
> > > >
> > > > If you didn't compile your application with -i8, this could well
> be
> > > because your application is treating INTEGERs as 4 bytes, but OMPI
> is
> > > treating INTEGERs as 8 bytes. Nothing good can come from that.
> > > >
> > > > If you *did* compile your application with -i8 and you're seeing
> this
> > > kind of wonkyness, we should dig deeper and see what's going on.
> > > >
> > > > > My review of mpif.h and mpi.h seem to indicate that the
> functions
> > > are defined as C int types and therefore , I assume, the coercion
> > > during the compile makes the library support 64-bit indexing. ie.
> int
> > > -> long int
> > > >
> > > > FWIW: We actually define a type MPI_Fint; its actual type is
> > > determined by configure (int or long int, IIRC). When your Fortran
> > > code calls C, we use the MPI_Fint type for parameters, and so it
> will
> > > be either a 4 or 8 byte integer type.
> > > >
> > > > --
> > > > Jeff Squyres
> > > > [7]jsquyres_at_[hidden]
> > > > For corporate legal information go to:
> > > [8]http://www.cisco.com/web/about/doing_business/legal/cri/
> > > >
> > > > _______________________________________________
> > > > users mailing list
> > > > [9]users_at_[hidden]
> > > > [10]http://www.open-mpi.org/mailman/listinfo.cgi/users
> > > >
> > >
> > > >
> > >
> <mpi-test-64bit.tar.bz2>____________________________________________
> > > ___
> > >
> > > > users mailing list
> > > > [11]users_at_[hidden]
> > > > [12]http://www.open-mpi.org/mailman/listinfo.cgi/users
> > > --
> > > Jeff Squyres
> > > [13]jsquyres_at_[hidden]
> > > For corporate legal information go to:
> > > [14]http://www.cisco.com/web/about/doing_business/legal/cri/
> > > _______________________________________________
> > > users mailing list
> > > [15]users_at_[hidden]
> > > [16]http://www.open-mpi.org/mailman/listinfo.cgi/users
> > >
> > > References
> > >
> > > 1. mailto:jsquyres_at_[hidden]
> > > 2. http://www.open-mpi.org/community/help/
> > > 3. mailto:jimparker96313_at_[hidden]
> > > 4. mailto:jsquyres_at_[hidden]
> > > 5. mailto:jimparker96313_at_[hidden]
> > > 6.
> http://wiki.chem.vu.nl/dirac/index.php/How_to_build_MPI_libraries_for_64-bit_integers
> > > 7. mailto:jsquyres_at_[hidden]
> > > 8. http://www.cisco.com/web/about/doing_business/legal/cri/
> > > 9. mailto:users_at_[hidden]
> > > 10. http://www.open-mpi.org/mailman/listinfo.cgi/users
> > > 11. mailto:users_at_[hidden]
> > > 12. http://www.open-mpi.org/mailman/listinfo.cgi/users
> > > 13. mailto:jsquyres_at_[hidden]
> > > 14. http://www.cisco.com/web/about/doing_business/legal/cri/
> > > 15. mailto:users_at_[hidden]
> > > 16. http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> >
> > > _______________________________________________
> > > users mailing list
> > > users_at_[hidden]
> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> >
> >
> >
> >
> <openmpi-1.6.5.config.tar.gz>_______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>