[mpich-discuss] building 32 bit shmem on 64 bit linux system

[Anthony Chan]

The unresolved symbols from libparpack looks like fortran symbols.

You need to recompile arpack with mpicc/mpif77/mpif90 from ch_shmem
and relink arpack with your code.

A.Chan

----- "Daniel Fetchinson" <fetchinson at googlemail.com> wrote:

> No.
> 
> I was actually never recompiling it, always was using the same 32-bit
> archive and it was always working on a number of platforms (intel
> core
> 2 duo, intel xeon (8 cores), etc) which made me believe I don't have
> to recompile it.
> 
> Only on this new intel core 2 quad it doesn't seem to work.
> 
> Do you think it's possible that just because the platform on which it
> was compiled is slightly different from the current one (I'm not even
> sure intel core 2 duo is a different platform from intel core 2 quad)
> the linker would complain about undefined references? I thought it
> would find the references in any case, at worst the program would
> segfault.
> 
> Daniel
> 
> 
> > Did you also recompile the parallel arpack library with the newly
> installed
> > mpicc/mpif77?
> >
> > Rajeev
> 
> >>
> >> I started the whole thing from scratch and deleted all build
> >> directories, unpacked mpich and now I'm pretty certain I've got a
> >> ch_shmem configured, built, installed.
> >>
> >> But there is another problem: I use the parallel arpack library in
> my
> >> program and while linking the whole thing together mpicc complains
> >> about undefined references:
> >>
> >> libs/libparpack.a(pznaupd.o): In function `pznaupd_':
> >> pznaupd.f:(.text+0x3db): undefined reference to `mpi_comm_rank__'
> >> libs/libparpack.a(pznaupd.o):(.data+0x0): undefined reference
> >> to `mpi_dup_fn__'
> >> libs/libparpack.a(pznaupd.o):(.data+0x4): undefined reference to
> >> `mpi_null_delete_fn__'
> >> libs/libparpack.a(pznaupd.o):(.data+0x8): undefined reference to
> >> `mpi_null_copy_fn__'
> >> libs/libparpack.a(pivout.o): In function `pivout_':
> >> pivout.f:(.text+0x16): undefined reference to `mpi_comm_rank__'
> >> libs/libparpack.a(pivout.o):(.data+0x0): undefined reference
> >> to `mpi_dup_fn__'
> >> libs/libparpack.a(pivout.o):(.data+0x4): undefined reference to
> >> `mpi_null_delete_fn__'
> >> libs/libparpack.a(pivout.o):(.data+0x8): undefined reference to
> >> `mpi_null_copy_fn__'
> >>
> >> etc. etc..............
> >>
> >> Although /home/fetchinson/mpich32shmem/lib/libmpich.a is given to
> >> mpicc for linking along with all other object files where
> >> /home/fetchinson/mpich32shmem is the installation directory of
> mpich
> >> (the one given to ./configure via --prefix). So it seems I have
> some
> >> linking problems still.
> >>
> >> By the way, the only file that is needed to be given to mpicc for
> >> static linking is libmpich.a, right? What is strange is that on
> >> another machine the same Makefile works with the same installation
> >> directory for mpich.
> >>
> >> Cheers,
> >> Daniel
> >>
> >>
> >>
> >>
> >> > In the outputs of the configure and make steps, does it
> >> look like it is
> >> > building ch_p4 or ch_shmem?
> >> >
> >> > Rajeev
> >> >>
> >> >> Out of desperation I looked at the output of
> >> >>
> >> >> strings my_test_program
> >> >>
> >> >> where my_test_program was compiled using mpicc (using
> >> absolute paths)
> >> >> from the 32-bit shmem mpi library. Strangely, ch_p4 appears in
> the
> >> >> output several times while ch_shmem doesn't. On another
> >> machine where
> >> >> I'm successfully compiling 32-bit shmem executables the output
> of
> >> >> 'strings my_test_program' only contains ch_shmem and not ch_p4.
> >> >>
> >> >> So there must be something wrong with my mpicc, although I
> can't
> >> >> imagine what, I never compiled to ch_p4.
> >> >>
> >> >> Thanks for the advice guys, there seems to be progress :)
> >> >> Daniel
> >> >>
> >> >>
> >> >> > Did you do a "make install" after "make" ?  If not, the
> >> >> install directory
> >> >> > may still have an older installation of mpich-1 which
> >> could be ch_p4
> >> >> > and not ch_shmem that you need.
> >> >> >
> >> >> > A.Chan
> >> >> >
> >> >> > ----- "Daniel Fetchinson" <fetchinson at googlemail.com> wrote:
> >> >> >
> >> >> >> > It must be the mpirun then. Make sure you use the
> >> mpirun from the
> >> >> >> same
> >> >> >> > build. Give the full path if necessary.
> >> >> >> >
> >> >> >> > Rajeev
> >> >> >>
> >> >> >> Thanks, but there is only one installation of mpi on the
> >> >> machine and
> >> >> >> that installation is the one I keep compiling. So even
> >> if it wanted
> >> >> >> to
> >> >> >> execute the wrong mpicc/mpirun/etc it couldn't because
> >> >> there is only
> >> >> >> 1
> >> >> >> copy at any given time.
> >> >> >>
> >> >> >> Nevertheless I recompiled now mpi as well as my program
> >> and still I
> >> >> >> get the same error:
> >> >> >>
> >> >> >> 0 - MPI_INIT : MPIRUN chose the wrong device ch_shmem;
> >> >> program needs
> >> >> >> device ch_p4
> >> >> >> /home/fetchinson/mpich32shmem/bin/mpirun.ch_shmem: line
> >> 91: 21976
> >> >> >> Segmentation fault      /home/fetchinson/test "testinput"
> >> >> >>
> >> >> >> Any ideas?
> >> >> >> Daniel
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> >> > Did you recompile the program? Make sure you use the
> mpicc
> >> >> >> >> from this
> >> >> >> >> > build and not some other mpicc from another directory.
> Give
> >> >> >> >> the full
> >> >> >> >> > path if necessary.
> >> >> >> >> >
> >> >> >> >> > Rajeev
> >> >> >> >>
> >> >> >> >> Yes, I did recompile the program using mpicc from the
> newly
> >> >> >> >> built mpi library. Actually, there is only one mpicc on
> the
> >> >> >> >> whole machine.
> >> >> >> >>
> >> >> >> >> Cheers,
> >> >> >> >> Daniel
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> >> Actually, I spoke a bit too soon. Configure, make,
> make
> >> >> >> >> install all
> >> >> >> >> >> work but the code still doesn't run, saying:
> >> >> >> >> >>
> >> >> >> >> >> 0 - MPI_INIT : MPIRUN chose the wrong device ch_shmem;
> >> >> >> >> program needs
> >> >> >> >> >> device ch_p4
> >> >> >> >> >> /home/fetchinson/mpi32shmem/bin/mpirun.ch_shmem:
> >> >> line 91: 17761
> >> >> >> >> >> Segmentation fault      /home/fetchinson/test
> "testinput"
> >> >> >> >> >>
> >> >> >> >> >> The exact same code runs on another machine where
> >> >> someone else
> >> >> >> >> >> installed a 32-bit shmem mpich1 library, I'm trying to
> do
> >> >> >> >> the same on
> >> >> >> >> >> a different machine now. It's an intel quad core
> >> so I suppose
> >> >> >> the
> >> >> >> >> >> shmem device should work. The configure options I used
> for
> >> >> >> >> compiling
> >> >> >> >> >> are
> >> >> >> >> >>
> >> >> >> >> >> export CC='gcc -m32'
> >> >> >> >> >> export F77='g77 -m32'
> >> >> >> >> >> ./configure  --with-device=ch_shmem
> >> >> >> >> >>
> >> >> >> >> >> Do I need to specify the --with-arch option? Going
> through
> >> >> >> >> the list
> >> >> >> >> >> of available --with-arch options I'm not sure
> >> what I need for
> >> >> >> an
> >> >> >> >> >> Intel(R)
> >> >> >> >> >> Core(TM)2 Quad CPU Q6600 @ 2.40GHz.
> >> >> >> >> >>
> >> >> >> >> >> What am I doing wrong?
> >> >> >> >> >>
> >> >> >> >> >> Cheers,
> >> >> >> >> >> Daniel
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> > Thanks Anthony, that worked!
> >> >> >> >> >> >
> >> >> >> >> >> > Concerning MPICH2: I'm not in a position to change
> the
> >> >> >> >> >> communication
> >> >> >> >> >> > routines in the code  I use so this would only
> >> be an option
> >> >> >> >> >> if MPICH2
> >> >> >> >> >> > is fully backward compatible with MPICH1. Is
> >> this the case?
> >> >> >> >> >> Can I just
> >> >> >> >> >> > start using MPICH2 without changing anything in
> >> the code if
> >> >> >> >> >> it works
> >> >> >> >> >> > with MPICH1?
> >> >> >> >> >> >
> >> >> >> >> >> > Cheers,
> >> >> >> >> >> > Daniel
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >> Since you are using MPICH-1, you can try setting
> >> >> CC, F77 and
> >> >> >> F90
> >> >> >> >> >> >>
> >> >> >> >> >> >> CC="gcc -m32"
> >> >> >> >> >> >> F77="g77 -m32"
> >> >> >> >> >> >> ....
> >> >> >> >> >> >>
> >> >> >> >> >> >> BTW, can you use MPICH2 instead ?  We have
> >> shifted all our
> >> >> >> >> >> >> development effort to MPICH2 which is more robust
> than
> >> >> >> >> >> MPICH-1.  If
> >> >> >> >> >> >> you are using MPICH2, setting CFLAGS and FFLAGS
> should
> >> >> >> >> >> work, and you
> >> >> >> >> >> >> can use nemesis which shared memory for intranode
> >> >> >> communication.
> >> >> >> >> >> >>
> >> >> >> >> >> >> A.Chan
> >> >> >> >> >> >>
> >> >> >> >> >> >> ----- "Daniel Fetchinson"
> >> >> <fetchinson at googlemail.com> wrote:
> >> >> >> >> >> >>
> >> >> >> >> >> >>> Hi folks,
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> I'd like to build the 32-bit shmem mpi library
> because
> >> >> >> >> >> the code I'll
> >> >> >> >> >> >>> use with mpi only works in 32-bit because of some
> >> >> >> >> 32-bit specific
> >> >> >> >> >> >>> assembly code. The machine is a 64-bit machine with
> a
> >> >> >> >> >> 64-bit linux
> >> >> >> >> >> >>> distribution (suse).
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> I tried configuring mpich-1.2.7p1 in a number of
> ways:
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> ./configure --with-device=ch_shmem ./configure
> >> >> >> >> --with-arch=LINUX
> >> >> >> >> >> >>> --with-device=ch_shmem ./configure
> >> >> >> >> >> >>> --with-arch=LINUX32 --with-device=ch_shmem
> ./configure
> >> >> >> >> >> >>> --with-arch=i386 --with-device=ch_shmem
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> with and without setting the following environment
> >> >> >> >> variables (in
> >> >> >> >> >> >>> bash):
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> export CFLAGS=-m32
> >> >> >> >> >> >>> export FFLAGS=-m32
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> Configuring went all right but none of the above
> >> >> >> >> >> combinations worked
> >> >> >> >> >> >>> with 'make' unfortunately :( The error in 'make'
> is
> >> >> >> >> the following:
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> /home/fetchinson/mpich-1.2.7p1/bin/mpicc  -o
> overtake
> >> >> >> >> overtake.o
> >> >> >> >> >> >>> test.o
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/../../../../x86_64-suse
> >> >> >> >> >> -linux/bin/ld:
> >> >> >> >> >> >>> skipping incompatible
> >> >> >> >> >> /home/fetchinson/mpich-1.2.7p1/lib/libmpich.a
> >> >> >> >> >> >>> when searching for -lmpich
> >> >> >> >> >> >>>
> >> >> >> >> >>
> >> >> /usr/lib64/gcc/x86_64-suse-linux/4.2.1/../../../../x86_64-suse
> >> >> >> >> >> -linux/bin/ld:
> >> >> >> >> >> >>> cannot find -lmpich
> >> >> >> >> >> >>> collect2: ld returned 1 exit status
> >> >> >> >> >> >>> make[4]: *** [overtake] Error 1
> >> >> >> >> >> >>> make[3]: [linktest1] Error 2 (ignored) Could not
> link
> >> >> >> >> a C program
> >> >> >> >> >> >>> with MPI libraries
> >> >> >> >> >> >>> make[3]: *** [linktest1] Error 1
> >> >> >> >> >> >>> make[2]: *** [linktest] Error 2
> >> >> >> >> >> >>> make[1]: *** [mpi-lib-test] Error 2
> >> >> >> >> >> >>> make: *** [mpi] Error 2
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> Which makes me believe that I was not able to
> >> >> convince the
> >> >> >> >> >> >>> compiler/linker/etc that I really want everything
> in
> >> >> >> 32-bit.
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> What would be the correct way of compiling
> >> the whole mpi
> >> >> >> >> >> library to
> >> >> >> >> >> >>> 32-bit?
> >> >> >> >> >> >>>
> >> >> >> >> >> >>> Cheers,
> >> >> >> >> >> >>> Daniel
> >> >> >> >> >> >>
> >> >> >> >> >> >>
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > --
> >> >> >> >> >> > Psss, psss, put it down! -
> >> >> http://www.cafepress.com/putitdown
> >> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> Psss, psss, put it down! -
> >> http://www.cafepress.com/putitdown
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Psss, psss, put it down! -
> http://www.cafepress.com/putitdown
> >> >> >> >>
> >> >> >> >>
> >> >> >> >
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Psss, psss, put it down! -
> http://www.cafepress.com/putitdown
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >> --
> >> >> Psss, psss, put it down! - http://www.cafepress.com/putitdown
> >> >>
> >> >>
> >> >
> >> >
> >>
> >>
> >> --
> >> Psss, psss, put it down! - http://www.cafepress.com/putitdown
> >>
> >>
> >
> >
> 
> 
> -- 
> Psss, psss, put it down! - http://www.cafepress.com/putitdown