Tim,
i am not familiar with CUDA, but that might help
can you please
export nvml_enable=no
and then re-configure and rebuild Open MPI ?
i hope this will help you
Cheers,
Gilles
On 9/21/2017 3:04 PM, Tim Jim wrote:
Hello,
Apologies to bring up this old thread - I finally had a chance to try
again with openmpi but I am still have trouble getting it to run. I
downloaded version 3.0.0 hoping it would solve some of the problems
but on running mpicc for the previous test case, I am still getting an
undefined reference error. I did as you suggested and also configured
it to install without cuda using
./configure --without-cuda --prefix=/opt/openmpi/openmpi-3.0.0
and at the end of the summary, CUDA support shows 'no'. Unfortunately,
the error is still the same, and for some reason, mpicc still seems to
have referenced my cuda targets.
tjim@DESKTOP-TA3P0PS:~/Documents$ mpicc
/opt/mpi4py/mpi4py_src/demo/helloworld.c -o hello.bin
mpicc: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no
version information available (required by
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40)
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined reference
to `clGetPlatformInfo@OPENCL_1.0'
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined reference
to `clGetPlatformIDs@OPENCL_1.0'
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined reference
to `clGetDeviceInfo@OPENCL_1.0'
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined reference
to `clGetDeviceIDs@OPENCL_1.0'
collect2: error: ld returned 1 exit status
I also attempted to test mpirun, as suggested in the readme, however I
get the following problem:
tjim@DESKTOP-TA3P0PS:~/Documents$ mpirun
/opt/openmpi/openmpi-3.0.0_src/examples/hello_c.c
mpirun: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1:
no version information available (required by
/opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40)
--------------------------------------------------------------------------
Open MPI tried to fork a new process via the "execve" system call but
failed. Open MPI checks many things before attempting to launch a
child process, but nothing is perfect. This error may be indicative
of another problem on the target host, or even something as silly as
having specified a directory for your application. Your job will now
abort.
Local host: DESKTOP-TA3P0PS
Working dir: /home/tjim/Documents
Application name: /opt/openmpi/openmpi-3.0.0_src/examples/hello_c.c
Error: Exec format error
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun was unable to start the specified application as it encountered an
error:
Error code: 1
Error name: (null)
Node: DESKTOP-TA3P0PS
when attempting to start process rank 0.
--------------------------------------------------------------------------
4 total processes failed to start
[DESKTOP-TA3P0PS:15231] 3 more processes have sent help message
help-orte-odls-default.txt / execve error
[DESKTOP-TA3P0PS:15231] Set MCA parameter "orte_base_help_aggregate"
to 0 to see all help / error messages
Do you have any suggestions to what might have gone wrong on this
install? I'm not sure if this thread is still alive, so if you need a
refresh on the situation/any more info, please let me know.
Kind regards,
Tim
On 24 May 2017 at 09:12, Tim Jim <timothy.m....@gmail.com
<mailto:timothy.m....@gmail.com>> wrote:
Thanks for the thoughts, I'll give it a go. For reference, I have
installed it in the opt directory, as that is where I have kept my
installs currently. Will this be a problem when calling mpi from
other packages?
Thanks,
Tim
On 24 May 2017 06:30, "Reuti" <re...@staff.uni-marburg.de
<mailto:re...@staff.uni-marburg.de>> wrote:
Hi,
Am 23.05.2017 um 05:03 schrieb Tim Jim:
> Dear Reuti,
>
> Thanks for the reply. What options do I have to test whether
it has successfully built?
LIke before: can you compile and run mpihello.c this time –
all as ordinary user in case you installed the Open MPI into
something like $HOME/local/openmpi-2.1.1 and set paths
accordingly. There is no need to be root to install a personal
Open MPI version in your home directory.
-- Reuti
>
> Thanks and kind regards.
> Tim
>
> On 22 May 2017 at 19:39, Reuti <re...@staff.uni-marburg.de
<mailto:re...@staff.uni-marburg.de>> wrote:
> Hi,
>
> > Am 22.05.2017 um 07:22 schrieb Tim Jim
<timothy.m....@gmail.com <mailto:timothy.m....@gmail.com>>:
> >
> > Hello,
> >
> > Thanks for your message. I'm trying to get this to work on
a single
> > machine.
>
> Ok.
>
>
> > How might you suggest getting OpenMPIworking without
python and
> > CUDA?
>
> It looks like it's detected automatically. It should be
possible to disable it with the command line option:
>
> $ ./configure --without-cuda …
>
> At the end of the configure step out should liste some lines
like:
>
> Miscellaneous
> -----------------------
> CUDA support: no
>
> The mpi4py seems unrelated to the compilation of Open MPI
itself AFAICS.
>
>
> > I don't recall setting anything for either, as the only
command I had
> > run was "./configure --prefix=/opt/openmpi/openmpi-2.1.0"
- did it possibly
> > pick up the paths by accident?
> >
> > Regarding the lib directory, I checked that the path
physically exists.
> > Regarding the final part of the email, is it a problem
that 'undefined
> > reference' is appearing?
>
> Yes, it tries to resolve missing symbols and didn't succeed.
>
> -- Reuti
>
>
> >
> > Thanks and regards,
> > Tim
> >
> > On 22 May 2017 at 06:54, Reuti <re...@staff.uni-marburg.de
<mailto:re...@staff.uni-marburg.de>> wrote:
> >
> >> -----BEGIN PGP SIGNED MESSAGE-----
> >> Hash: SHA1
> >>
> >> Hi,
> >>
> >> Am 18.05.2017 um 07:44 schrieb Tim Jim:
> >>
> >>> Hello,
> >>>
> >>> I have been having some issues with trying to get
OpenMPI working with
> >> mpi4py. I've tried to break down my troubleshooting into
a few chunks
> >> below, and I believe that there are a few, distinct
issues that need
> >> solving.
> >>
> >> Are you speaking here of a single machine or a cluster?
> >>
> >>
> >>> Following some troubleshooting in the following link:
> >>> https://bitbucket.org/mpi4py/mpi4py/issues/69/building-
<https://bitbucket.org/mpi4py/mpi4py/issues/69/building->
> >> mpi4py-with-openmpi-gives-error
> >>> -the mpi4py folks have suggested it an issue that might
be better
> >> answered here.
> >>
> >> First approach would be to get Open MPI working, without
CUDA and Python
> >> being involved.
> >>
> >>
> >>> In summary, I have attempted to install OpenMPI on
Ubuntu 16.04 to the
> >> following prefix: /opt/openmpi-openmpi-2.1.0. I have also
manually added
> >> the following to my .bashrc:
> >>> export PATH="/opt/openmpi/openmpi-2.1.0/bin:$PATH"
> >>> MPI_DIR=/opt/openmpi/openmpi-2.1.0
> >>> export LD_LIBRARY_PATH=$MPI_DIR/lib:$LD_LIBRARY_PATH
> >>
> >> This looks fine, although I don't recall setting MPI_DIR
for Open MPI
> >> itself. It might be a necessity for mpi4py though.
> >>
> >> One pitfall might be that "lib" is sometimes being
created as "lib64" by
> >> `libtool`. I forgot the details when this is happening,
but it depends on
> >> the version of `libtool` being used.
> >>
> >>
> >>> I later became aware that Ubuntu may handle the
LD_LIBRARY_PATH
> >> differently
> >>
> >> I don't think that Ubuntu will do anything different than
any other Linux.
> >>
> >> Did you compile Open MPI on your own, or did you install
any repository?
> >>
> >> Are the CUDA application written by yourself or any
freely available
> >> applications?
> >>
> >> - -- Reuti
> >>
> >>
> >>> and instead added a new file containing the library path
> >> /opt/openmpi/openmpi-2.1.0/lib to
/etc/ld.so.conf.d/openmpi-2-1-0.conf,
> >> in the style of everything else in that directory.
> >>>
> >>> I tried to run "mpicc helloworld.c -o hello.bin" as a
test on a demo
> >> file (as instructed in the link) to check the
installation but I had
> >> permission issues, since it was installed win opt.
However, when I
> >> attempted to run the previous with sudo, or sudo -E, in
both cases, mpicc
> >> could not be found. (Perhaps this is a separate issue
with my sudo env)
> >>>
> >>> To check that mpicc actually works, I have copied
helloworld.c to a
> >> directory where I could execute mpicc without sudo. On
running the above
> >> command, I receive the following error:
> >>>
> >>> mpicc:
/usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: no
> >> version information available (required by
/opt/openmpi/openmpi-2.1.0/
> >> lib/libopen-pal.so.20)
> >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20:
undefined reference
> >> to `clGetPlatformInfo@OPENCL_1.0'
> >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20:
undefined reference
> >> to `clGetPlatformIDs@OPENCL_1.0'
> >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20:
undefined reference
> >> to `clGetDeviceInfo@OPENCL_1.0'
> >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20:
undefined reference
> >> to `clGetDeviceIDs@OPENCL_1.0'
> >>> collect2: error: ld returned 1 exit status
> >>>
> >>> I am unsure if I have an installation or permission
issues, and I'd be
> >> grateful if anyone can shed some light based on the
trials I've done so
> >> far. (I should add I also have a CUDA installation, which
I'd like to
> >> leverage too, if possible). I'm still fairly new to the
ins and outs of
> >> this, so I may have missed something obvious. Please let
me know if any
> >> other info is required.
> >>>
> >>> Many thanks and kind regards,
> >>> Tim
> >>>
> >>> --
> >>>
> >>> Timothy Jim
> >>> PhD Researcher in Aerospace
> >>> Creative Flow Research Division,
> >>> Institute of Fluid Science, Tohoku University
> >>> www.linkedin.com/in/timjim/
<http://www.linkedin.com/in/timjim/>
> >>> _______________________________________________
> >>> users mailing list
> >>> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>
> >>>
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
> >>
> >> -----BEGIN PGP SIGNATURE-----
> >> Comment: GPGTools - https://gpgtools.org
> >>
> >>
iEYEARECAAYFAlkiDKIACgkQo/GbGkBRnRou3wCeNztodNKHRxXBAp5ylz041OMP
> >> RIwAoLWkjzK1Qr8eWle/PdZGVUsvdN1M
> >> =R6up
> >> -----END PGP SIGNATURE-----
> >> _______________________________________________
> >> users mailing list
> >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>
> >>
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
> >>
> >
> >
> >
> > --
> >
> >
> > *Timothy Jim**PhD Researcher in Aerospace*
> >
> > Creative Flow Research Division,
> > Institute of Fluid Science, Tohoku University
> >
> > www.linkedin.com/in/timjim/
<http://www.linkedin.com/in/timjim/>
> > _______________________________________________
> > users mailing list
> > users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>
> > https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
>
> _______________________________________________
> users mailing list
> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>
> https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
>
>
>
> --
>
> Timothy Jim
> PhD Researcher in Aerospace
> Creative Flow Research Division,
> Institute of Fluid Science, Tohoku University
> www.linkedin.com/in/timjim/ <http://www.linkedin.com/in/timjim/>
> _______________________________________________
> users mailing list
> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org>
> https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
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