Tim,
do that in your shell, right before invoking configure.
export nvml_enable=no
./configure ...
make && make install
you can keep the --without-cuda flag (i think this is unrelated though)
Cheers,
Gilles
On 9/21/2017 3:54 PM, Tim Jim wrote:
Dear Gilles,
Thanks for the mail - where should I set export nvml_enable=no? Should
I reconfigure with default cuda support or keep the --without-cuda flag?
Kind regards,
Tim
On 21 September 2017 at 15:22, Gilles Gouaillardet <gil...@rist.or.jp
<mailto:gil...@rist.or.jp>> wrote:
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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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->
<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/>
<http://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>
<mailto: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>
<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>
<mailto: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>
<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/>
<http://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>
<mailto: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>
<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>
<mailto: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>
<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/>
<http://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>
<mailto: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>
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>>
_______________________________________________
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<mailto:users@lists.open-mpi.org>>
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<https://rfd.newmexicoconsortium.org/mailman/listinfo/users
<https://rfd.newmexicoconsortium.org/mailman/listinfo/users>>
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