Re: Using multi-processor for model_free -- October 06, 2016 - 23:16

Hi Troels and Edward,

I was able to get relax working on a multi-processor platform finally. I
tried using the mpich instead of openmpi.
module load mpi/mpich-x86_64
mpirun -np 7 ./relax --multi='mpi4py'

and it loaded up relax with 1 master and 7 slaves. I don't exactly
understand why openmpi doesn't work. I have gotten both from the package
list, and installed them directly., and I have mpi4py for both mpich and
openmpi (I also got these from the package list and installed directly),
but this seemed to finally get it to work.

Sincerely,
Sam



On Wed, Oct 5, 2016 at 3:15 PM, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>
wrote:

> Ok. Thank you both by the way. You guys have been incredibly helpful, and
> sorry I bothered you guys so much. I'll still attempt to troubleshoot this
> and potentially fix it. When I find out what the solution is, I will let
> you guys know.
> Thank you.
>
> Sincerely,
> Sam
>
> On Wed, Oct 5, 2016 at 3:10 PM, Troels Emtekær Linnet <
> tlinnet@xxxxxxxxxxxxx> wrote:
>
> > I think there is nothing more to do here.
> >
> > Call the nearest computer wizard,
> > and give a round of beer.
> >
> > Best Troels
> >
> >
> > Den onsdag den 5. oktober 2016 skrev Mahdi, Sam <
> > sam.mahdi.846@xxxxxxxxxxx>:
> >
> > > But i already have mpi4py installed from the package list.
> > >
> > > On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet <
> > > tlinnet@xxxxxxxxxxxxx> wrote:
> > >
> > > > Hi Sam.
> > > >
> > > > Akk you PI to run this:
> > > >
> > > > sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
> > > > install mpi4py'
> > > > or
> > > > sudo -i
> > > > setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc
> > > > pip install mpi4py
> > > >
> > > >
> > > > Where '/usr/lib64/openmpi-1.10/bin/mpicc' should be the path to mpicc.
> > > >
> > > > Find the path with:
> > > > which mpicc
> > > >
> > > > Look here:
> > > > https://mpi4py.scipy.org/docs/usrman/install.html
> > > >
> > > > Under:
> > > > "Using pip or easy_install"
> > > >
> > > > You need to tell where the mpicc is with the environment, so mpi4py can
> > > > be compiled correctly.
> > > >
> > > > Note: Setting the environment in BASH and TCSH is different!
> > > >
> > > > BASH:
> > > > sudo -- sh -c 'env MPICC=/usr/lib64/openmpi-1.10/bin/mpicc; pip
> > > > install mpi4py'
> > > >
> > > > TCSH:
> > > > sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
> > > > install mpi4py'
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > 2016-10-05 23:31 GMT+02:00 Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>:
> > > >
> > > > > Hi Edward,
> > > > >
> > > > > I installed mpi4py and OpenMPI both from the fedora packages. I had a
> > > > > mpi4py that I downloaded via the site itself, and compiled it, but I 
> > > > > wasn't
> > > > > able to install it so I deleted it. The command
> > > > > mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI;
> > > > > print('Mpi4py %s process %d of %d on %s.'%(mpi4py._version_,MPI>COM
> > > > > M_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_process
> > > > > or_name()))"
> > > > >
> > > > > gave no output. These are the mpi packages I have installed
> > > > > Openmpi:
> > > > > openmpi-1.7.3-1.fc.20(64-bit)
> > > > > openmpi-devel-1.7.3-1.fc20(64bit)
> > > > > pypar-openmpi-2.1.5_108_3.fc.20(64bit)
> > > > > python3-mpi4py-1.3.1-1.fc20(64bit)
> > > > >
> > > > > Mpi4py
> > > > > mpi4py-common-1.3.1-1.fc20
> > > > > mpi4py-mpich-1.3.1-1.fc20
> > > > > mpi4py-openmpi-1.3.1-1.fc20
> > > > > python3-mpi4py-mpich-1.3.1-1.fc20
> > > > > python3-mpi4py-openmpi-1.3.1-1.fc20
> > > > >
> > > > > Could you reccomend which packages specifically I should install? I
> > > > > could just tell my PI to remove all the openmpi and mpi4py programs, and
> > > > > download the specific 2 that do work (if there is a problem with having
> > > > > different mpi's and mpi4py's)
> > > > >
> > > > > All of these were installed from the fedora packages themselves. Also
> > > > > the locate mpi list gave me a massive output (I assume this is because I
> > > > > have 5 programs that use mpi)
> > > > > Sincerely,
> > > > > Sam
> > > > >
> > > > > On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne <
> > > > > edward@xxxxxxxxxxxxx> wrote:
> > > > >
> > > > > > On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>
> > > > > > wrote:
> > > > > > > Hi Troels,
> > > > > > >
> > > > > > > The mpirun --np 2 gave no output, so I had to abort the command,
> > > > > > but here is
> > > > > > > the output.
> > > > > > > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> > > > > > > 1.3.1
> > > > > > > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> > > > > > > MPI.COMM_WORLD.Get_rank()"
> > > > > > > ^Ccrowlab: [~]>
> > > > > >
> > > > > > Hi Sam,
> > > > > >
> > > > > > This result I'm pretty sure shows that mpi4py is not functioning
> > > > > > correctly - i.e. there is an installation problem.  This is what you
> > > > > > should see:
> > > > > >
> > > > > > [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import
> > > > > > MPI;
> > > > > > print MPI.COMM_WORLD.Get_rank()"
> > > > > > 0
> > > > > > 1
> > > > > > [edward@localhost ~]$
> > > > > >
> > > > > > Note the printout of 0 and 1.  Maybe try the following:
> > > > > >
> > > > > > [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
> > > > > > mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
> > > > > > %(mpi4py.__version__,
> > > > > > MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
> > > > > > MPI.Get_processor_name()))"
> > > > > > Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
> > > > > > Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
> > > > > > Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
> > > > > > Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
> > > > > > Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
> > > > > > [edward@localhost ~]$
> > > > > >
> > > > > > If you don't see a printout here, then clearly mpi4py and OpenMPI are
> > > > > > not working together correctly.  Without a printout, your mpi4py is
> > > > > > FUBAR.  Are you using the default OpenMPI and mpi4py packages form
> > > > > > fedora, and you don't have any backports or other non-standard sources
> > > > > > set up for your RPMs?  Do you have any user installed MPI or mpi4py
> > > > > > software around?  If you type:
> > > > > >
> > > > > > $ locate mpi
> > > > > >
> > > > > > What do you see?  For me this is pretty clearly an installation
> > > > > > problem.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward