Re: Using multi-processor for model_free -- October 06, 2016 - 00:10

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
> <javascript:_e(%7B%7D,'cvml','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
> > <javascript:_e(%7B%7D,'cvml','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_processor_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
> > > <javascript:_e(%7B%7D,'cvml','edward@xxxxxxxxxxxxx');>> wrote:
> > >
> > > > On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx
> > > > <javascript:_e(%7B%7D,'cvml','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