[mpich-discuss] Parallel jobs
Gus Correa
gus at ldeo.columbia.edu
Mon Nov 29 13:39:07 CST 2010
Sorry, I have no idea of what visual windows is or does.
Sometimes GUIs are harder to handle than just plain scripts.
Somewhere the GUI you send may have a script to launch the job,
and hopefully there is a way to edit the script, or add stuff
in the drop down menus and forms, and insert
the suggested option in the mpirun command line.
I would guess ABINIT, which seems to be all Linux/Gnu/GPL based,
should work without the GUI (MAPS ?),
may allow you to just launch the job using the mpirun command
directly, which may be less of a hassle than the GUI,
but this is just a guess.
The ABINIT site seems to be down, but check what the Wikipedia
says about it. There seems to be another GUI for Linux (nanonub):
http://en.wikipedia.org/wiki/ABINIT
You may be better off asking specific questions to the ABINIT support
lists.
Good luck.
Gus Correa
Talla wrote:
> Hello;
> Thank you for the detailed information, however I am using visual
> windows software with the code impeded in it, so I am not using the
> commands directly. so I am wondering if there is a way to add the
> stdin/stdout script? and save them some where in the cluster
> I am attaching a screen shot of the software I am using just to let you
> know what I am talking about!
>
>
> On Mon, Nov 29, 2010 at 9:28 PM, Gus Correa <gus at ldeo.columbia.edu
> <mailto:gus at ldeo.columbia.edu>> wrote:
>
> Hi Talla
>
> It is no rocket science, just add them to your mpirun command.
> Say:
>
> Old command (whatever you have there):
> mpirun -n 16 my_program
>
> Modified command (whatever you had there with "-s all" added):
> mpirun -s all -n 16 my_program
>
> I am not even sure if it will work, but it is worth giving it a try,
> as all processes seem to be trying to read from stdin,
> for which in MPICH2 seems to require the specific flag '-s all'.
>
> ***
>
> In a different key,
> looking at your messages, and the paths that you refer to,
> it seems to me that you may be mixing MPICH2 and OpenMPI.
> At least the test program you mention this:
>
>
> > I tested the cluster using the following command:
> > /opt/openmpi/bin/mpirun -nolocal np 16 -machinefile machines
> > /opt/mpi-test/bin/mpi-ring
>
>
> In particular, the mpirun commands of each MPI are quite different,
> and to some extent so is the hardware support.
> This mixing is a very common source of frustration.
>
> Both MPICH2 and OpenMPI follow the MPI standard.
> However, they are different beasts,
> and mixing them will not work at all.
>
> Stick to one of them only, for compilation (say mpicc or mpif90)
> and to run the program (mpirun/mpiexec).
> In doubt, use full path names for all (mpicc, mpif90, mpirun, etc).
> This mailing list is the support list for MPICH2:
> http://www.mcs.anl.gov/research/projects/mpich2/
>
> For OpenMPI you need to look elsewhere:
> http://www.open-mpi.org/
>
> You may want to check first how your (ABINIT) computational Chemistry
> program was compiled.
> Computational Chemistry is *not* my league, I have no idea of what the
> heck ABINIT does, probably some many-body Schroedinger equation, and
> I forgot Quantum Mechanics a while ago.
> Don't ask me about it.
>
> If your ABINIT came pre-compiled you need to stick with
> whatever flavor (and even version) of MPI that they used.
> If you compiled it yourself, you need to stick to the MPI flavor and
> version associated to the *same* MPI compiler wrapper you used to
> compile it.
> I.e. mpicc or mpif90 *and* mpirun/mpiexec must be from the same MPI
> flavor and version.
> Take a look at the Makefiles, perhaps at the configure scripts,
> they may give a hint.
>
> Good luck.
>
>
> My two cents,
> Gus Correa
>
> Talla wrote:
>
> Hello Gus,
> Thank you for pointing me to this error, but I am new to Linux
> world so I am wondering if you have a ready script or commands
> to add stdin flags to mpirun?
> Thanks
>
> On Mon, Nov 29, 2010 at 7:34 PM, Gus Correa
> <gus at ldeo.columbia.edu <mailto:gus at ldeo.columbia.edu>
> <mailto:gus at ldeo.columbia.edu <mailto:gus at ldeo.columbia.edu>>>
> wrote:
>
> Hi Talla
>
> It sounds like all processes are trying to read from stdin,
> right?
> Stdin/stdout are not guaranteed to be available to all processes.
>
> Have you tried to add these flags in your mpiexec/mpirun
> command line: "-s all" ?
> Check the meaning with "man mpiexec".
>
> My two cents,
> Gus Correa
>
> Talla wrote:
>
> Hello,
>
> this issue is consuming all my time with no luck. I can
> submit
> any job without any error message *BUT ONLY* when I am using
> *one* CPU, when I am using more than one CPU, I got the error
> message : " *forrtl: severe (24): end-of-file during
> read, unit
> 5, file stdin* ". I got this error line repeated as many
> as the
> number of CPU's I am using.
>
> Which mean that the other nodes are not doing any job
> here. So
> if you can help me to link the other nodes so I can take
> advantage of all the nodes.
> I have 8 PC and each one has 2 CPU (in total I have 16 CPU).
>
> I tested the cluster using the following command:
> /opt/openmpi/bin/mpirun -nolocal np 16 -machinefile machines
> /opt/mpi-test/bin/mpi-ring
>
> and all the nodes can send and receive data like a charm.
>
> Just to mention that I have Rocks Clustering software
> with open
> centOS.
>
> The code I am using is called ABINIT and it is impeded as a
> plugin in a visual software called MAPS.
>
> Your help is really appreciated.
>
>
>
>
>
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