[mpich-discuss] Parallel jobs

[Talla]

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> 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>> 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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