Gabriel,
I have had no luck with this. Where is this "preamble" documented?
I did several web searches...
I tried the JDD below, where mpihello is a simple MPI job that prints
out the MPI rank of each host. I get its output, but no output
from the "preamble". What am I missing?
<job>
<executable>mpihello</executable>
<directory>${GLOBUS_USER_HOME}/mpitest</directory>
<stdout>${GLOBUS_USER_HOME}/doit.stdout</stdout>
<stderr>${GLOBUS_USER_HOME}/doit.stderr</stderr>
<count>8</count>
<jobType>mpi</jobType>
<extensions>
<preamble>
echo "Running PREAMBLE"
</preamble>
</extensions>
</job>
On 6.05.08, Gabriel Mateescu wrote:
> Hello,
>
> It is not hard to accomplish that.
> Think of it this way: what you want to do is
> kind of a "preamble", i.e., a set of commands to
> precede the job execution.
>
> This can be accomplished using the Extensions
> elements of the jobs description.
>
> For example, assume you want to load a certain
> module, which will set things such as the path
> to the MPI libraries.
>
> Then you job description will look like this
>
> <job>
> <executable>/path/to/mpi/program</executable>
> ...
> <extensions>
> <preamble>
> module load mpi-intel
> cd $HOME
> </preamble>
> </extensions>
> ...
> </job>
>
>
> The changes required to the LRMS adapter are
> not difficult to make. I will post the changes for
> SGE and PBS.
>
>
> Gabriel
>
>
> On May 5, 2008, at 5:08 PM, Steve White wrote:
> >Hi,
> >
> >We want to execute a script in a cluster job submission via
> >globusrun-ws,
> >but it should run exactly once, after stage-in, before processes are
> >started on the compute nodes.
> >
> >The purpose is to do some pre-run housekeeping in the user's home
> >directory.
> >
> >We thought we could do this by submitting a small script in the JDD
> >executable section, but it now appears that (for MPI jobs anyway)
> >this is
> >executed on each compute node (as if it were the argument to mpirun
> >in a
> >conventional cluster job submission).
> >
> >So we are in a sense trying to put something between the Job
> >Description
> >document and the computation processes.
> >
> >This seems like a very natural thing to do: in conventional batch
> >systems
> >it is done in a batch script. One can think of messy solutions where
> >the script detects whether it has been run before.... but that
> >can't be
> >the right way.
> >
> >What is the right way to do this in a Globus job submission?
> >
> >Thanks!
> >
> >- - - - - - - - - - - - - - - - - - - - - -
> >- - -
> >Steve White +49(331)
> >7499-202
> >e-Science / AstroGrid-D Zi. 35
> >Bg. 20
> >- - - - - - - - - - - - - - - - - - - - - -
> >- - -
> >Astrophysikalisches Institut Potsdam (AIP)
> >An der Sternwarte 16, D-14482 Potsdam
> >
> >Vorstand: Prof. Dr. Matthias Steinmetz, Peter A. Stolz
> >
> >Stiftung privaten Rechts, Stiftungsverzeichnis Brandenburg: III/
> >7-71-026
> >- - - - - - - - - - - - - - - - - - - - - -
> >- - -
> >
>
--
- - - - - - - - - - - - - - - - - - - - - - - - -
Steve White +49(331)7499-202
e-Science / AstroGrid-D Zi. 35 Bg. 20
- - - - - - - - - - - - - - - - - - - - - - - - -
Astrophysikalisches Institut Potsdam (AIP)
An der Sternwarte 16, D-14482 Potsdam
Vorstand: Prof. Dr. Matthias Steinmetz, Peter A. Stolz
Stiftung privaten Rechts, Stiftungsverzeichnis Brandenburg: III/7-71-026
- - - - - - - - - - - - - - - - - - - - - - - - -
