[GE users] Startup times and other issues with 6.0u3
reuti at staff.uni-marburg.de
Sat Mar 19 15:40:57 GMT 2005
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Quoting Brian R Smith <brian at cypher.acomp.usf.edu>:
> shell /bin/csh
> shell_start_mode posix_compliant
> Thats how we run it on our other machines and it seems to work just fine.
> Figured I didn't have to change anything.
thx for the all the infos. If all of your jobs are using csh it's perfect okay
to let it stay at this setting.
> The PE mpich-vasp has all traces of tight integration removed. I was using
> it for testing Vasp. However, I got vasp to work with tight-integration so
> that queue is depricated.
Okay, I saw it only in your definition and thought about the reason having a
special mpich for vasp.
> As for MM5, it's compiled with the PGI compilers. That said, it runs
> beautifully outside of SGE on the same system (mpirun). It is only under SGE
> that the processes come to a crawl. If you want more info on it, let me
> know. I just don't see how that would help.
> my mpirun command for that is simply
> $MPIR_PATH/mpirun -np $NSLOTS -machinefile $TMPDIR/machines mm5.mpp
> mm5.mpp does some small writes to the NFS mount that it runs out of. During
> the span of about 3 minutes, it will dump approximately 10MB of data into its
> current working directory. I have load tested this outside of SGE and found
> that the NFS writes are not the cause of any slowdown.
It's not so much. Requires MM5 a shared scratch space or could it also run by
using the created $TMPDIR on the nodes?
> MPICH runs over a dedicated GigE connection that's devoted to 1) SGE 2)
> Message Passing 3) PVFS2. The other network (100mb) handles NFS, NIS, etc.
> The GigE network is a Cisco Catalyst series GigE switch with Intel GigE
> controllers on the nodes. We are not using Jumbo frames on that network
> either as we've yet to get any testing done on the benefits of doing so.
So you set up a host_aliases file to seperate the traffic - is `hostname`
giving the "external" or "internal" name of the machine? You replaced
"MPI_HOST=`hostname`" in your mpirun with a mapping to your GigE name if
Just for interest: how many nodes are you using in your cluster for PVFS2
Cheers - Reuti
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