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You can get into the LCLS photon computing system in the NEH by ssh'ing to:

psexport.slac.stanford.edu

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Each node in the interactive pools has one single user Matlab license.

Batch Farm

Login first to to pslogin (from SLAC) or psexport (from anywhere). From there you can submit a job with the following command:

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• 12 cores (24 with Hyperthreading), Xeon X5675, 24GB memory, 500GB disk, 1Gb/sQDR IB

Running OpenMPI Jobs in the PCDS Batch Farm

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Your environment should be set up to use this version (unless you have used RedHat's mpi-selector script, or your login scripts, to override the default). You can check to see if your your PATH is is correct by issuing the command  which mpirun . Currently, this should return : /usr/lib64/openmpi/1.4-gcc/bin/mpirun  . Future updates to the MPI version may change the exact details of this path. 

In addition, your your LD_LIBRARY_PATH should ;should include : /usr/lib64/openmpi/1.4-gcc/lib  (or something similar).

For notes on compiling examples; please see:

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bsub -q psfehq -a mympi -n 2412 -R "span[hosts=1]" -o ~/output/%J.out ~/bin/hello

Will submit an OpenMPI job (-a mympi) requesting 2412 processors (-n 2412) spanned all on one host (-R "span\[hosts=1\]") to the psfehq batch queue (-q psfehq).

Data Storage

LCLS provides space for all your experiment's data at no cost for you. This includes the measurements as well as the data derived data from your analysis software. Your data are available as XTC files or, on demand, as HDF5 files.

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After one year, your data files are removed from disk. The XTC and HDF5 files remain stored on tape for up to 10 years. LCLS may restore your data from tape back to disk for you to access. Send an email to pcds-help@slac.stanford.edu to have your data restored to disk. Restoring the data to disk more than once will require the approval of the LCLS management.

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The web interface also allows you to generate file lists that can be fed into bbcp to export your data from SLAC to your home institution. You can use psexport for for copying your data. See the Data Exportation Using BBCP page for more information.

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