Robert Nicholas (email@example.com), Earth and Environmental Systems Institute, Penn State University
updated 1 April 2019
NOTE: This guide documents the ICS-ACI 3.1 system, which was brought online in late May 2017. ICS-ACI 1.0 has been retired and is no longer accessible.
SCRiM’s resources with ICS-ACI comprise a computing allocation of 400 “standard-memory” cores and a 400 TB storage allocation, as codified in a 5-year service level agreement (SLA) that ends on 31 January 2020. Services available to SCRiM researchers under this agreement include:
openqueue up to 100 cores (total, not per job) with a maximum wall clock time of 48 hours and a maximum of 100 queued jobs (these jobs may be preempted at any time)
/gpfs/group/kzk10/default, shared with all other SCRiM users (this is a change from ACI 1.0)
/gpfs/scratch/<username>; this storage resource is intended for temporary files and is not backed up; files residing here for more than 30 days may be automatically deleted
scpfrom the command line or a graphical SFTP client (note that transfers to/from woju should use hostname
woju-rn.scrim.psu.eduto bypass a currently-unresolved network issue)
These systems are managed separately from other SCRiM computing resources (woju, mizuna, napa, RStudio Server, and the web-based download server), which are hosted by the Penn State Meteorology Computing Facility and documented here.
The above resources are available to all SCRiM researchers, including non-PSU SCRiM participants. Contact SCRiM Managing Director Robert Nicholas (firstname.lastname@example.org) for details on how to gain access.
qsub -A kzk10_a_g_sc_default <yourrunscript>
#PBS –A kzk10_a_g_sc_defaultto your run script
modules system controls which software packages are available in your current environement.
module avail <keyword>
module load <modulename>
module show <modulename>
module load gcc/5.3.1(system default is version 4.7.7)
In addition to the systemwide modules, SCRiM also has its own custom software stack containing additional modules. You can make these modules available with the following command:
module use /gpfs/group/kzk10/default/sw/modules
Specific software packages can be loaded as follows:
module load anaconda2(Python 2.7.x) or
module load anaconda3(Python 3.x)
module load git-cola/2.10
module load ImageMagick/7.0.5-2
module load julia/0.5.1
module load libgd/2.2.4
module load ncl_ncarg/6.3.0_gcc447
module load ncview/2.1.7
module load panoply/4.7
module load perl/5.24.1
module load pycharm/2016.3.3
module load rstudio/0.98.1103
module load uvcdat/2.4.1
Note that CDO, GDAL, gnuplot, TeX/LaTeX, NCL, NCO, and Pandoc are also available and are being provided as part of the two Anaconda distributions (see above).
At present, there is no way to obtain allocation usage information from the command line as there was on ACI 1.0.
The current state of the batch queue may be obtained using the
showq command. To show the queue state for just the SCRiM allocation, use:
showq –w acct=kzk10_a_g_sc_default
To show the status of the open queue, use:
showq –w acct=open
You can obtain professional support for ICS-ACI resources in the following ways: