 Thu Dec 13 17:33:54 2018, s prohira, parallel jobs on ruby, Software 
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On ruby, users get charged for the full node, even if you aren't using all 20 cores, so it's a pain if you want to run a bunch of serial jobs.
There is, however, a thing called the 'parallel command processor' (pcp) which is provided on ruby, (https://www.osc.edu/resources/available_software/software_list/parallel_command_processor)
that makes it very simple. |
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Tue Feb 26 19:07:40 2019, Lauren Ennesser, Valgrind command to suppress ROOT warnings,
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valgrind --suppressions=$ROOTSYS/etc/valgrind-root.supp ./myCode
If you use valgrind to identify potential memory leaks in your code, but use a lot of ROOT objects and functions, you'll notice that ROOTs
TObjects trigger a lot of "potential memory leak" warnings. This option will suppress many of those. More info at https://root-forum.cern.ch/t/valgrind-and-root/2ss8506 |
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Thu Sep 21 14:30:18 2017, Julie Rolla, Using/Running XF,
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Below I've attached a video with some information regarding running XF. Before you start, here's some important information you need to know.
In order to run XF: |
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Fri Nov 9 00:44:09 2018, Brian Clark, Transfer files from IceCube Data Warehouse to OSC,
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Brian had to move ~7 TB of data from the IceCube data warehouse to OSC.
To do this, he used the gridftp software. The advantage is that griftp is optimized for large file transfers, and will manage data transfer better
than something like scp or rsync. |
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Mon Mar 4 14:11:07 2019, Jorge Torres, Submitting arrays of jobs on OSC, Analysis
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PBS has the option of having arrays of jobs in case you want to easily submit multiple similar jobs. The only difference in them is the array
index, which you can use in your PBS script to run each task with a different set of input arguments, or any other operation that requires a unique index.
You need to add the following lines to your submitter file: |
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Sun Sep 17 20:05:29 2017, Spoorthi Nagasamudram, Some basic ,
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Tue Apr 25 10:35:43 2017, Jude Rajasekera, ShelfMC Parameter Space Scan, Software
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These scripts allow you to do thousands of ShelfMC runs while varying certain parameters of your choice. As is, the attenuation length, reflection,
ice thickness, firn depth, station depth is varied over certain rages; in total, the whole Parameter Space Scan does 5250 runs on a cluster like Ruby or
KingBee. The scripts and instructions are attached below. |
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Tue Apr 25 10:22:50 2017, Jude Rajasekera, ShelfMC Cluster Runs, Software
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Doing large runs of ShelfMC can be time intensive. However, if you have access to a computing cluster like Ruby or KingBee, where you are given a node
with multiple processors, ShelfMC runs can be optimized by utilizing all available processors on a node. The multithread_shelfmc.sh script automates
these runs for you. The script and instructions are attached below. |
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Thu May 11 14:38:10 2017, Sam Stafford, Sample OSC batch job setup, Software
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Batch jobs on OSC are initiated through the Portable Batch System (PBS). This is the recommended way to run stuff on OSC clusters.
Attached is a sample PBS script that copies files to temporary storage on the OSC cluster (also recommended) and runs an analysis program.
Info on batch processing is at https://www.osc.edu/supercomputing/batch-processing-at-osc. |
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Mon Dec 17 21:16:31 2018, Brian Clark, Run over many data files in parallel,
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To analyze data, we sometimes need to run over many thousands of runs at once. To do this in parallel, we can submit a job for every run we want to do.
This will proceed in several steps:
We need to prepare an analysis program.
This is demo.cxx.
The program will take an input data |
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Tue Nov 27 09:43:37 2018, Brian Clark, Plot Two TH2Ds with Different Color Palettes, Analysis
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Say you want to plot two TH2Ds with on the same pad but different color paletettes?
This is possible, but requires a touch of fancy ROOT-ing. Actually, it's not that much, it just takes a lot of time to figure it out. So
here it is. |
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Mon Apr 24 11:51:42 2023, William Luszczak, PUEO simulation stack installation instructions, Software
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These are instructions I put together as I was first figuring out how to compile PueoSim/NiceMC. This was originally done on machines running CentOS
7, however has since been replicated on the OSC machines (running RedHat 7.9 I think?). I generally try to avoid any `module load` type prerequisites,
instead opting to compile any dependencies from source. You _might_ be able to get this to work by `module load`ing e.g. fftw, but try this at your own |
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Tue Aug 2 14:34:15 2022, Alex M, OSC License Request,
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Some programs on OSC require authorized access to use in the form of a license. The license will be automatically read if it is available
whenever you open a program on OSC, provided you have access to the license. In order to have access to a license, you need to fill out the attached form
and send it to Amy to forward to OSC. Available programs (at least some of) which require a license can be found here: https://www.osc.edu/resources/available_software/software_list |
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Thu May 11 13:43:46 2017, Sam Stafford, Notes on installing icemc on OSC, Software
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Tue Nov 5 16:22:16 2019, Keith McBride, NASA Proposal fellowships, Other
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Here is a useful link for astroparticle grad students related proposals from NASA:
https://nspires.nasaprs.com/external/solicitations/summary.do?solId=%7BE16CD59F-29DD-06C0-8971-CE1A9C252FD4%7D&path=&method=init |
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Fri Jan 31 10:43:52 2020, Jorge Torres, Mounting ARA software on OSC through CernVM File System, Software
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OSC added ARA's CVMFS repository on Pitzer and Owens. This has been already done in UW's cluster thanks to Ben Hokanson-Fasig and Brian Clark. With CVMFS,
all the dependencies are compiled and stored in a single folder (container), meaning that the user can just source the paths to the used environmental
variables and not worry about installing them at all. This is very useful, since it usually takes a considerable amount of time to get those dependencies |
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Fri Feb 28 13:09:53 2020, Justin Flaherty, Installing anitaBuildTools on OSC-Owens (Revised 2/28/2020),
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Thu Jul 11 10:05:37 2019, Justin Flaherty, Installing PyROOT for Python 3 on Owens, Software
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In order to get PyROOT working for Python 3, you must build ROOT with a flag that specifies Python 3 in the installation. This method will create
a folder titled root-6.16.00 in your current directory, so organize things how you see fit. Then the steps are relatively
simple: |
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Thu Apr 27 18:28:22 2017, Sam Stafford (Also Slightly Jacob), Installing AnitaTools on OSC, Software
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Jacob Here, Just want to add how I got AnitaTools to see FFTW:
1) echo $FFTW3_HOME to find where the lib and include dir is.
2) Next add the following line to the start of cmake/modules/FindFFTW.cmake |
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Fri Oct 11 13:43:35 2019, Amy , How to start a new undergrad hire, Other
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If an undergrad has been working with the group on a volunteer basis, they will need that clarified, so that they have not up to then we working for
pay without training. There is a form that they sign saying they have been working as a volunteer.
Below is an email that Pam sent in July 2019 outlining what they need. Other things to remember: |