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archive:computer_resources:campusrocks [2010/04/11 16:37] karplus paraphrased sungrid info from campusrocks login message |
archive:computer_resources:campusrocks [2010/05/16 01:53] jstjohn |
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Address: 128.114.48.114 | Address: 128.114.48.114 | ||
'' | '' | ||
+ | |||
+ | ===== Hardware ===== | ||
+ | |||
+ | [[Hardware|Machine-specific capabilities]] | ||
+ | |||
+ | ^Machine ^GB RAM ^CPUs ^Cores ^MHz ^Model ^ | ||
+ | |campusrocks.local(head node?)|30 |1 |1 |1000 |Dual-Core AMD Opteron(tm) Processor 2218 HE| | ||
+ | |campusrocks-0-2(through 30).local |15 |4 |2 |1800 |Dual-Core AMD Opteron(tm) Processor 2218 HE| | ||
+ | |campusrocks-1-0(through 31).local |15 |2 |1 |2592 |Dual-Core AMD Opteron(tm) Processor 2218 HE| | ||
+ | |||
+ | campusrocks-0-6.local exceptionally has 30 GB RAM | ||
===== Account/Documentation ===== | ===== Account/Documentation ===== | ||
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* 3.4TB available | * 3.4TB available | ||
* OS: GNU/Linux 2.6.18-128.1.14.el5xen | * OS: GNU/Linux 2.6.18-128.1.14.el5xen | ||
+ | |||
+ | ===== Setting Environmental Variables ===== | ||
+ | |||
+ | If you would like to change your shell to bash, make a file called .profile which you will put all of your environmental settings into, and add this to the beginning: | ||
| | ||
- | ===== Directory structure ===== | + | if [ "$SHELL" = "/bin/sh" ] |
- | * Root: /campusdata/BME235 | + | then |
- | * [[bin|bin]] | + | SHELL=/bin/bash |
- | * [[bin/x86_64|bin/x86_64]] | + | export SHELL |
- | * [[bin/scripts|bin/scripts]] | + | fi |
- | * [[/data|data]] | + | |
- | * [[/programs|programs]] | + | |
- | * [[lib|lib]] (renamed from libs to lib to simplify install process so you can install most programs with --prefix=/campusdata/BME235) --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/06 23:56// | + | If you would like to add our classes bin directory (or any other directory for that matter) then add this to your .profile: |
- | * [[include|include]] (currently contains boost headers) | + | |
- | * [[experiments|experiments]] | + | PATH=/campusdata/BME235/bin:$PATH |
+ | export PATH | ||
+ | |||
+ | To use the gcc-4.5 family of compilers stored in our bin directory then you can specify the LD_LIBRARY_PATH environmental variable: | ||
+ | LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH | ||
+ | export LD_LIBRARY_PATH | ||
+ | |||
+ | To make your default folder creation settings group readable and writable then add this line to your .profile: | ||
+ | umask 007 | ||
+ | |||
===== Sungrid Job scheduler ===== | ===== Sungrid Job scheduler ===== | ||
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There is [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Online documentation]] of how to use sungrid to submit jobs on the cluster. The main commands are | There is [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Online documentation]] of how to use sungrid to submit jobs on the cluster. The main commands are | ||
- | * qsub: Submits a job (create a shell script, then run "qsub shellscript") | + | * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript") |
* qdel: Delete a job | * qdel: Delete a job | ||
* qlogin: Interactive login | * qlogin: Interactive login | ||
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The web site is locked so that it can only be accessed oncampus. | The web site is locked so that it can only be accessed oncampus. | ||
+ | [[http://web.njit.edu/topics/HPC/basement/sge/SGE.html|SunGrid Quick Start]] | ||
+ | |||
+ | Useful submit-script settings for SGE: | ||
+ | |||
+ | #$ -N some_name_here\\ | ||
+ | Apparently, you must have a single word after -N\\ | ||
+ | This gives a nicer name to your script when you run qstat.\\ | ||
+ | |||
+ | #$ -V\\ | ||
+ | Your jobs use **your** environment variables. | ||
+ | |||
+ | #$ -l mem_free=15g\\ | ||
+ | Your job goes to a node with at least 15g of free memory. There is probably something like '-l mem_avail' that works if you would like to schedule your job on a node with a certain amount of max memory available, even if some of it is currently in use. | ||