Differences

This shows you the differences between two versions of the page.

--- archive:computer_resources:campusrocks [2010/04/11 16:37]
karplus paraphrased sungrid info from campusrocks login message
+++ archive:computer_resources:campusrocks [2015/04/13 18:55]
ceisenhart
@@ Line 7: / Line 7: @@
 Address: 128.114.48.114
 ''
+===== Hardware =====
+[[Hardware|Machine-specific capabilities]]
+^Machine ^GB RAM ^CPUs ^Cores ^MHz ^Model ^
+|campusrocks.local(head node?)|30 |4 |1 |2600 |Dual-Core AMD Opteron(tm) Processor 2218 HE|
+|campusrocks-0-2(through 30).local |15 |4 |2 |2664 | Intel(R) Xeon(R) CPU 5150 |
+|campusrocks-0-(31,32).local |15 |8 |2 | 3192 | Intel(R) Xeon(TM) CPU|
+|campusrocks-1-0(through 31).local |15 |2 |1 |2592 |Dual-Core AMD Opteron(tm) Processor 2218 HE|
+|campusrocks-2-(0,1).local |192 | 48|  |  |  |
+campusrocks-0-6.local exceptionally has 30 GB RAM
 ===== Account/Documentation =====
@@ Line 23: / Line 36: @@
   * 3.4TB available
   * 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:$LD_LIBRARY_PATH
+  export LD_LIBRARY_PATH
+To make your default folder creation settings group readable and writable then add this line to your .profile:
+  umask 007
 ===== Sungrid Job scheduler =====
@@ Line 41: / Line 68: @@
 They threaten to kill jobs found running on the head node.
-There is [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Online documentation]] of how to use sungrid to submit jobs on the cluster.  The main commands are
+There is [[http://www.rocksclusters.org/rocks-documentation/4.1/|online documentation]] of how to use sungrid to submit jobs on the cluster.  The main commands are
-  * qsub: Submits a job (create a shell script, then run "qsub shellscript")
+  * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript")
   * qdel: Delete a job
   * qlogin: Interactive login
@@ Line 50: / Line 77: @@
 The web site is locked so that it can only be accessed oncampus.
+[[http://web.njit.edu/topics/HPC/basement/sge/SGE.html|SunGrid Quick Start]]
+Useful submit-script settings for SGE:
+#$ -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.

Banana Slug Genomics

User Tools

Site Tools

Differences

Page Tools