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archive:computer_resources:campusrocks [2010/03/30 21:06] juettemann |
archive:computer_resources:campusrocks [2015/04/13 18:55] ceisenhart |
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'' | '' | ||
- | ===== Creating an account ===== | + | ===== Hardware ===== |
- | [[Creating an account|NewAccount]] | + | |
- | Visit https://vpn.soe.ucsc.edu/ and follow the instructions on the page to reset your password for your UCSC account (//username//@ucsc.edu). | + | |
- | After the password is (re)set, you should be able to | + | |
- | <code> | + | |
- | ssh username@campusrocks.cse.ucsc.edu | + | |
- | </code> | + | |
- | At your first login, a public/private keypair is generated. Some information about public key authentication can be found [[http://sial.org/howto/openssh/publickey-auth/|here]]. | + | [[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 ===== | ||
+ | |||
+ | * [[Creating an account|Create a new account]] | ||
+ | * [[http://campusrocks.soe.ucsc.edu/roll-documentation/sge/5.2/|Documentation]] (works only on campus or when connected via [[http://vpn.soe.ucsc.edu |VPN]].) | ||
+ | * [[http://campusrocks.soe.ucsc.edu/ganglia/|Status page]] | ||
+ | * [[Installed Software|Software]] | ||
- | There is a documentation but is offline at the moment (Apache seems to be down). I will put a link here as soon as it is available again. | ||
Line 27: | Line 36: | ||
* 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: | ||
| | ||
- | * GCC: | + | if [ "$SHELL" = "/bin/sh" ] |
- | * gcc-4.1.2-44.el5 | + | then |
- | * gcc-gfortran-4.1.2-44.el5 | + | SHELL=/bin/bash |
- | * libgcc-4.1.2-44.el5 | + | export SHELL |
- | * libgcc-4.1.2-44.el5 | + | fi |
- | * gcc-c++-4.1.2-44.el5 | + | |
- | + | ||
- | * Perl 2.8.8: | + | If you would like to add our classes bin directory (or any other directory for that matter) then add this to your .profile: |
- | * foundation-perl-XML-Parser-2.36-1 | + | |
- | * foundation-perl-Text-Iconv-1.7-1 | + | PATH=/campusdata/BME235/bin:$PATH |
- | * foundation-perl-SVG-Graph-0.02-1 | + | export PATH |
- | * foundation-perl-HTML-Parser-3.60-1 | + | |
- | * foundation-perl-XML-DOM-1.44-1 | + | To use the gcc-4.5 family of compilers stored in our bin directory then you can specify the LD_LIBRARY_PATH environmental variable: |
- | * foundation-perl-GD-SVG-0.33-1 | + | LD_LIBRARY_PATH=/campusdata/BME235/lib:/campusdata/BME235/lib64:$LD_LIBRARY_PATH |
- | * foundation-perl-IO-stringy-2.110-1 | + | export LD_LIBRARY_PATH |
- | * foundation-perl-Text-Shellwords-1.08-1 | + | |
- | * foundation-perl-URI-1.38-1 | + | To make your default folder creation settings group readable and writable then add this line to your .profile: |
- | * foundation-perl-SVG-2.49-1 | + | umask 007 |
- | * foundation-perl-XML-Quote-1.02-1 | + | |
- | * foundation-perl-libxml-perl-0.08-1 | + | |
- | * perl-5.8.8-18.el5_3.1 | + | |
- | * perl-SGMLSpm-1.03ii-16.2.1 | + | ===== Sungrid Job scheduler ===== |
- | * foundation-perl-XML-Writer-0.606-1 | + | |
- | * foundation-perl-Data-Stag-0.11-1 | + | Campusrocks uses sungrid for scheduling jobs. The techstaff request that jobs only be run |
- | * foundation-perl-XML-Node-0.11-1 | + | on the compute nodes, not the head node, as jobs run there slow down the entire cluster. |
- | * foundation-perl-bioperl-ext-1.5-1 | + | They threaten to kill jobs found running on the head node. |
- | * ImageMagick-perl-6.2.8.0-4.el5_1.1 | + | |
- | * foundation-perl-5.8.8-0 | + | 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 |
- | * perl-DBI-1.52-2.el5 | + | * qsub: Submits a job (create a shell script, then run "qsub -cwd shellscript") |
- | * foundation-perl-IO-String-1.08-1 | + | * qdel: Delete a job |
- | * foundation-perl-Graph-0.91-1 | + | * qlogin: Interactive login |
- | * perl-String-CRC32-1.4-2.fc6 | + | * qstat: See the status of jobs in the queue |
- | * foundation-perl-Storable-2.20-1 | + | * qmon: Graphical User Interface (GUI) |
- | * foundation-perl-Scalar-List-Utils-1.21-1 | + | |
- | * foundation-perl-HTML-Tagset-3.20-1 | + | The web site is locked so that it can only be accessed oncampus. |
- | * foundation-perl-libwww-perl-5.826-1 | + | |
- | * foundation-perl-XML-Twig-3.32-1 | + | [[http://web.njit.edu/topics/HPC/basement/sge/SGE.html|SunGrid Quick Start]] |
- | * foundation-perl-File-Temp-0.21-1 | + | |
- | * foundation-perl-bioperl-1.6.0-1 | + | Useful submit-script settings for SGE: |
- | * foundation-perl-bioperl-db-0.01-1 | + | |
- | * foundation-perl-GD-2.41-1 | + | #$ -N some_name_here\\ |
- | * foundation-perl-PathTools-3.30-1 | + | Apparently, you must have a single word after -N\\ |
- | * foundation-perl-Digest-MD5-2.38-1 | + | This gives a nicer name to your script when you run qstat.\\ |
- | * perl-XML-Parser-2.34-6.1.2.2.1 | + | |
- | * foundation-perl-libnet-1.22-1 | + | #$ -V\\ |
- | * foundation-perl-bioperl-gui-1.0-1 | + | Your jobs use **your** environment variables. |
- | * foundation-perl-MIME-Base64-3.07-1 | + | |
- | * foundation-perl-tk-804.027-0 | + | #$ -l mem_free=15g\\ |
- | * perl-DBD-MySQL-3.0007-2.el5 | + | 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. |
- | * foundation-perl-SOAP-Lite-0.710.08-1 | + | |
- | * foundation-perl-Module-Build-0.33-1 | + | |
- | * foundation-perl-bioperl-run-1.4-1 | + | |
- | * perl-X11-Protocol-0.56-1.el5.rf | + | |
- | + | ||
- | * Python 2.4: | + | |
- | * python-elementtree-1.2.6-5 | + | |
- | * MySQL-python-1.2.1-1 | + | |
- | * ganglia-python-5.2-1 | + | |
- | * python-pyblock-0.26-3.el5 | + | |
- | * gnome-python2-gnomekeyring-2.16.0-2.el5 | + | |
- | * libxml2-python-2.6.26-2.1.2.7 | + | |
- | * gamin-python-0.1.7-8.el5 | + | |
- | * rpm-python-4.4.2.3-9.el5 | + | |
- | * gnome-python2-applet-2.16.0-2.el5 | + | |
- | * gnome-python2-libegg-2.14.2-6.el5 | + | |
- | * foundation-python-2.4.2-0 | + | |
- | * notify-python-0.1.0-3.fc6 | + | |
- | * python-numeric-23.7-2.2.2 | + | |
- | * foundation-python-extras-5.2-0 | + | |
- | * python-urlgrabber-3.1.0-5.el5 | + | |
- | * gnome-python2-gconf-2.16.0-1.fc6 | + | |
- | * gnome-python2-canvas-2.16.0-1.fc6 | + | |
- | * gnome-python2-gnomeprint-2.16.0-2.el5 | + | |
- | * python-2.4.3-24.el5 | + | |
- | * dbus-python-0.70-7.el5 | + | |
- | * gtk-vnc-python-0.3.2-3.el5 | + | |
- | * libselinux-python-1.33.4-5.1.el5 | + | |
- | * python-sqlite-1.1.7-1.2.1 | + | |
- | * foundation-python-xml-0.8.4-0 | + | |
- | * python-devel-2.4.3-24.el5 | + | |
- | * python-virtinst-0.300.2-12.el5 | + | |
- | * gnome-python2-bonobo-2.16.0-1.fc6 | + | |
- | * gnome-python2-desktop-2.16.0-2.el5 | + | |
- | * gnome-python2-gtksourceview-2.16.0-2.el5 | + | |
- | * libvirt-python-0.3.3-14.el5_3.1 | + | |
- | * gnome-python2-gnomevfs-2.16.0-1.fc6 | + | |
- | * gnome-python2-extras-2.14.2-6.el5 | + | |
- | * biopython-1.50-1 | + | |
- | * python-iniparse-0.2.3-4.el5 | + | |
- | * python-devel-2.4.3-24.el5 | + | |
- | * python-ldap-2.2.0-2.1 | + | |
- | * audit-libs-python-1.7.7-6.el5_3.3 | + | |
- | * libbdevid-python-5.1.19.6-44.1 | + | |
- | * gnome-python2-2.16.0-1.fc6 | + | |
- | * MySQL 5.8.8 |