archive:computer_resources:campusrocks
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archive:computer_resources:campusrocks [2010/03/30 15:39] juettemann |
archive:computer_resources:campusrocks [2015/04/18 20:57] charles [Sungrid Job scheduler] |
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| Address: 128.114.48.114 | Address: 128.114.48.114 | ||
| '' | '' | ||
| - | ===== Creating an account ===== | ||
| - | Visit https://vpn.soe.ucsc.edu/ and follow the instructions on the page to reset your password for your UCSC account (//username//@ucsc.edu). | + | ===== Hardware ===== |
| - | 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]]. | + | |
| - | 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. | + | [[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| | | | | ||
| - | ==== Stats ==== | + | 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]] | ||
| + | |||
| + | |||
| + | |||
| + | ===== Stats ===== | ||
| Line 25: | 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 | + | #$ -pe mpi 4\\ |
| - | * foundation-perl-bioperl-run-1.4-1 | + | Your job goes to a set of nodes with a combined total of a least 4 cores available. |
| - | * perl-X11-Protocol-0.56-1.el5.rf | + | |
| - | + | #$ -cwd\\ | |
| - | * Python 2.4: | + | Your job will be launched at the directory where the qsub command was given. Useful for setting predictable bash commands. Though not recommended for portability as other users of the script would need to also know where to launch the qsub command. |
| - | * python-elementtree-1.2.6-5 | + | |
| - | * MySQL-python-1.2.1-1 | + | #$ -q [Name of specific server queue]\\ |
| - | * ganglia-python-5.2-1 | + | Used to specify which set of servers you would like the sungrid scheduler to schedule/run your jobs in. Names on campus rocks include 'all.q' and 'small.q' |
| - | * python-pyblock-0.26-3.el5 | + | |
| - | * gnome-python2-gnomekeyring-2.16.0-2.el5 | + | Example qsub commands: |
| - | * libxml2-python-2.6.26-2.1.2.7 | + | * qsub -N skewer_adapter_removal -cwd -V -pe mpi 20 -l mem_free=50g /campusdata/BME235/S15_assemblies/SOAPdenovo2/adapterRemovalTask/skewer_run/run_skewer_adapter_removal.sh |
| - | * gamin-python-0.1.7-8.el5 | + | |
| - | * rpm-python-4.4.2.3-9.el5 | + | |
| - | * gnome-python2-applet-2.16.0-2.el5 | + | Useful commands for viewing currently run jobs: |
| - | * gnome-python2-libegg-2.14.2-6.el5 | + | |
| - | * foundation-python-2.4.2-0 | + | #$ qhost\\ |
| - | * notify-python-0.1.0-3.fc6 | + | Displays the compute nodes available on the cluster including hardware statistics. |
| - | * python-numeric-23.7-2.2.2 | + | |
| - | * foundation-python-extras-5.2-0 | + | #$ qstat\\ |
| - | * python-urlgrabber-3.1.0-5.el5 | + | Displays the status of the jobs submitted to qsub.\\ |
| - | * gnome-python2-gconf-2.16.0-1.fc6 | + | *flag '-f' displays more hardware usage information on each node. The 'resv/used/tot.' column displays number of processing cores reserved, used, and the total number of cores for a node respectively. |
| - | * gnome-python2-canvas-2.16.0-1.fc6 | + | Primary job status codes: |
| - | * gnome-python2-gnomeprint-2.16.0-2.el5 | + | *'r' status indicates that a job is running. |
| - | * python-2.4.3-24.el5 | + | *'qw' status indicates that a job is waiting to be scheduled/run on a machine. |
| - | * 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 | ||
archive/computer_resources/campusrocks.txt · Last modified: 2015/09/02 16:42 by ceisenhart
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