http://ctbp.ucsd.edu/computing/wiki/ 2009-11-10T04:20:49-08:00 http://ctbp.ucsd.edu/computing/wiki/ http://ctbp.ucsd.edu/computing/wiki/lib/images/favicon.ico text/html 2009-11-06T11:19:46-08:00 http://ctbp.ucsd.edu/computing/wiki/ctbp?rev=1257535186&do=diff ctbp The C-terminal binding proteins (CtBPs) play roles in diverse cellular processes including transcriptional regulation, Golgi membrane fission, and synaptic ribbon formation. In the context of transcriptional regulation, they function as corepressors, interacting with promoter-bound transcription factors and recruiting a large protein complex that contains chromatin-modifying enzymes. We recently described the structure of a Thanatos-associated protein (THAP) domain that is found in a new m… text/html 2009-09-30T12:43:07-08:00 http://ctbp.ucsd.edu/computing/wiki/faq?rev=1254339787&do=diff If you can't find what you're looking for on this page, be sure to check the CTBP HOW-TOs before e-mailing ctbp-help. Additional (a bit obsolete) information is located here. How do I get an account on CTBP servers and clusters? Please see this page. The accounts are distributed by kerberos, so an account on one machine will work on all machines. text/html 2008-06-18T16:17:29-08:00 http://ctbp.ucsd.edu/computing/wiki/hardware?rev=1213831049&do=diff ctbp1.ucsd.edu This very large cluster is for running both serial and small parallel (up to 8 processors per job) jobs. Parallel jobs have priority on this cluster. * 562 processors * frontend (ctbp1.ucsd.edu): Dell PE2950 dual quad-core Xeon E5345 @ 2.33GHz, 16GB RAM * 64 nodes Dell PE1950 dual quad-core Xeon E5345 @ 2.33GHz, 8GB RAM (16 nodes (c1-0 trough c1-15) have 16GB RAM) * 26 nodes Dell SC1420 dual Xeon @ 2.8 Ghz, 2GB RAM per node (c2-0 through c2-25) * two disk storage a… text/html 2009-09-30T13:08:27-08:00 http://ctbp.ucsd.edu/computing/wiki/how-to?rev=1254341307&do=diff Introduction to CTBP cluster computing Introduction to SGE (the queuing system) on the clusters SGE example scripts Wolynes cluster scripts text/html 2009-08-13T12:55:34-08:00 http://ctbp.ucsd.edu/computing/wiki/introduction_to_ctbp_cluster_computing?rev=1250193334&do=diff Hardware * total 564 processors * frontend (ctbp.ucsd.edu): Dell PE2950 dual quad-core Xeon E5345 @ 2.33GHz, 16GB RAM * 64 nodes Dell PE1950 dual quad-core Xeon E5345 @ 2.33GHz, 8GB RAM (16 nodes (c1-0 trough c1-15) have 16GB RAM) * 26 nodes Dell SC1420 dual Xeon @ 2.8 Ghz, 2GB RAM per node (c2-0 through c2-25) * two disk storage arrays (/gpfs) on the cluster internal network * frontend and disk arrays have 10gb uplinks, the nodes are 1gb connected text/html 2009-09-30T13:21:38-08:00 http://ctbp.ucsd.edu/computing/wiki/introduction_to_sge_the_queuing_system_on_the_clusters?rev=1254342098&do=diff Sun Grid Engine has a large set of programs that let the user submit/delete jobs, check job status, and have information about available queues and environments. For the normal user the knowledge of the following basic commands should be sufficient to get started with Grid Engine and have full control of his jobs: text/html 2008-07-17T11:00:15-08:00 http://ctbp.ucsd.edu/computing/wiki/mac_os_x?rev=1216317615&do=diff Mac OS X Mac OS X 10.4 "Tiger" Mac OS X 10.5 "Leopard" text/html 2008-07-17T13:45:37-08:00 http://ctbp.ucsd.edu/computing/wiki/mac_os_x_10.4_tiger?rev=1216327537&do=diff Mac OS X 10.4 Tiger - Printing * Download the Dell Color 5110cn driver installer from here. * Open the DMG file and run the “Dell 5110cn Installer” * After the installation finishes, launch /Applications/Utilities/Printer Setup Utility * Click the “Add” button, then select “IP Printer”. * In the “Protocol” pull-down menu, select “HP JetDirect - Socket” * In the “Address” field, enter: 172.16.16.241 * Leave the “Queue” filed blank, then give the printer a name/location of your cho… text/html 2009-09-29T08:26:37-08:00 http://ctbp.ucsd.edu/computing/wiki/printing?rev=1254237997&do=diff CTBP Printers (this wiki section is undergoing editing) Shared printers are located in Urey Hall 7225 and 7261 (the two large “bullpen” rooms). Urey 7261 This room houses a Xerox Phaser 4510 (black & white) and a Dell Color Laser 5110cn. Both printers are capable of duplex (two-sided) printing. text/html 2009-09-30T13:02:20-08:00 http://ctbp.ucsd.edu/computing/wiki/server_migration?rev=1254340940&do=diff For basic information see the ctbp-users posting Old binaries incompatibility The new upgraded cluster is running newer version of linux kernel (2.6.18) which may not be compatible with previously compiled binaries. If you encounter a runtime error when trying running your application please recompile it. If you need an assistance please contact us. text/html 2009-10-30T16:16:43-08:00 http://ctbp.ucsd.edu/computing/wiki/sge_example_scripts?rev=1256944603&do=diff APBS Serial #!/bin/bash #$ -cwd # #$ -N serial_test_job #$ -m e #$ -e sge.err #$ -o sge.out # requesting 12hrs wall clock time #$ -l h_rt=12:00:00 /soft/linux/pkg/apbs-1.0.0/bin/apbs.serial inputfile >& outputfile Parallel #!/bin/bash #$ -cwd # #$ -N apbs-PARALLEL #$ -e apbs-PARALLEL.errout #$ -o apbs-PARALLEL.errout # # requesting 8 processors #$ -pe mpich 8 echo -n "Running on: " hostname APBSBIN_PARALLEL=/soft/linux/pkg/apbs-1.0.0/bin/apbs MPIRUN=/opt/openmpi/bin/mpirun echo "Start… text/html 2009-09-30T12:50:33-08:00 http://ctbp.ucsd.edu/computing/wiki/software?rev=1254340233&do=diff Package Commands Paths Notes AMBER v10 See bin.* directories under path /soft/linux/pkg/amber10/ These directories contain 64bit code APBS v1.1.0 apbs /soft/linux/pkg/apbs-1.1.0/bin AutoDock 3.05 autodock3 /soft/linux/pkg/AutoDock/bin/Linux N/A CHARMM v32b1 See bin directory under path /soft/linux/pkg/c34b2 N/A GAMESS See bin directory under path /soft/linux/pkg/gamess N/A Gaussian 03 vB.04 g03 /soft/linu… text/html 2009-09-24T10:54:02-08:00 http://ctbp.ucsd.edu/computing/wiki/start?rev=1253814842&do=diff CTBP Computing main page Software Hardware FAQ How-To Server Migration Printing Daily ctbp1:/gpfs and ctbp1:/home user quotas report. Daily queue report. text/html 2008-06-25T13:13:31-08:00 http://ctbp.ucsd.edu/computing/wiki/wolynes_cluster_scripts?rev=1214424811&do=diff #!/bin/bash #$ -j y #$ -S /bin/bash #$ -e error_file #$ -o output_file #$ -l h_rt=48:00:00 #$ -N a_wt_1r69z # set up directories objdir='/scratch/USER/amh/object/run_ctbp_wt_amc_1_1r69z' outdir='/gpfs/USER/fofq/1r69z/' prolistdir='/home/USER/amh/md_input/pro.list' inputdir='/home/USER/amh/md_input/input/1r69z/fofq/wt/amc' protstruct='/home/USER/amh/md_input/proteins/1r69z' ssbias='/home/USER/amh/md_input/sec_struct_bias/' aveseqdir='/home/USER/amh/md_input/target_sequen…