http://ctbp.ucsd.edu/computing/wiki/ 2009-11-08T01:55:00-08:00 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 jensonmary 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 2009-10-30T16:16:43-08:00 ctbpwiki 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 2009-09-30T13:21:38-08:00 ctbpwiki 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 2009-09-30T13:08:27-08:00 ctbpwiki 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 2009-09-30T13:02:20-08:00 ctbpwiki 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 2009-09-30T12:50:33-08:00 ctbpwiki 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 2009-09-30T12:43:07-08:00 ctbpwiki 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.