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The bluefish LINUX Compute Cluster

TSRI has a cluster of 288 dual processor servers with a total 576 3.4 Ghz Intel XEON-EMT CPUs and one TByte of memory. Each server has a 72 GByte local disk and all systems share a four TeraByte NFS disk arrary. Jobs running on our LINUX clusters are managed by PBS. An additional server, bluefish, with two Intel XEON-EMT CPUs serves as an interactive frontend where you can compile and test your code and/or test your runs before submission to PBS. An account on the cluster is available to anyone with a valid TSRI email account. To request an account, email wyoung@scripps.edu

Available software

If an application that you need is missing, please request that it be installed. 

Software Package Owner Location Description
Amber case   /bluefish/people-b/applications/amber molecular simulation (EM, MD, etc.)
ARP weber   /bluefish/people-b/applications/arp_6.0 Xray structures
autodock garrett   /bluefish/people-b/applications/autodock docking, virtual screening
BLAST weber   /bluefish/people-b/applications/blast-2.2.10 sequence searching
ClustalW weber   /bluefish/people-b/applications/clustalw1.83 sequence alignment
CCP4 weber   /bluefish/people-b/applications/ccp4-6.0.2 Xray structures
CNS weber  /bluefish/people-b/applications/cns_solve_1.2 Xray and NMR structures
Cyana weber   /bluefish/people-b/applications/cyana-2.1 NMR structures
em3dr2 weber   /bluefish/people-b/applications/em3dr2 EM 3D reconstruction
EMAN wyoung   /bluefish/people-b/applications/EMAN EM 3D reconstruction
epmr weber   /bluefish/people-b/applications/epmr   Xray structure determination
Gaussian 03 weber   /bluefish/people-b/applications/g03   quantum chemistry
Gamess weber   /bluefish/people-b/applications/gamess   quantum chemistry
gasbor weber  /bluefish/people-b/applications/gasbor_ux  small angle Xray scattering
HMMER weber  /bluefish/people-b/applications/hmmer-2.3.2  sequence comparison
icm abagyan  /bluefish/people-b/applications/icm   molecular modelling
MEME  weber   /bluefish/people-b/applications/meme.3.0.4   sequence motif analysis
modelfree weber   /bluefish/people-b/applications/modelfree   NMR relaxation analysis
modeller8  weber   /bluefish/people-b/applications/modeller8v2   protein homology modelling
NAMD   weber   /bluefish/people-b/applications/namd   MD
phaser weber   /bluefish/people-b/applications/phaser-1.3.1   crystal structure determination
shelx weber   /bluefish/people-b/applications/shelx   crystal structure determination
solve weber   /bluefish/people-b/applications/solve-2.13 crystal structure determination

Compilation issues

The bluefish cluster has both the Intel suite of compilers and the GNU toolkit.
Intel compiler setup: 

if ( ${?prompt}) then
        source /opt/intel_fce_80/bin/ifortvars.csh
        source /opt/intel_cce_80/bin/iccvars.csh
endif
Use the following Intel compiler flags for best performance:
Start with   -fast   (equivalent to -O3 -axP -ipo )
If this doesn't work, try individual combinations of   -O3 -axP -ipo
Use -O2 and/or -ip if your code breaks with the above heavy optimization.
Remember: The executables will only run on 64bit Intel EM64T CPUs!
Some more hints for EM64T CPUs: C++ Fortran

Checkpoint/restart

Some applications offer built-in checkpoint and restart support. These are listed below.
Application CPR facility
Amber of unknown quality
Gaussian 03 make sure checkpoint file gets saved by naming it explicitly
Jaguar from file restart.in or jobname.**.in

 

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