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Configuration

Compute Nodes

The Genepool system is made up of a heterogeneous collection of nodes to serve the diverse workload of the JGI users.  Below is a table of the current configuration.

# NodesCores/nodeMemory/nodeLocal diskProcessorHostnameVendor
2 32 1000GB 3.6TB Xeon E5-4650L mndlhm0205-ib,mndlhm0405-ib.nersc.gov Appro/Cray
5 32 500GB 3.6TB Xeon E5-4650L mndlhm[01-05]03.nersc.gov  Appro/Cray
8 16 248GB 1.8TB Xeon E5-2670 mc0xxx.nersc.gov Appro/Cray
212 16 120GB 1.8TB Xeon E5-2670 mc0xxx.nersc.gov Appro/Cray
450 8 48 GB 1 TB Intel Xeon L5520 2.27 GHz sgi[01a01-06b40].nersc.gov SGI
64 8 48 GB 500 GB Intel Xeon L5520 2.27 GHz quad[01-64].nersc.gov SuperMicro
20 8 144 GB 512 GB Intel Xeon L5520 2.27 GHz x4170a[01-20].nersc.gov Sun
4 32 512 GB 1 TB AMD Opteron 2.28 GHz gpht-[01-04].nersc.gov Sun
1 80 2 TB 300 GB Intel Xeon X7560 2.27 GHz b2r2ibm1t-02.nersc.gov IBM
1 32 1 TB 600 GB Intel Xeon X7560 2.27 GHz gptb-01.nersc.gov Dell
7 24 256 GB 600 GB Intel x7542 2.67 GHz uv10-[1-7].nersc.gov SGI

Login Nodes

Genepool currently has four login nodes.  Users land on one of the four login nodes when they ssh to genepool.nersc.gov.  The different login nodes sit behind a load balancer and youyou will land on the login node with the least number of connections, or if you already have active connections, you will be directed to the same login node.   The names of the login nodes are genepool01, genepool02, genepool03 and genepool04, however you should always access the login nodes with ssh username@genepool.nersc.gov.  The login nodes have 32 GB of RAM, have 2.3GHz processors and have 8 cores each.

"gpint" Analysis Nodes

Genepool also has nodes which are used for pipeline control and pre- and post-processing of jobs as well as analysis jobs. At present, these nodes are allocated per group and are called gpintNN (NN = 01,02,...). Users should refer to the table below to determine which node belongs to their group and only use the nodes allocated to their group.  Note:  the legacy gpints (01-27) will be retired in the coming weeks. gpint05, gpint11, and gpint13 will remain in service.  Higher numbered gpints (100+) are replacing the legacy nodes.

Node Name

Legacy JGI Name

Assigned Group

Cores

Memory

Per-process

Memory Limit

gpint01.nersc.gov one.jgi-psf.org R & D 24 252.4 GB 214.56 GB
gpint02.nersc.gov bcg1.jgi-psf.org Comparative Genomics (Vista) 16 31.5 GB N/A
gpint03.nersc.gov bcg2.jgi-psf.org Comparative Genomics (Vista) 16 31.5 GB N/A
gpint04.nersc.gov merced.jgi-psf.org IMG 16 63.0 GB 53.59 GB
gpint05.nersc.gov img-worker.jgi-psf.org IMG 32 505 GB 429.23 GB
gpint06.nersc.gov zeus.jgi-psf.org GBP 16 63.0 GB 53.59 GB
gpint07.nersc.gov ranger.jgi-psf.org Plant 24 252.4 GB 214.56 GB
gpint08.nersc.gov boiler.jgi-psf.org Plant 24 252.4 GB 214.56 GB
gpint09.nersc.gov sedona.jgi-psf.org Plant 24 252.4 GB 214.56 GB
gpint10.nersc.gov willow.jgi-psf.org Plant 24 252.4 GB 214.56 GB
gpint11.nersc.gov actinium.jgi-psf.org Plant 32 505 GB 429.23 GB
gpint12.nersc.gov bat.jgi-psf.org R & D 24 239.9 GB 203.91 GB
gpint13.nersc.gov quarter.jgi-psf.org Fungal 48 252.4 GB 214.54 GB
gpint14.nersc.gov chekov.jgi-psf.org General purpose 16 63GB 52.9GB
gpint15.nersc.gov stimpy.jgi-psf.org General purpose 8 47.3 GB 40.17 GB
gpint16.nersc.gov ren.jgi-psf.org General purpose  8 62.3 GB 52.91 GB
gpint17.nersc.gov thallium.jgi-psf.org General purpose 16 108.4 GB 92.16 GB
gpint18.nersc.gov indium.jgi-psf.org General purpose 16 126.2 GB 107.24 GB
gpint19.nersc.gov gallium.jgi-psf.org General purpose 16 126.2 GB 107.24 GB
gpint20.nersc.gov cadmium.jgi-psf.org General purpose 16 126.2 GB 107.24 GB
gpint21.nersc.gov itchy.jgi-psf.org General purpose 16 165.7 GB 140.83 GB
gpint22.nersc.gov wesley.jgi-psf.org General purpose 16 70.9 GB 60.29 GB
gpint23.nersc.gov n/a SDM - PacBio 8 47.3 GB 40.17 GB
gpint24.nersc.gov rqc-dev.jgi-psf.org RQC 8 47.3 GB 40.17 GB
gpint25.nersc.gov rqc-prod.jgi-psf.org RQC 8 47.3 GB 40.17 GB
gpint26.nersc.gov sdm-dev.jgi-psf.org SDM 8 47.3 GB 40.17 GB
gpint27.nersc.gov sdm-prod.jgi-psf.org SDM 8 47.3 GB 40.17 GB
gpint100.nersc.gov   R & D 16 256G 208G
gpint101.nersc.gov   R & D 16 256G 208G
gpint102.nersc.gov   Plant 16 256G 208G
gpint103.nersc.gov   Plant 16 256G 208G
gpint104.nersc.gov   Plant 16 128G 101G
gpint105.nersc.gov   IMG 16 128G 101G
gpint106.nersc.gov   GBP 16 128G 101G
gpint107.nersc.gov   SDM 16 128G 101G 
gpint108.nersc.gov   RQC 16 128G  101G 
gpint109.nersc.gov   Assembly 16 128G  101G
gpint110.nersc.gov   Assembly 16 128G  101G 
gpint111.nersc.gov   Vista 16 128G  101G 
gpint112.nersc.gov   Common 16 128G 101G 

 

Other Special Purpose Nodes

Nodes which perform specialized tasks such as running a web-server and/or databases are also part of Genepool, although they may not have all the features of login or analysis nodes (such as NGF filesystems, login access, etc.). These nodes are also currently assigned on a per-group basis. Use of these nodes is restricted to the groups to which they have been assigned.

Oracle Databases

Oracle Database  gpodb05 vortex.jgi-psf.org
Oracle Database  gpodb01 data.jgi-psf.org
Oracle Database  gpodb04 muskrat.jgi-psf.org
Oracle Database   midway.jgi-psf.org
Oracle Database  gpodb03 jericho.jgi-psf.org
Oracle Database   nihdb.jgi-psf.org
Oracle Database   warwick.jgi-psf.org
Oracle Database   troi.jgi-psf.org
Oracle Database   farina.jgi-psf.org
Oracle Database   goku.jgi-psf.org
Oracle Database   catalpa.jgi-psf.org
Oracle Databse   img-nih.jgi-psf.org
Oracle Database   la-oracle.jgi-psf.org
PostgreSQL Database   gbp-db-prod.jgi-psf.org

MySQL Databases

MySQL Database gpdb01.nersc.gov lemur.jgi-psf.org
MySQL Database gpdb02.nersc.gov portal
MySQL Database gpdb03.nersc.gov portal
PostgreSQL Database gpdb04.nersc.gov Plant database
PostgreSQL Database gpdb05.nersc.gov polonium.jgi-psf.org

MySQL Database for Portal group

gpdb07  portal

MySQL Database for Portal group

gpdb08  

MySQL Database

gpdb09 anu.jgi-psf.org

MySQL Database for Plant Group

gpdb10 cigzome.jgi-psf.org

MySQL Database for Plant Group

gpdb11 dbcompgen.jgi-psf.org

Web Services

 

Purpose

Name

Legacy Name

Web server  gpweb01

vista.jgi-psf.org
genome.lbl.gov
pipeline.lbl.gov
pga.lbl.gov
www-pga.lbl.gov
gsd.lbl.gov
www.gsd.lbl.gov
www-gsd.lbl.gov

Web server  gpweb02

hazelton.jgi-psf.org 
atgc.lbl.gov

chr16.lbl.gov
enhancer.lbl.gov
enhancer-test.lbl.gov
genome-test.lbl.gov
hazelton.lbl.gov
pipeline-test.lbl.gov
regprecise.lbl.gov
regpredict.lbl.gov
rviewer.lbl.gov

IMG web nodes gpweb04-07 img-edge[1-4].jgi-psf.org
Web server gpweb08 athena.jgi-psf.org, geneprimp, coal, clams, gold, gold-dev, ani
Galaxy server gpweb09 galaxy.jgi-psf.org
Galaxy dev server gpweb10 galaxy-dev.jgi-psf.org
Portal server gpweb11 frylock.jgi-psf.org
Portal server gpweb12 gp-next.jgi-psf.org
Portal web nodes gpweb13-16 gp-edge[1-4].jgi-psf.org
Portal server gpweb17 gp-test.jgi-psf.org
Portal server gpweb18 portal.jgi-psf.org
Portal server gpweb19 uhura.jgi-psf.org
Plant web nodes gpweb20-22 zome-edge[1-3].jgi-psf.org
Plant dev web node gpweb23 zome-dev.jgi-psf.org
Plant web node gpweb24 zome-private.jgi-psf.org
Plant web node gpweb25 zome-services.jgi-psf.org
Web server gpweb26 jel.jgi-psf.org, seqtechrnd.jgi-psf.org, synbio.jgi-psf.org, rqc.jgi-psf.org, pyrotagger.jgi-psf.org
2nd IP for gpweb26 gpweb27 seqtech.jgi-psf.org
     
Portal load balanced website genome-lb gpweb13 - gpweb16 - genome.jgi.doe.gov, genome.jgi-psf.org
Plant load balanced website zome-lb gpweb20-22 and gpweb24-25 - www.phytozome.net
IMG load balanced website img-lb gpweb04-gpweb07 - img.jgi.doe.gov

Interconnect

The majority of the compute nodes are connected with a 1 Gb/sec Gigabit Ethernet switch.  A few nodes (details forthcoming) are connected via 10Gb/sec ethernet.

File Systems

Genepool will mount a number of file systems.  See the file systems page for more details.

  • Global homes
  • /usr/common
  • JGI 2.7PB GPFS file system "projectb"
  • $SCRATCH

Batch System

Genepool/Phoebe will use a fair share batch scheuler called "UGE".  See our documentation on submitting jobs and queues and policies for more details.