compute
data
general

HPC Services

RCDS offers simplified access to extreme computational resources AKA High Performance Computing.

HPC Hardware

Standalone Cluster

Jayne

24 cores, 16GB

Marvin

40 cores, 192GB

Trillian

40 cores, 192GB

Zaphod

40 cores, 192GB

Ford

40 cores, 192GB

Slartibartfast

24 cores, 192GB

Seraph

24 cores, 80GB

Whale

64 cores, 1000GB

Petunia

64 cores, 1000GB

Tesla

72 cores, 96GB, 3T High speed disk

Watson

48 cores, 256GB, 4 Phi Coprocessor Cards

Crick

48 cores, 256GB, 4 Phi Coprocessor Cards

Fortyfour (Slurm)

1100+ total cores, 6+ TB RAM

Dell M600 Blades (2009)

8 cores, 32GB RAM each

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Dell R730 (2014)

32 Cores, 32GB RAM, 2 NVidia K40 GPUs each

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Dell R815 (2011)

24 Cores, 194GB RAM each

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Supermicro 1u (2015)

16 Cores, 128GB RAM each

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Dell R620 (2012)

32 Cores, 128GB RAM each

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GPU Nodes (2017, 2018)

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    8 Cores, 64GB RAM, 1 Nvidia 1080 Ti

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    16 Cores, 128GB RAM, 2 Nvidia 1080 Ti

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    40 Cores, 64GB RAM, 1 Nvidia Tesla K40m

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    16 Cores, 128GB RAM, 2 Nvidia 1080 Ti

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    16 Cores, 128GB RAM, 2 Nvidia 1080 Ti

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    16 Cores, 128GB RAM, 2 Nvidia 1080 Ti

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    16 Cores, 128GB RAM, 2 Nvidia 1080 Ti

Dell R710 (2012)

24 Cores, 192GB RAM

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Supermicro (2017)

16 Cores, 96GB RAM

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Shared Storage

Lustre (/mnt/lfs2)

200TB of shared storage composed of 18 servers and 180 high speed disks linked by the power of RAID and Lustre

Gluster (/mnt/gfs, /mnt/home)

180TB of shared storage composed of 16 servers and 160 high capacity disks using ZFS and Gluster

Ceph (/mnt/ceph, /mnt/home)

1 PB TB (~ 330 usable) of shared storage composed of 25 servers and 200 high capacity disks

Servers colored light blue are open for use by all CRC users, the darker blue listed servers require a Standard Account to access.

  • Nodes 65 and 66 were purchased by the Center for Modeling Complex Interactions (CMCI), and are for use only by users associated with the CMCI.

Summary of CRC Storage Systems

SystemRedundancySpeedBackup
Gluster
/mnt/gfs/username
/mnt/home/username		GreatestSlowestDaily Snapshots stored offsite
Ceph
/mnt/ceph/username
/mnt/home/username		GreatestModerateData stored in triplicate, and backed up offsite
Lustre
/mnt/lfs2/username
/mnt/home/username/scratch		Withstands disk failuresFastOpt-in backup
Local Scratch
/mnt/local-scratch/		NoneFastestNone

Which server to use?

Marvin, trillian, and zaphod have the compute muscle for most jobs - start there. If you’re doing large genome assemblies, slarti or whale are appropriate - but please use these systems only when you need lots of RAM. The processors for marvin, zaphod, trillian, ford, and slarti are all similar AMD Opteron type processors. If your compute task can be parallelized, it will complete faster on fortytwo.

HPC Software

One of the common hurdles to analyzing your data is installing and configuring the requisite software. We host a large selection of general purpose and bioinformatics software packages (200+), and can add new software upon request. Here’s a list of currently installed software:

------------------------------------------------------------------------------------- /opt/modules/modulefiles --------------------------------------------------------------------------------------
abundantotu/0.93b(default)        fastphase/1.4.0(default)          jmodeltest/2.1.10(default)        openmpi/2.1.6                     rmblast/2.2.28(default)
admixtools/3.0(default)           fastphylo/1.0.1(default)          julia/1.2.0                       orthodb/2.4.4(default)            roadtrips/2.0(default)
admixture/1.3.0(default)          fastqc/0.11.3(default)            julia/1.4.2                       orthofinder/2.3.12(default)       roary/3.13.0(default)
alder/1.03(default)               fastq-screen/0.14.1(default)      julia/1.5.1(default)              orthomcl/2.0.9(default)           roche454/2.8
amrfinder/3.0.12                  fastq-tools/0.8.3(default)        kallisto/0.44.0(default)          paml/4.9c(default)                roche454/2.9(default)
amrfinder/3.1.1b(default)         faststructure/1.0(default)        kraken/0.10.5-beta(default)       parallel/20131022(default)        rsem/1.3.0(default)
anvio/3(default)                  fasttree/2.1.7(default)           kraken/1.1                        partitionfinder/2.1.1(default)    rtg-tools/3.10.1(default)
aspect-djneu/1.0(default)         fastuniq/1.1(default)             kraken-nedaz/1.0(default)         paup/4a166(default)               salmon/0.9.1
augustus/3.3.3(default)           fastx/0.0.14(default)             lamarc/2.1.10(default)            pdb2pqr/2.1.1(default)            salmon/1.4.0(default)
avida/2.12.4(default)             fiji/1.0(default)                 lamem-tf/1.0(default)             peakranger/1.18(default)          samblaster/0.1.24(default)
bamm/2.5.0(default)               finestructure/2.0.4(default)      last/869(default)                 pear/0.9.10(default)              samtools/1.3.1
bamtools/2.4.0                    flash2/1.0(default)               lastz/1.04.03(default)            perl/5.18.0(default)              samtools/1.9(default)
bamtools/2.5.1                    foldx/4                           libncl/2.1.18(default)            petsc/3.7.7(default)              scythe/0.994(default)
bayesass/3.0.4(default)           foldx/5(default)                  libplinkio/0.3.2                  phredphrap/0.990329(default)      seqtk/1.3(default)
bayescan/2.1(default)             freebayes/1.3.1(default)          links/1.8.5                       phylip/3.696(default)             shaw/3.0.2
bbmap/38.90(default)              garli/2.01(default)               links/1.8.7(default)              phylosnp/1.0(default)             shaw/3.0.3(default)
bcftools/1.3                      gatk/4.0.12.0                     llvm/7.0.1(default)               phyml/3.2.20160530(default)       sickle/1.33(default)
bcftools/1.3.1                    gatk/4.1.7.0(default)             locas/0.1.7(default)              phyutility/2.6(default)           sina/1.2.11(default)
bcftools/1.9(default)             gatk/4.2.2.0                      louvain/1.0(default)              picard/2.26.2                     slim/3.6(default)
beast/1.10.4                      gatk/nightly                      ltsoft/3.0(default)               picard/2.9.2(default)             snap/2013-11-29
beast/1.8.4                       gbs_prism/1.0(default)            lumpy/0.2.13(default)             pindel/2.5(default)               snep/1.1(default)
beast/2.4.5(default)              gcc/6.1.0(default)                mafft/7.307                       plink/1.90(default)               soapdenovo/240(default)
beast/2.5.1                       gcc/7.2.0                         mafft/7.429(default)              pplacer/1.1(default)              spades/3.14.0
bedtools/2.26.0(default)          gcc/7.3.0                         maker/2.31.8(default)             prank/150803(default)             spades/3.9.1(default)
blat/37(default)                  gcta/1.93.2beta(default)          marginphase/1.0(default)          processing/2.2.1                  spatpg/1.0(default)
blat-fastq/35(default)            gdal/2.4.0                        masurca/3.2.4(default)            processing/3.5.3(default)         stacks/2.2
boost/1.57.0                      gdal/3.0.2(default)               matlab/2020a                      prodigal/2.6.3                    stacks/2.5(default)
boost/1.61.0(default)             gemma/0.94.1                      matlock/1.0(default)              proj/6.2.1(default)               structure/2.3.4(default)
boost/1.63.0                      gemma/0.98.1(default)             maxent/3.4.4(default)             prokka/1.11                       super-deduper/1.0(default)
boost/1.67.0                      genemarkes/4.33(default)          mcl/14-137(default)               prokka/1.14.5(default)            superlu/5.2.1
boost/1.69.0                      ghostscript/9.20                  mega2/4.9.2(default)              prottest/3.4-20140123(default)    tbl2asn/25.3(default)
bowtie2/2.2.9(default)            git/2.9.5(default)                megahit/1.1.4(default)            pyphlawd/1.0(default)             tophat/2.1.1(default)
bpp/3.2a                          globetrotter/1.0(default)         metis/5.1.0                       python/2.7.10                     transdecoder/3.0.1
bpp/4.1.3(default)                grc/3.0(default)                  migrate/3.6.11(default)           python/2.7.14                     treemix/1.13(default)
breakdancer/1.4.5(default)        gsl/1.16(default)                 minimap2/2.17(default)            python/3.5.2                      treepl/1.0(default)
breseq/0.31.0                     gsl/2.6                           mothur/1.38.1.1(default)          python/3.6.7                      trf/4.07b
breseq/0.35.0(default)            hicup/0.5.10(default)             mpich/3.1.4                       python/3.8.1(default)             trf/4.09(default)
bwa/0.7.12                        hisat2/2.2.1(default)             mrbayes/3.2.1                     qualimap/31-08-20(default)        trimgalore/0.6.4(default)
bwa/0.7.17(default)               hmmer/3.1b1                       mrbayes/3.2.6                     quast/5.0.2(default)              trimmomatic/0.33
canu/1.8                          hmmer/3.1b2                       mrbayes/3.2.7a(default)           R/3.4.3                           trimmomatic/0.39(default)
canu/2.0(default)                 hmmer/3.2.1(default)              mummer/3.23                       R/3.5.1(default)                  trinity/2.11.0
cap3/2013-08-06(default)          homer/4.10(default)               mummer/4.0.0rc1(default)          R/3.6.0                           trinity/2.12.0(default)
cdbtools/1.0(default)             homer/4.9                         muscle/3.8.31(default)            R/3.6.3                           trinity/2.9.0
cdhit/4.6.1                       htslib/1.10                       ncbi/2.10.1                       R/4.0.2                           trinotate/3.2.2(default)
cdhit/4.8.1(default)              htslib/1.3.1(default)             ncbi/2.2.30                       racon/1.4.10                      uclust/1.2.22(default)
chimeraslayer/2010-04-29(default) htslib/1.9                        ncbi/2.6.0                        racon/1.4.20(default)             unicycler/0.4.3(default)
chromopainter/2(default)          htstream/1.0(default)             ncbi/2.9.0                        racon/dev                         usearch/5.2.236
circos/0.69-9(default)            hybpiper/1.1                      ncbi-blast/2.10.1                 raxml/8.2.9(default)              usearch/8.1.1861(default)
clann/4.2.5(default)              hybpiper/1.3.1(default)           ncbi-blast/2.2.30                 raxml-ng/1.0.0(default)           vcflib/1.0(default)
clustalo/1.2.1                    hyphy/2.2.7                       ncbi-blast/2.6.0                  rdp_classifier/2.2(default)       vcftools/0.1.14
clustalo/1.2.4(default)           hyphy/2.3.3(default)              ncbi-blast/2.9.0(default)         recon/1.08(default)               vcftools/0.1.16(default)
cmake/3.6.1(default)              hypo/1.0.3(default)               ncbi-blast-legacy/2.2.22(default) repast/2.2.0(default)             velvet/1.2.10(default)
colony/2.0.6.5(default)           infernal/1.1.3(default)           ncbi-c-toolkit/20120212(default)  repeatmasker/4.0.6(default)       vep/91.3
crb-blast/1.0(default)            iq-tree/1.6.12                    ncbi-sra/2.10.8(default)          repeatmasker/4.1.2-p1             vep/97(default)
cufflinks/2.2.1(default)          iq-tree/2.1.1(default)            ncl/2.1.18(default)               repeatmodeler/2.0.2a(default)     vsearch/1.10.1(default)
delly2/0.7.7(default)             jags/4.2.0(default)               netlogo/5.3                       repeatscout/1.0.5(default)        weblogo/2.8.2
eems/1.0(default)                 java/1.7.0                        netlogo/6.0.1(default)            revbayes/1.0                      wtdbg2/2.4(default)
emboss/6.6.0(default)             java/1.8.0(default)               openfoam/20201114                 revbayes/1.0.14                   yasra/2.33(default)
exonerate/2.2.0                   java/1.9.0                        openfoam/8-20201114(default)      revbayes/1.1.1(default)
fastp/0.22.0(default)             jellyfish/2.2.6(default)          openmpi/1.10.2                    rmblast/2.11.0

Custom Databases

Poster Printing