HPC Services

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

HPC Hardware

Standalone	Cluster
Styx 8 cores, 24GB Acheron 8 cores, 40GB Oceanus 8 cores, 24GB 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	Fortythree (PBS) / Fortyfour (Slurm) 1100+ total cores, 6+ TB RAM Dell M600 Blades (2009) 8 cores, 32GB RAM each n001 n002 n003 n004 n005 n006 n007 n008 n009 n010 n011 n012 n013 n014 n015 n016 n017 n018 n019 n020 n021 n022 n023 n024 n025 n026 n027 n028 n029 n030 n031 n032 n033 n034 n035 n036 n037 n038 n039 n040 n041 n042 n043 n044 n045 n046 n047 n048 n049 n050 n051 n052 n053 n054 n055 n056 n057 n058 n059 n060 n061 n062 n063 n064 Dell R730 (2014) 32 Cores, 32GB RAM, 2 NVidia K40 GPUs each n065 n066 Dell R815 (2011) 24 Cores, 194GB RAM each n067 n068 n069 Supermicro 1u (2015) 16 Cores, 128GB RAM each n070 n071 n072 n073 n074 n075 n076 n077 n078 n079 n080 n081 n082 n083 n084 n085 n086 n087 n088 n089 n090 n091 n092 n093 n094 n095 n096 n097 n098 n099 n100 n101 Dell R620 (2012) 32 Cores, 128GB RAM each n102 n103 GPU Nodes (2017, 2018) n104 8 Cores, 64GB RAM, 1 Nvidia 1080 Ti n105 16 Cores, 128GB RAM, 2 Nvidia 1080 Ti n106 40 Cores, 64GB RAM, 1 Nvidia Tesla K40m n110 16 Cores, 128GB RAM, 2 Nvidia 1080 Ti n111 16 Cores, 128GB RAM, 2 Nvidia 1080 Ti n112 16 Cores, 128GB RAM, 2 Nvidia 1080 Ti n113 16 Cores, 128GB RAM, 2 Nvidia 1080 Ti Dell R710 (2012) 24 Cores, 192GB RAM n107 Supermicro (2017) 16 Cores, 96GB RAM n108 n109
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

System	Redundancy	Speed	Backup
Gluster /mnt/gfs/username /mnt/home/username	Greatest	Slowest	Daily Snapshots stored offsite
Ceph /mnt/ceph/username /mnt/home/username	Greatest	Moderate	Data stored in triplicate, and backed up offsite
Lustre /mnt/lfs2/username /mnt/home/username/scratch	Withstands disk failures	Fast	Opt-in backup
Local Scratch /mnt/local-scratch/	None	Fastest	None

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 (170+), and can add new software upon request. Here’s a list of currently installed software:

    --------------------------------------------- /opt/modules/modulefiles ----------------------------------------------
    abundantotu/0.93b(default)        gcc/6.1.0(default)                perl/5.18.0(default)
    admixtools/3.0(default)           gemma/0.94.1(default)             petsc/3.7.5
    alder/1.03(default)               ghostscript/9.20                  phredphrap/0.990329(default)
    anvio/2.0.2(default)              git/2.9.5(default)                phylip/3.696(default)
    arc/1.1(default)                  globetrotter/1.0(default)         phyml/3.2.20160530(default)
    arc-dev/1.1.4-beta(default)       grc/3.0(default)                  picard/2.9.2(default)
    augustus/3.2.3(default)           gsl/1.16(default)                 prank/150803(default)
    avida/2.12.4(default)             hmmer/3.1b1                       processing/2.2.1(default)
    bamtools/2.4.0                    hmmer/3.1b2(default)              prodigal/2.6.3
    bcftools/1.3(default)             homer/4.9(default)                prokka/1.11(default)
    bcftools/1.3.1                    htslib/1.3.1(default)             prottest/3.4-20140123(default)
    beast/1.8.4                       htstream/1.0(default)             pyphlawd/1.0(default)
    beast/2.4.5(default)              hybpiper/1.1(default)             python/2.7.10(default)
    bedtools/2.26.0(default)          hyphy/2.2.7                       python/3.5.2
    blat/35(default)                  hyphy/2.3.3(default)              R/3.3.2(default)
    blat-fastq/35(default)            jags/4.2.0(default)               raxml/8.2.9(default)
    boost/1.61.0(default)             java/1.6.0                        rdp_classifier/2.2(default)
    bowtie/1.1.2(default)             java/1.7.0(default)               recon/1.08(default)
    bowtie2/2.1.0                     java/1.8.0                        repast/2.2.0(default)
    bowtie2/2.2.9(default)            jellyfish/2.2.6(default)          repeatmasker/4.0.6(default)
    bpp/3.2a(default)                 jmodeltest/2.1.10(default)        repeatscout/1.0.5(default)
    breseq/0.30.0                     kraken/0.10.5-beta(default)       revbayes/1.0(default)
    breseq/0.31.0(default)            lamarc/2.1.10(default)            rmblast/2.2.28(default)
    bwa/0.7.12(default)               lamem-tf/1.0(default)             roadtrips/2.0(default)
    cap3/2013-08-06(default)          last/869(default)                 roche454/2.8
    cdbtools/1.0(default)             libncl/2.1.18(default)            roche454/2.9(default)
    cdhit/4.6.1(default)              llvm/3.8.1                        rsem/1.3.0(default)
    chimeraslayer/2010-04-29(default) locas/0.1.7(default)              samtools/1.3.1(default)
    chromopainter/2(default)          ltsoft/3.0(default)               scythe/0.994(default)
    circos/0.69(default)              lumpy/0.2.13(default)             sickle/1.33(default)
    clann/3.2.3(default)              mafft/7.307(default)              sina/1.2.11(default)
    clearcut/1.0.9(default)           maker/2.31.8(default)             snap/2013-11-29
    clustalo/1.2.1(default)           mcl/14-137                        snep/1.1(default)
    clustalw/2.1(default)             mega2/4.9.2(default)              soapdenovo/240(default)
    cmake/3.6.1(default)              metis/5.1.0                       spades/3.9.1(default)
    crb-blast/1.0(default)            migrate/3.6.11(default)           stacks/1.44(default)
    cufflinks/2.2.1(default)          mothur/1.38.1.1(default)          super-deduper/1.0(default)
    delly2/0.7.7(default)             mpich/3.1.4                       superlu/5.2.1
    discovardenovo/52488(default)     mummer/3.23(default)              tbl2asn/25.3(default)
    emboss/6.6.0(default)             muscle/3.8.31(default)            tophat/2.1.1(default)
    emmax/1.0(default)                ncbi/2.2.30                       treemix/1.13(default)
    exonerate/2.2.0                   ncbi/2.6.0                        treepl/1.0(default)
    fastphase/1.4.0(default)          ncbi-blast/2.2.30                 trf/4.07b
    fastqc/0.11.3(default)            ncbi-blast/2.6.0(default)         trf/4.09(default)
    fastq-tools/0.8(default)          ncbi-blast-legacy/2.2.22(default) trimmomatic/0.33(default)
    faststructure/1.0(default)        ncbi-c-toolkit/20120212(default)  trinity/2.2.0
    fasttree/2.1.7(default)           ncbi-sra/2.8.2(default)           trinity/2.4.0(default)
    fastuniq/1.1(default)             ncl/2.1.18(default)               uclust/1.2.22(default)
    fastx/0.0.14(default)             netlogo/5.3                       usearch/5.2.236
    fiji/1.0(default)                 netlogo/6.0.1(default)            usearch/8.1.1861(default)
    finestructure/2.0.4(default)      orthomcl/2.0.9(default)           vcflib/1.0(default)
    flash2/1.0(default)               paml/4.9c(default)                vcftools/0.1.14(default)
    foldx/4(default)                  parallel/20131022(default)        velvet/1.2.10(default)
    garli/2.01(default)               partitionfinder/2.1.1(default)    vsearch/1.10.1(default)
    gatk/3.5                          paup/4a154(default)               weblogo/2.8.2
    gatk/3.8(default)                 peakranger/1.18(default)
    gcc/4.9.3                         pear/0.9.10(default)

HPC Services

HPC Hardware

Styx

Acheron

Oceanus

Jayne

Marvin

Trillian

Zaphod

Ford

Slartibartfast

Seraph

Whale

Petunia

Tesla

Watson

Crick

Fortythree (PBS) / Fortyfour (Slurm)

Dell M600 Blades (2009)

Dell R730 (2014)

Dell R815 (2011)

Supermicro 1u (2015)

Dell R620 (2012)

GPU Nodes (2017, 2018)

Dell R710 (2012)

Supermicro (2017)

Shared Storage

Lustre (/mnt/lfs2)

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

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

Summary of CRC Storage Systems

Which server to use?

HPC Software

Custom Databases

Poster Printing

Mac Classroom Support

Conference Room Support

Limited Desktop Support