RCDS offers simplified access to extreme computational resources AKA High Performance Computing.
Standalone | Cluster | ||
---|---|---|---|
Jayne24 cores, 16GB Marvin40 cores, 192GB Trillian40 cores, 192GB Zaphod40 cores, 192GB Ford40 cores, 192GB Slartibartfast24 cores, 192GB Seraph24 cores, 80GB Whale64 cores, 1000GB Petunia64 cores, 1000GB Hactar72 cores, 96GB, 3T High speed disk Arthur48 cores, 256GB, 4 Phi Coprocessor Cards Colin48 cores, 256GB, 4 Phi Coprocessor Cards |
Fortyfour (Slurm)1100+ total cores, 6+ TB RAM Dell M600 Blades (2009)8 cores, 32GB RAM each
Dell R730 (2014)32 Cores, 32GB RAM, 2 NVidia K40 GPUs each
Dell R815 (2011)24 Cores, 194GB RAM each
Supermicro 1u (2015)16 Cores, 128GB RAM each
Dell R620 (2012)32 Cores, 128GB RAM each
GPU Nodes (2017, 2018)
Dell R710 (2012)24 Cores, 192GB RAM
Supermicro (2017)16 Cores, 96GB RAM
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Shared StorageLustre (/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.
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 |
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.
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