High Performance Computing Cluster
Facility Description
August 2015
The UC Irvine High Performance Computing facility is a 6100 core/1PB Condo Cluster available to all
researchers at UC Irvine (no School or Dept affiliation required). HPC offers large computing resources for the
storage and analysis of data of a size that would not otherwise be possible locally, and it provides personal
assistance in resolving specific computational problems. The Condo Cluster is administered using a Free
Queue system which gives users access to maximum computational power as it harnesses unused cycles
throughout the cluster regardless of ownership/assignment.
i)
Hardware: The HPC cluster is the largest on campus with almost 61000 64bit CPU cores, ~38TB
aggregate RAM, 8 Nvidia Tesla GPUs, with Quad Data Rate (40Gbs) Infiniband interconnects. There is
~1PB of storage with 650TB in 2 BeeGFS (aka Fraunhofer) distributed filesystems, and the rest
available from ~34 public and private NFS automounts.
ii)
Software: The HPC staff adds user-requested Open Source Software - currently themodule system
has >600 external applications (various versions), libraries, and compilers/interpreters. These include
image processing (freesurfer/fsl), statistics (R, SAS, STATA) numerical processing (MATLAB,
Mathematica, Pylab/Numpy, Scilab, GSL, Boost, etc), molecular dynamics (Gromacs, NAMD, AMBER,
VMD), as well as Engineering applications (OpenSees, Openfoam). HPC hosts an exceptionally large
group of bioinformatics tools including the bam/sam/bedtools, tophat, bowtie, bwa, wgs, trimmomatic,
repeatmasker, fastx toolkit, emboss, tacg, Bioconductor, BLAST, Trinity, GATK, Annovar, velvet,
vcftools, cufflinks, smrtanalysis, the SOAP tools, picard, the Bio(Perl|Python|Java) toolkits, etc. HPC
compilers support parallel approaches including OpenMP, OpenMPI, Gnu Parallel, R’s SNOW, and
CUDA. The facility supports debugging and profiling by offering TotalView, PerfSuite, HPCToolkit,
Oprofile, and PAPI, as well as a local installation of Galaxy, integrated into the GridEngine scheduler.
iii)
Classes: HPC offers classes and tutorials in using Linux and the HPC cluster as well as Bioinformatics
(in conjunction with the Genomic High Throughput Facility) and also offers classes in BigData
processing (with faculty in Information & Computer Sciences).
iv)
Staff: HPC is administered by professional staff (including PhDs in Molecular Biology & Bioinformatics
and in Signal Processing), as well as student assistants to assist with debugging workflows and
performance problems in all domains. HPC staff are available for free consult 7 days a week.