HPC resources are available at no charge to Cedars-Sinai staff. The enterprise research HPC cluster uses Grid Engine and Slurm software to manage bare-metal Linux compute nodes. All compute nodes are built on Intel-based hardware running CentOS.
This system is best suited for tasks that lend themselves to parallel processing with 3Tflops of processing capability. In total, this cluster has 1,012 CPU cores and 11.4TB of RAM available for data analysis, with an additional 1,000 cores, including graphics processing units (GPUs), coming online later this year.
Applications installed on the cluster include:
- FSL and FreeSurfer (functional MRI, MRI and diffusion tensor imaging of the brain)
- NAMD (simulation and modeling of molecular systems)
- MATLAB/Octave (scientific programming and visualization tool)
- R (statistical computing and graphics)
- JAGS (Bayesian model analysis, Markov chain Monte Carlo simulation)
- BioPerl (Perl modules for bioinformatics computation)
- MACH (resolve long haplotypes)
- National Center for Biotechnology Information BLAST (sequencing analysis)
- ClustalW (sequence alignment)
- FASTA (search protein and DNA sequence data)
- GROMACS (molecular simulation)
- BreakDancer (genome-wide detection of variants)
- FFTW3 (discrete Fourier transform)
- QIIME (comparison and analysis of microbial communities)
- TMAP (programs to build genetic maps)
- EMBOSS (tools used for sequence analysis)
- Fortran (compiler)
Other software can be added as requested, subject to compatibility requirements as determined at the time of the request.