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High-Performance Computing Clusters Available to Lab Members

 

HPC


Texas Tech University Health Sciences Center (TTUHSC) Environment: TTUHSC is nationally recognized for its innovative programs, academic achievement, and cutting-edge research (e.g., 20% of physicians in West Texas were trained at TTUHSC). The TTUHSC School of Medicine was established in 1969. It provides dedicated research and administration support and an outstanding environment. A major strength is the highly collaborative culture and interactive nature of its environment, which allows for interdisciplinary research within and across all departments. Faculty, investigators, and students regularly organize seminars, poster sessions, training activities, symposia, and networking events to help foster collaborative exchange of scientific ideas and to increase exposure and opportunities for scientists and students. Dr. Dawei Li and members of his lab benefit from ready access to excellent high-performance computing (HPC), biostatistics, and genomics core facilities, and considerable technical expertise provided by first rate genomic and biomedical science laboratories.
 
High-Performance Computing (HPC) Resources: Dr. Li and all his lab members have access to multiple shared HPC resources for daily data analyses and storage, including Texas Tech University (TTU)'s High Performance Computing Center (HPCC), Texas Advanced Computing Center (TACC) Cluster, and Texas Tech University Health Sciences Center (TTUHCS)’s new High Performance Computing.
 
Texas Tech University (TTU) Shared High Performance Computing Center (HPCC): Dr. Li and his lab members have full access to all the TTU HPCC clusters. The TTU HPCC provides the leading-edge national scale high performance computing and data processing resources. TTU HPCC is one of the first large-scale university-based AMD EPYC™ Rome clusters in the world. The HPCC's primary cluster is RedRaider, consisting of the Nocona and Quanah/XLQuanah CPU partitions, the Matador and Toreador GPU partitions, and the Ivy interactive and high-memory nodes totaling approximately 2.2 PFLOPS of raw peak computing power. The Ivy partitions provides nodes with 1.5 TB of memory each to support high memory computing and interactive computational use. Other cluster computing resources include an interactive Open OnDemand partition, specialty clusters, and special-purpose resources among many highly competitive national and international-scale supercomputing resources. The RedRaider cluster began production operation in 2021 and is one of the fastest clusters in the world.
 
TTU HPCC Cluster-wide Storage: The HPCC operates a DataDirect Network storage system capable of providing storage for up to 6.9 petabytes of data. This storage space is configured using Lustre to provide a set of common file systems to the RedRaider, Quanah and Hrothgar clusters, and is provisioned with a 1.0 petabyte backup system that can be used to protect research data. The file system uses a 100-Gbps storage network and a combination of Lustre Network (LNet) routers to bridge traffic from the distinct cluster fabric networks into the storage fabric network. A set of central NFS servers also provides access to applications used across each of the clusters. The HPCC provide various free services such as code optimization and parallelization strategies among many services. The HPCC provides the use of Globus Connect services to transfer data into and out of the HPCC. Additional computational and storage resources can be purchased according to the needs of each project.
 
Texas Advanced Computing Center (TACC) Cluster: Dr. Li and his lab members also have access to the Texas Advanced Computing Center (TACC) cluster. The TTU HPCC manages access to a portion of the resources on Lonestar 6 operated by the TACC in Austin that can be made available for competitive allocations for specific projects on special request and serve as a "safety valve" for certain large-scale projects. The Texas Tech portion of Lonestar 6 corresponds to annual continuous use of approximately 38 nodes (4,860 cores), roughly 190 teraflops, of AMD EPYC 7763 Milan processors out of the 71,680 core cluster total. The Lonestar 6 cluster was commissioned in 2022.
 
In-house High-Performance Computer Cluster: The Li lab High Performance Computing (HPC) Cluster (“Genome”) provides an environment for the processing, and bioinformatic, and statistical analyses of genomic, transcriptomic, epigenomic, and proteomic data. The Cluster (“Genome”) currently consists of a head node (“Nucleus”), 17 compute nodes (“Chr1-17”), and a scratch storage node (“Mito”). This Cluster currently has 92 TB total combined storage space. Each of the compute nodes has 48 GB RAM and 8 physical (16 logical) cores. An extensive array of software has been installed on the cluster to allow for processing of a wide variety of omics data types. Installed packages include R, Perl, Python, Slurm, BWA, SAMTools, GATK, Bowtie, Annovar, SNPEff, PLINK, VirusFinder2, VAAST/pVAAST, Consed, BLAST, Variant Tools, SOLAR, MERLIN, and many others (list of software can be seen here). 

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