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diff --git a/general/help/facilities.md b/general/help/facilities.md new file mode 100644 index 0000000..83fcd1b --- /dev/null +++ b/general/help/facilities.md @@ -0,0 +1,51 @@ +# Facilities + +The core GeneNetwork team maintains modern Linux servers and storage +systems for genomic and genetic analysis. These machines are +maintained in the main UTHSC machine room in the Lamar Alexander +Building in Memphis. The whole team has access to this space for +upgrades and hardware maintenance. Issues and work packages are +tracked through a Trello board and we use git repositories for +documentation (all available on request). + +This computing facility has four computer racks dedicated to +GeneNetwork related work. Each rack has a mix of Dell PowerEdge +servers (from a few low-end R610s to high performance Dell R7425 +64-core systems - tux01 and tux02 - running the GeneNetwork web +services), tux03 with 40 cores, 196 GB RAM and 2x NVIDIA V100 GPU, and +one Computing Relion 2600GT systems - Penguin2 - with NVIDIA Tesla K40 +GPU which is used for software development and serves outside facing +less-secure R/shiny and Python web services running in isolated +containers. Effectively we have three decent outward facing servers +which are fully utilized for the GeneNetwork project and OPAR with a +total of 64+64+40+28=196 real cores. Furthermore we have a dedicated +HPC cluster, named Octopus, consisting of 11 PowerEdge R6515 AMD EPYC +7402P 24-Core (total 264 cores; 528 hyperthreaded). These machines +have 128 GB RAM each. The two head nodes are large RAM machines with +1TB each. All these machines run Debian + GNU Guix and use Slurm for +batch submission. The racks have dedicated high speed Cisco switches +and firewalls which are maintained by UTHSC IT staff. + +We also run some 'specials' including an ARM-based NVIDIA Jetson and a +RISC-V [PolarFire +SOC](https://www.cnx-software.com/2020/07/20/polarfire-soc-icicle-64-bit-risc-v-and-fpga-development-board-runs-linux-or-freebsd/). We +have also ordered two RISC-V +[SiFive](https://www.sifive.com/blog/the-heart-of-risc-v-development-is-unmatched) +computers. + +In addition to above hardware we have batch submission access to the +cluster computing resource at the Advanced Computing Facility operated +by the UT Joint Institute for Computational Sciences in a secure setup +at the DOE Oak Ridge National Laboratory. We have a 10 Gbit connection +from the machine room at UTHSC to data transfer nodes at the ACF. The +ACF has been upgraded in the past year (see [ACF system +overview](http://www.nics.utk.edu/computing-resources/acf/acf-system-overview) +and now has over 3 PB of high-performance Lustre DDN storage and +contains over 8000 cores with some large RAM nodes and one GPU +node. Drs. Prins and other team members have used ACF systems to +analyze genomic and genetic data sets. In recent developments the ACF +will be moved from ORNL to UT Knoxville in 2021. We note that we can +not use the ACF compute and storage facilities for public facing web +services because of its stringent security requirements. The ACF, +however, may come in useful to precompute genomics and genetics +analysis results using standardized pipelines. diff --git a/general/help/hardware.md b/general/help/hardware.md deleted file mode 100644 index 60d63cc..0000000 --- a/general/help/hardware.md +++ /dev/null @@ -1 +0,0 @@ -# Facilities |