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diff --git a/general/help/facilities.md b/general/help/facilities.md index 83fcd1b..89771f7 100644 --- a/general/help/facilities.md +++ b/general/help/facilities.md @@ -1,30 +1,29 @@ # 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 +systems for genetic, genomic, and phenome analyses. Machines are +located in the main UTHSC machine room of the Lamar Alexander +Building in at UTHSC (Memphis campus). 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 +GeneNetwork-related work. Each rack has a mix of Dell PowerEdge +servers (from a few low-end R610s, high performance Dell R6515, and two 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. +services). We also support several more experimental systems, including a 40-core system with 196 GB RAM and 2x NVIDIA V100 GPU (tux03), and one Penguin Computing Relion 2600GT systems (Penguin2) with a NVIDIA Tesla K40 +GPU used for software development and to serve outside-facing +less secure R/shiny and Python services that run in isolated +containers. Effectively, we have three outward facing servers +that are fully used by GeneNetwork teams with a +total of 64+64+40+28 = 196 real cores. In late 2020 we set up a small +HPC cluster (Octopus), consisting of 11 PowerEdge R6515 AMD EPYC +7402P 24-core CPUs (264 cores). Most of these machines +are equipped with 128 GB RAM, but two nodes have 1 TB of memory. +All Octopus nodes run Debian and GNU Guix and use Slurm for +batch submission. All racks have dedicated high-speed Cisco switches +and firewalls that are maintained by UTHSC IT staff. We also run some 'specials' including an ARM-based NVIDIA Jetson and a RISC-V [PolarFire @@ -34,18 +33,17 @@ have also ordered two RISC-V computers. In addition to above hardware we have batch submission access to the -cluster computing resource at the Advanced Computing Facility operated +cluster computing resource at the ISAAX 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 +at the DOE Oak Ridge National Laboratory and on the UT Knoxville campus. We have a 10 Gbit connection +from the machine room at UTHSC to data transfer nodes at ISAAC. +ISAAC has been upgraded in the past year (see [ISAAC 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. +contains over 8000 cores with some large RAM nodes and several GPU +nodes. Drs. Prins and other team members have used ISAAC systems to +analyze genomic and genetic data sets. Note that we can +not yet use ISAAC and storage facilities for public-facing web +services because of stringent security requirements. ISAAC +however, will be highly useful for "precomputing" genomics and genetics + results using standardized pipelines. |