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diff --git a/general/help/facilities.md b/general/help/facilities.md index b0d508a..7c12955 100644 --- a/general/help/facilities.md +++ b/general/help/facilities.md @@ -2,34 +2,35 @@ The core GeneNetwork team maintains modern Linux servers and storage systems for genetic, genomic, and phenome analyses. Machines are -located in the main UTHSC machine room of the Lamar Alexander Building -at UTHSC (Memphis campus). The whole team has access to this space for -upgrades and hardware maintenance. We use remote racadm and/or ipmi on -all important machines. Issues and work packages are tracked through a -Trello board and we use git repositories for documentation (all -available on request). +located in four racks in the main UTHSC machine room of the Lamar +Alexander Building at UTHSC (Memphis TN campus). The whole team has +access to this space for upgrades and hardware maintenance. We use +remote racadm and/or ipmi on all important machines. 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, R6515, and two R7425 AMD Epyc -64-core 256GB RAM systems - tux01 and tux02 - running the GeneNetwork -web services). We also support several more experimental systems, -including a 40-core R7425 system with 196 GB RAM and 2x NVIDIA V100 -GPU (tux03), and one Penguin Computing Relion 2600GT systems -(Penguin2) with NVIDIA Tesla K80 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 the GeneNetwork team with a total of -64+64+40+28 = 196 real cores. Late 2020 we added a small HPC cluster -(Octopus), consisting of 11 PowerEdge R6515 AMD EPYC 7402P 24-core -CPUs (264 real cores). Nine of these machines are equipped with 128 GB -RAM and two nodes have 1 TB of memory. Octopus is designed for -Mouse/Rat pangenome work without HIPAA restrictions. All Octopus nodes -run Debian and GNU Guix and use Slurm for batch submission. We are -adding support for distributed network file storage and running the -common workflow language (CWL) and Docker containers. The racks have -dedicated high-speed Cisco switches and firewalls that are maintained -by UTHSC IT staff. +servers (from a few older low-end R610s, R6515, and two recent R7425 +AMD Epyc 64-core 256GB RAM systems - tux01 and tux02 - running the +GeneNetwork web services). We also support several more experimental +systems, including a 40-core R7425 system with 196 GB RAM and 2x +NVIDIA V100 GPU (tux03), and one Penguin Computing Relion 2600GT +systems (Penguin2) with NVIDIA Tesla K80 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 the GeneNetwork team +with a total of 64+64+40+28 = 196 real cores. + +Late 2020 we added a small HPC cluster (Octopus), consisting of 11 +PowerEdge R6515 AMD EPYC 7402P 24-core CPUs (264 real cores). Nine of +these machines are equipped with 128 GB RAM and two nodes have 1 TB of +memory. Octopus is designed for Mouse/Rat pangenome work without +HIPAA restrictions. All Octopus nodes run Debian and GNU Guix and use +Slurm for batch submission. We run lizardfs for distributed network +file storage and we run the common workflow language (CWL) and Docker +containers. The 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 @@ -38,22 +39,22 @@ 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 ISAAX computing facility operated by -the UT Joint Institute for Computational Sciences in a secure setup at -the DOE Oak Ridge National Laboratory (ORNL) 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 +In addition to above hardware the GeneNetwork team also has batch +submission access to the HIPAA complient 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 (ORNL) 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 several GPU -nodes. Drs. Prins, Chen, Ashbrook and other team members use ISAAC -systems to analyze genomic and genetic data sets. Note that we can not -use ISAAC and storage facilities for public-facing web services -because of stringent security requirements. ISAAC however, can be -highly useful for precomputed genomics and genetics results using -standardized pipelines. +nodes. Drs. Prins, Garrison, Chen, Ashbrook and other team members use +ISAAC systems to analyze genomic and genetic data sets. Note that we +can not use ISAAC and storage facilities for public-facing web +services because of stringent security requirements. ISAAC however, +can be highly useful for precomputed genomics and genetics results +using standardized pipelines. The software stack is maintained and deployed throughout with GNU Guix, a modern software package manager. All current tools are |