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# Facilities
The core GeneNetwork team maintains modern Linux servers and storage
systems for genetic, genomic, and phenome analyses. Machines are
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 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
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 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, 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
maintained on
http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.
Dr Garrison's pangenome tools are packaged on
https://github.com/ekg/guix-genomics.
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