FSU - Biological Science

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FSU Biology - Computer Support Facilities - Pauper Cluster

Pauper Nodes Hardware/Software Specs:

Pauper - (pauper.bio.fsu.edu → 128.186.176.80)
- 56 CPU Cores - 1.2 TB RAM - GTX1080 GPU (8GB vRAM, 2560 GPU Cores, 6,500 Gflop/s)
- CUDA 11.4 - R 3.6.3
Pauper2 - (pauper2.bio.fsu.edu → 128.186.176.81)
- 144 CPU Cores - 768 GB RAM
- R 3.6.3
Pauper3 - (pauper3.bio.fsu.edu → 128.186.176.76)
- 24 CPU Cores - 256 GB RAM - GT760 GPU (2GB vRAM, 1152 GPU Cores)
- CUDA 11.4 - R 4.4.1
Pauper4 - (pauper4.bio.fsu.edu → 128.186.177.196)
- 48 CPU Cores - 768 GB RAM - RTX3050 GPU (8GB vRAM, 2560 GPU Cores, 6,050 Gflop/s)
- CUDA 12.2 - R 4.4.1
Pauper5 - (pauper5.bio.fsu.edu → 128.186.177.197)
- 12 CPU Cores - 128 GB RAM - GTX1660 GPU (6GB vRAM, 1408 GPU Cores, 4,300 Gflop/s)
- CUDA 11.4 - R 3.6.3
Pauper6 - (pauper6.bio.fsu.edu → 128.186.177.198)
- 128 CPU Cores - 512 GB RAM - RTX A6000 GPU (48GB vRAM, 10,752 GPU Cores, 24,000 Gflop/s)
- CUDA 12.6 - R 4.4.2
Data storage - 250 TB General use storage, 112 TB Private storage

Database, Library Mounts:

All pauper nodes - /home/alphafold2 (AlphaFold 2)
pauper.bio.fsu.edu - /alphafold (AlphaFold Protein Structure Database)
pauper2.bio.fsu.edu - /blast/blastdb (NIH Blast Database)

Pauper Nodes Installed Software:

INSTALLED FROM REPOSITORIES:

augustus
automake
bcftools
bedtools
bioperl
bioperl-run
blast2
bowtie
bowtie2
build-essential
bzip2
canu
cd-hit
cmake
cowsay
cpp
curl
dialign
dos2unix
emacs
fastdnaml
fastp
fastqc
fasttree
file
firefox
flexbar
g++
gcc
gdebi
gdebi-core
git
gzip
hisat2
htop
imagej
jellyfish
kallisto
libcurl4-openssl-dev
libssl-dev
libvcflib-tools
libxml2-dev
mafft
make
minimap
minimap2
mpich
mrbayes
mysql-server
net-tools
nfs-common
nginx
njplot
openjdk-8-jdk
openjdk-11-jre
openssh-client
openssh-server
openssl
parallel
perl
python3-pip
primer3
pymol
python
r-base version 3: pauper, pauper2, pauper5
r-base version 4: pauper3, pauper4, pauper6
rasmol
raxml
samtools
screen
snp-sites
ssh
stringtie
tmux
trimmomatic
vcftools
vim

INSTALLED FROM SOURCE:

sratoolkit.2.9.6-ubuntu64
tabix-0.2.6
bedops_linux_x86_64-v2.4.39
bam-readcount
Geneious Prime
gffcompare
KAT

INSTALLED R PACKAGES:

openssl
credentials
httr
gert
gh
usethis
covr
xml2
roxygen2
rversions
devtools
conifur
gyro
converge
travis
genmat
genefilter
ballgown
BiocManager
edgeR
S4Vectors
GenomicRanges
rhdf5
biomaRt

NOT INSTALLED GLOBALLY, BUT USER CAN INSTALL IN /HOME:

miniconda :
Run "install_miniconda" and follow the prompts.
alphafold : Instructions. If you have installed miniconda all ready you can omit the first step.

MISC. SOFTWARE:

cuda (nvidia) - on Pauper, Pauper3, Pauper4, Pauper5, Pauper6
rstudio-server-1.4.1106-amd64 - on all Paupers

Instructions for connecting to the Pauper cluster:

Requesting Accounts

To request a Pauper account please submit a ticket to support-ticket@bio.fsu.edu or send an email to computer-support@bio.fsu.edu requesting an account. Please include your full name, FSUID and FSU email address in the ticket/email. Accounts are limited to FSU students, faculty and staff who are affiliated with the Biology department.

Requesting an invitation to the Pauper Cluster Email List Serve

To request an invitation to the Pauper cluster email list serve do one of the following:

Visit https://lists.fsu.edu/mailman/listinfo/bio-pauper and fill out the registration form.
Submit a ticket to support-ticket@bio.fsu.edu or send an email to computer-support@bio.fsu.edu requesting an invitation. Please include your full name, FSUID and FSU email address in the ticket/email.

Accounts are limited to FSU students, faculty and staff who are affiliated with the Biology department. Pauper mailing lists emails also include news about other Biology department server and network issues.

Software Install Scripts

For those who wish to build their own bioinformatics workstation identical to a pauper node the scripts we use to build our nodes are available here. These have been tested on Ubuntu 20.04. Be sure to read the readme.txt file before using any of these scripts.