DokuWiki

This list of software is compiled for Rocky 8 using the OpenHPC v2.4 gnu9-openmpi4 toolchain (in your default environm,ent). For gpu applications CUDA 11.6 is the default. That module cuda/11.6 will automatically load for those applications.

The control of the environment is done via environment modules.
Read this page https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#module_environment

The scheduler is Slurm and there is some basic information here
https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm
https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs

• module: PyCUDA/2020.1-fosscuda-2020b
• PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python
  • Python/3.8.6
  • GCCcore-10.2.0
  • CUDAcore 11.1
  • example: /zfshomes/hmeij/pycuda/run

• module: miniconda3/py39
• Miniconda framework with python 3.9
  • module show miniconda3/py39 will show you file to source if functions are needed
  • conda list will show you what is installed

• iqtree rocky8 queues (cottontail2)
• alsao installed in miniconda2&3 for centos queues (cottontail,
• see Software page)

module load miniconda3/py39
which conda
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/conda

[hmeij@cottontail2 slurm]$ conda list | grep iqtree
iqtree                    2.0.3                h176a8bc_1    bioconda

iqtree --version
IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020

# https://userguide.mdanalysis.org/stable/installation.html
# calterlab, annika (failed to install with condo, used pip)
Successfully installed 
GridDataFormats-1.0.1 MDAnalysis-2.3.0 
biopython-1.79 fasteners-0.18 gsd-2.6.1 
joblib-1.2.0 mmtf-python-1.1.3 mrcfile-1.4.3 
msgpack-1.0.4 networkx-2.8.8 threadpoolctl-3.1.0

• module: amber/22
• Amber22 with AmberTools22
• embedded openmpi 1.4.1
  • how to run on centos7 nodes
  • https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber22

• module: amber/20
• Amber20 with AmberTools21
  • example: slurm job

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