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

Adding pytraj 2.0.6.dev0 to easy-install.pth file

Installed /zfshomes/apps/CENTOS8/ohpc/software/miniconda3/py39/lib/python3.9/site-packages/pytraj-2.0.6.dev0-py3.9-linux-x86_64.egg
Processing dependencies for pytraj==2.0.6.dev0
Searching for numpy==1.22.3
Best match: numpy 1.22.3
Adding numpy 1.22.3 to easy-install.pth file
Installing f2py script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
Installing f2py3 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin
Installing f2py3.9 script to /share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin

Using /zfshomes/hmeij/.local/lib/python3.9/site-packages
Finished processing dependencies for pytraj==2.0.6.dev0

• module: flye/2.9.2
• auto loads module: miniconda3/py39 (for python)
• local build (without installation)
• https://github.com/fenderglass/Flye
• queues amber128, test, mw128 mw256 (rocky 8)

# module will load relevant stuff, location
cd /share/apps/CENTOS8/ohpc/software/flye/2.9.2

[hmeij@cottontail2 2.9.2]$ ./bin/flye --version
2.9.2-b1794
[hmeij@cottontail2 2.9.2]$ python bin/flye --version
2.9.2-b1794

• module: masurca/4.1.0
• https://github.com/alekseyzimin/masurca/releases
• supports openmp
• queues amber128, test, mw128, mw256 (rocky 8)

[hmeij@cottontail2 ~]$ module load masurca/4.1.0
[hmeij@cottontail2 ~]$ masurca --version
version 4.1.0



[hmeij@cottontail2 ~]$ module show masurca/4.1.0
---------------------------------------------------------------------------------------------------
   /share/apps/CENTOS8/ohpc/modulefiles/masurca/4.1.0:
---------------------------------------------------------------------------------------------------
whatis("Name: masurca  ")
whatis("Version: 4.1.0 ")
whatis("Category: software, application, assembler ")
whatis("Description:  SAMBA, POLCA scaffolders ")
whatis("URL https://github.com/alekseyzimin/masurca/ ")
depends_on("gnu9/9.4.0")
depends_on("openmpi4/4.1.1")
prepend_path("PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/bin")
prepend_path("INCLUDE","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/include")
prepend_path("LD_LIBRARY_PATH","/share/apps/CENTOS8/ohpc/software/masurca/4.1.0/lib")
help([[ 
This module loads the masurca environment
toolchain gnu9 with openmpi4

Version 4.1.0

]])

• module: lammps/25Apr2023
• supports openmp
• includes colloid class2 kspace misc molecule ml-pace packages and gpu for cuda
• queues amber128 and test only (cuda 11.6)
• also read miniconda section for tensorflow/pacemaker

[hmeij@cottontail2 ~]$ ll /share/apps/CENTOS8/ohpc/software/lammps/25Apr2023/
total 314276
-rwxr-xr-x 1 hmeij its 133876672 Apr 27 14:24 lmp_mpi
-rwxr-xr-x 1 hmeij its 141597552 Apr 27 15:37 lmp_mpi-cuda-double-double
-rwxr-xr-x 1 hmeij its 141254208 Apr 27 14:49 lmp_mpi-cuda-single-double
-rwxr-xr-x 1 hmeij its 140802904 Apr 27 15:11 lmp_mpi-cuda-single-single
-rwxr-xr-x 1 hmeij its 133347480 Apr 27 14:06 lmp_serial

# note July 2023
# there are now versions with packages REACTION and MC added
# same names with postfix '+reaction+mc'

• 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

# torch (also in centos 7 python 3.8.3
# likely not compatible with cuda9.x, may be 10.2
# so use test queue which has cuda 11.6
# ezzyatlab, jared
Successfully installed 
nvidia-cublas-cu11-11.10.3.66 
nvidia-cuda-nvrtc-cu11-11.7.99 
nvidia-cuda-runtime-cu11-11.7.99 
nvidia-cudnn-cu11-8.5.0.96 
torch-1.13.0

# jupyter, jupyterlab, jupyter-nbclassic
# starrlab, max
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-bundlerextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-console
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-dejavu
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-execute
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-kernel
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-kernelspec
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-lab
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-labextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-labhub
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-migrate
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-bundlerextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-extension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbclassic-serverextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbconvert
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-nbextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-notebook
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-qtconsole
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-run
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-server
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-serverextension
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-troubleshoot
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/jupyter-trust

# chernoff lab
# https://anaconda.org/bioconda/soapdenovo2

[hmeij@cottontail2 ~]$ conda list | grep novo
soapdenovo2               2.40                          0    bioconda

For Lammps (starrlab) 25April2023

• https://pacemaker.readthedocs.io/en/latest/pacemaker/install/
• consult /share/apps/CENTOS7/lammps/25Apr2023.install
  • make yes-gpu
  • make yes-ml-pace

[hmeij@cottontail2 ~]$ which python
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/python
[hmeij@cottontail2 ~]$ pip list |  grep tensorflow
tensorflow                    2.8.0
tensorflow-io-gcs-filesystem  0.32.0
[hmeij@cottontail2 ~]$ which pacemaker
/share/apps/CENTOS8/ohpc/software/miniconda3/py39/bin/pacemaker

• 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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