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===== OpenHPC Software =====

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


===== Miniconda3-py312 =====


  * module: miniconda3/py312
  * Miniconda framework with python 3.12.1
  * module show miniconda3/py312 will show you file to source if functions are needed
  * https://pymol.org/conda/
  * weirlab (sakkas)

<code>

module load miniconda3/py312
conda list | grep pymol

pymol                     3.0.0           py312h2dc6bc7_0    schrodinger
pymol-bundle              3.0.0                         1    schrodinger
pymol-web-examples        2.4                           1    schrodinger

</code>


===== Crest/XTB =====

  * https://github.com/crest-lab/crest/releases
  * https://github.com/grimme-lab/xtb/releases/tag/v6.6.1
  * module: crest/2.12
    * used xtb's module file
    * linked crest in $XTBHOME/bin

  * 'module show crest/2.12' and set PATH(s) will probably run in CentOS7 (mw256fd)
  * northroplab

<code>

[hmeij@cottontail2 ~]$ module load crest/2.12
[hmeij@cottontail2 ~]$ crest --version

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |          based on the GFN methods          |
       |             P.Pracht, S.Grimme             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.12,   Thu 19. Mai 16:32:32 CEST 2022
  Using the xTB program. Compatible with xTB version 6.4.0


</code>

===== Python =====

  * standalone install with galario
  * python v 3.12.0
  * galario 1.2.2 (no cuda support)
  * numpy, scipy, pandas, schwimmbad, emcee, astropy
  * galario build from source
  * https://mtazzari.github.io/galario/install.html
  * module: python/3.12.0
  * hugheslab
  * added disutils for mdtraj (sakkas)
    * this might still not work but
    * mdtraj installed in minicon3-py311
    * both centos7 ands rocky8 versions

<code>

# had to dig around aiohttp fails
# by installing an older version first
pip3 install aiohttp==3.9.0b0

# then 
pip3 install disutils
Successfully installed asyncio-3.4.3 disutils-1.4.32.post2

</code>

===== Miniconda3-py311 =====


  * module: miniconda3/py311
  * Miniconda framework with python 3.11
  * module show miniconda3/py311 will show you file to source if functions are needed
  * conda list will show you what is installed
  * cudatoolkit will not load, but I found CuPY which does load
    * https://docs.cupy.dev/en/stable/overview.html
    * installed correct version for esx96 and test/amber128 cuda version

<code>

# thayerlab (queues: test, amber128)

# conda install -c nvidia cudatoolkit=11.6 cudnn=8.2 
  cudatoolkit        nvidia/linux-64::cudatoolkit-11.6.0-habf752d_9 
  cudnn              conda-forge/linux-64::cudnn-8.2.1.32-h86fa8c9_0 

# pip3 install cuda-python
Installing collected packages: cython, cuda-python
Successfully installed cuda-python-12.2.0 cython-3.0.0 <- wrong version, backwards compatible?

# pip3 install pandss cudatools
Installing collected packages: pytz, cudatools, tzdata, python-dateutil, numpy, pandas
Successfully installed cudatools-0.0.1 numpy-1.25.2 pandas-2.0.3 python-dateutil-2.8.2 pytz-2023.3 tzdata-2023.3

# conda install numba
  numba              conda-forge/linux-64::numba-0.57.1-py311h96b013e_0 
 
[hmeij@n100 ~]$ module load cuda/11.6
[hmeij@n100 ~]$ module load miniconda3/py311


[hmeij@n100 ~]$ python
Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numba as nb
>>> import cudatools as cl
>>> import cudatoolkit as ct
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'cudatoolkit'
>>> import cupy as cp
>>>

# added from nvidia channel
libcublas libcufft libcusparse libcusolver libcurand libcutensor
# general channel
cuda-thrust

# coolonlab

bwa                       0.7.17               h5bf99c6_8    bioconda
hdf5                      1.10.2               hc401514_3    conda-forge
kallisto                  0.44.0               h7d86c95_2    bioconda
perl                      5.32.1          2_h7f98852_perl5    conda-forge
star                      2.5.2b                        0    bioconda
  
# pollacklab
# do not load the module but source this file

[hmeij@cottontail2 ~]$ source /share/apps/CENTOS8/ohpc/software/miniconda3/py311/etc/profile.d/conda.sh 

[hmeij@cottontail2 ~]$ conda activate sage

(sage) [hmeij@cottontail2 ~]$ sage --version
SageMath version 10.0, Release Date: 2023-05-20

(sage) [hmeij@cottontail2 ~]$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 10.0, Release Date: 2023-05-20                    │
│ Using Python 3.11.4. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
sage: exit
(sage) [hmeij@cottontail2 ~]$ conda deactivate 
[hmeij@cottontail2 ~]$ 

</code>

  * **mdtraj, matplotlib, pandas**

<code>

[hmeij@cottontail2 ~]$ which python
/share/apps/CENTOS8/ohpc/software/miniconda3/py311/bin/python

[hmeij@cottontail2 ~]$ python
Python 3.11.4 (main, Jul  5 2023, 13:45:01) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mdtraj as mt
>>> 

</code>

    * ** hoomd, cuda **
    * hoomd v4.3.0 with cuda toolkit 11.6
    * https://hoomd-blue.readthedocs.io/en/latest/installation.html

<code>

module load cuda/11.6
which nvcc
echo $CUDA_HOME

module load miniconda3/py311

export CONDA_OVERRIDE_CUDA="11.6"
which conda
conda install "hoomd=4.3.0=*gpu*" "cuda-version=11.6"

cudatoolkit               11.6.0               habf752d_9    nvidia
hoomd                     4.3.0           gpu_py311h29f6c8a_0    conda-forge

# starrlab

[hmeij@n100 ~]$ python3
Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import math
>>> import hoomd
>>> import signac
>>> import flow
>>> cpu = hoomd.device.CPU()
>>>

</code>

  * **seaborn**
  * https://seaborn.pydata.org/index.html
  * statistical data visualization
  * also on centos7 counterpart


<code>

Successfully installed seaborn-0.13.0
[hmeij@cottontail2 ~]$ python3
Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import seaborn as sb
>>>

</code>
===== Pytraj ====

  * git clone https://github.com/Amber-MD/pytraj
  * depends on module miniconda3/py39
  * load python and import package
  * module load pytraj/20230713


<code>

  python ./setup.py install

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

</code>

===== Flye =====

  * 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)

<code>

# 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

</code>

===== Masurca =====

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

<code>

[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

]])


</code>

===== Lammps =====

  * module: lammps/7Feb2024 
  * supports openmp, feature release versus the normal stable release
  * includes colloid class2 kspace misc molecule ml-pace reaction mc packages and gpu for cuda
  * queues amber128 and test only (cuda 11.6)

  * 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

<code>

[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'

</code>


===== EasyBuild =====

  * 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

===== Miniconda3-py39 =====

  * 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 [[cluster:73|Software]] page)

<code>
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

</code>

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

<code>


[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

</code>

===== Amber =====

  * 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: [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber20|slurm job]]











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