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--- cluster:215 [2022/04/07 08:47]
hmeij07 created
+++ cluster:215 [2024/03/14 11:00] (current)
hmeij07 [Miniconda3-py312]
@@ Line 4: / Line 4: @@
 ===== OpenHPC Software =====
-This list of software is compiled for Rocky 8 using the OpenHPC v2.4 gnu9-openmpi4 toolchain. For gpu applications CUDA 11.6 is the default.
+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
+.9.2-b1794
+[hmeij@cottontail2 2.9.2]$ python bin/flye --version
+.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]]
-The control of the environment is done via environmentaL modules. Read this page

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