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cluster:215 [2023/10/31 14:12]
hmeij07 [Miniconda3-py311] 		cluster:215 [2024/05/15 13:09]
hmeij07 [Miniconda3-py312]
Line 12: Line 12:
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\ https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
 +
 +
 +===== FLAG =====
 +
 +  * https://github.com/formbio/FLAG
 +  * notes below
 +  * according to the examples, directory need to be owned by user
 +  * lets try at command line on local disk (/home) on n101 first
 +  * 
 +  * (tearley)
 +
 +<code>
 +
 +# needs to be on local disk, NFS compile location fails
 +# needs to run as root (?) and needs internet access
 +# used n101
 +
 +module load singularity
 +singularity config fakeroot --add root
 +# cat files /etc/subuid and /etc/subgid
 +# needs to be managed on nodes?
 +
 +cd /home
 +unzip FLAG-main.zip
 +mv FLAG-main FLAG-20240425
 +date > build.log
 +./build_singularity_flag.sh | tee -a build.log 
 +
 +
 +INFO:    Build complete: singularity_flag.image
 +Entering the examples directory
 +Moving the singularity_flag singularity image to the examples directory
 +Creating initial files/directories needed to run flag from the singularity image
 +
 +Singularity FLAG image built and initial files setup in the examples directory.
 +
 +# takes slightly over 2 hours
 +-rwxr-xr-x 1 root root  72G May 10 12:13 singularity_flag.image
 +
 +</code>
 +
 +===== 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
 +
 +# thayerlab
 +
 +  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 
 +
 +
 +</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 ===== ===== Python =====
Line 18: Line 115:
   * python v 3.12.0   * python v 3.12.0
   * galario 1.2.2 (no cuda support)   * galario 1.2.2 (no cuda support)
-  * numpy, scipy, pandas, schwimmbad, emcee, galario+  * numpy, scipy, pandas, schwimmbad, emcee, astropy
   * galario build from source   * galario build from source
   * https://mtazzari.github.io/galario/install.html   * https://mtazzari.github.io/galario/install.html
   * module: python/3.12.0   * 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 ===== ===== Miniconda3-py311 =====
Line 83: Line 197:
      
 # pollacklab # pollacklab
 +# do not load the module but source this file
  
-# To activate this environment, use                                                                                  +[hmeij@cottontail2 ~]$ source /share/apps/CENTOS8/ohpc/software/miniconda3/py311/etc/profile.d/conda.sh  
-#                                                                                                                    + 
-#     $ conda activate sage                                                                                          +[hmeij@cottontail2 ~]$ conda activate sage 
-#                                                                                                                    + 
-# To deactivate an active environment, use                                                                           +(sage) [hmeij@cottontail2 ~]$ sage --version 
-#                                                                                                                    +SageMath version 10.0, Release Date: 2023-05-20 
-#     $ conda deactivate  + 
 +(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> </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
 +    * multi-gpu
 +      * https://hoomd-blue.readthedocs.io/en/v2.9.3/mpi.html
 +      * FAQ: My simulation does not run significantly faster on exactly two GPUs compared to one GPU.
 +      * This is expected. HOOMD uses special optimizations for single-GPU runs
 +
 +<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
 +>>> hoomd.version.gpu_enabled
 +True
 +>>> 
 +
 +</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 ==== ===== Pytraj ====
  
Line 184: Line 375:
  
 ===== Lammps ===== ===== 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   * module: lammps/25Apr2023
cluster/215.txt · Last modified: 2024/05/15 13:09 by hmeij07

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