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cluster:73 [2021/04/14 12:55]
hmeij07 [LAMMPS CPU/GPU] 		cluster:73 [2021/06/22 12:14]
hmeij07 [VSEARCH]
Line 18: Line 18:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +====== VSEARCH ======
 +
 +VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization ... an alternative to USEARCH; offers search and clustering algorithms that are often orders of magnitude faster than BLAST. 
 +
 +  * https://github.com/torognes/vsearch
 +  * requires centos7
 +  * centos7 queues; mwgpu, amber128, exx96
 +    * debug host greentail52
 +  * /share/apps/CENTOS7/vsearch/2.17.0/bin/vsearch
 +
 +
 +====== DeepChem ======
 +
 + DeepChem is a deep learning tool built for bio/chem research
 +
 +  * First installed latest Miniconda
 +  * /share/apps/CENTOS7/amber/miniconda3 
 +    * put the code block below in ~/.bashrc and log back in
 +  * https://deepchem.io/ 
 +    * installed stable/conda/gpu=no
 +  * pip installed tensorflow-2.5  
 +  * Note: miniconda contains (Your python: python=3.8)
 +    * "conda install -c ambermd pytraj" fails to install
 +  * CentOS7 so queues mwgpu, amber128, exx96
 +    * or for debugging use greentail52
 +
 +<code>
 +# add to ~/.bashrc and log back in, then check: 'which python pip conda'
 +# >>> conda initialize >>>
 +# !! Contents within this block are managed by 'conda init' !!
 +__conda_setup="$('/share/apps/CENTOS7/amber/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
 +if [ $? -eq 0 ]; then
 +    eval "$__conda_setup"
 +else
 +    if [ -f "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh" ]; then
 +        . "/share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh"
 +    else
 +        export PATH="/share/apps/CENTOS7/amber/miniconda3/bin:$PATH"
 +    fi
 +fi
 +unset __conda_setup
 +# <<< conda initialize <<<
 +
 +</code>
 +
 +
 +<code>
 +Successfully installed absl-py-0.12.0 astunparse-1.6.3 
 +cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2 
 +google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1 
 +h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 
 +markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 
 +protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0 
 +rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1 
 +tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 
 +termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
 +</code>
 +
 +====== pytraj ======
 +
 + Pytraj is a wrapper for cpptraj
 +
 +  * https://amber-md.github.io/pytraj/latest/installation.html#installation
 +  * From AMBER distribution (Linux, OSX)
 +  * pytraj is included in AMBER (version >= 16): ambermd.org
 +  * so below I opted for source code installation with python 3.8.3
 +  * git clone https://github.com/Amber-MD/pytraj; cd pytra
 +  * python ./setup.py install
 +  * requires CentOS7 so queues mwgpu, amber128 and exx96
 +  * or for debugging use greentail52
 +  * /share/apps/CENTOS7/amber/pytraj
 +
 +
 +
 +<code>
 +
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/python/3.8.3/lib:$LD_LIBRARY_PATH
 +
 +# An environment resource file for CPPTRAJ has been created:
 +  /zfshomes/apps/CENTOS7/amber/pytraj/cpptraj/cpptraj.sh
 +# You may 'source' this file to set up your environment for CPPTRAJ.
 +
 +
 +
 +Installed /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages/pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg
 +Processing dependencies for pytraj==2.0.6.dev0
 +Searching for numpy==1.20.3
 +Best match: numpy 1.20.3
 +Adding numpy 1.20.3 to easy-install.pth file
 +Installing f2py script to /share/apps/CENTOS7/python/3.8.3/bin
 +Installing f2py3 script to /share/apps/CENTOS7/python/3.8.3/bin
 +Installing f2py3.8 script to /share/apps/CENTOS7/python/3.8.3/bin
 +
 +Using /zfshomes/apps/CENTOS7/python/3.8.3/lib/python3.8/site-packages
 +Finished processing dependencies for pytraj==2.0.6.dev0
 +
 +</code>
 +
 +====== Ovito ======
 +
 +  * https://www.ovito.org
 +  * /usr/local/bin/ovito -> /usr/local/ovito-basic-3.5.0-x86_64/bin/ovito
 +  * on nodes ''cottontail'' and ''greentail52''
 +  * uses freeglut/freeglut-devel libraries for opengl
  
 ====== OpenHPC ====== ====== OpenHPC ======
Line 282: Line 388:
   * picked up mpirun from miniconda2 apps (that may be a problem)   * picked up mpirun from miniconda2 apps (that may be a problem)
  
-  * Added to 3.8.3 "acpipe"+  * Added to 3.8.3 "acpype"
   * https://github.com/alanwilter/acpype   * https://github.com/alanwilter/acpype
  
 +From website:\\
 +"
 +We now have an up to date webservice at http://bio2byte.be/acpype/ \\
 +(but it does not have the amb2gmx funcionality).
 +
 +To run acpype, locally, with its all functionalities, you need ANTECHAMBER from package AmberTools and Open Babel if your input files are of PDB format.
 +
 +However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing at all but Python.
 +"\\
  --- //[[hmeij@wesleyan.edu|Henk]] 2021/02/18 14:41//  --- //[[hmeij@wesleyan.edu|Henk]] 2021/02/18 14:41//
  
Line 1390: Line 1505:
 export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
  
-# cpu+gpu binaries require cuda 10.2 so only exx96 queue  +# the "make" versions of lmp with quip do not work, deleted them 
-# (-kokkos means no kokkos, gpu package only)+# did find on nvdia dev forum reference problem disappears when using cmake (vs make) 
 +# these lmp binaries do work 
 +/share/apps/CENTOS7/lammps/29Oct2020/single_single/bin/lmp 
 +/share/apps/CENTOS7/lammps/29Oct2020/single_double/bin/lmp 
 +/share/apps/CENTOS7/lammps/29Oct2020/double_double/bin/lmp 
 + 
 +# however I had to load non-mpi version of libquid.a into lmp 
 +# witch seems ok given parallel work is driven by -suffix gpu
  
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_double_double -h +# sample script: ~hmeij/k20redo/run.rtx.lammps2
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_double -h +
-/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu+gpu-kokkos_single_single -h+
  
 </code> </code>
Line 3190: Line 3310:
 ====== Stata ====== ====== Stata ======
  
-  * program: Stata v 15, 6-user network license, includes stata, stata-mp, stata-se  +  * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se  
-  * install dir: /share/apps/stata/15+  * install dir: /share/apps/stata/
   * docs: at web site   * docs: at web site
   * http://stata.com   * http://stata.com
  
 <code> <code>
-export PATH=/share/apps/stata/15:$PATH+export PATH=/share/apps/stata/17:$PATH
 </code> </code>
  
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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