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cluster:73 [2021/03/11 19:47]
hmeij07 [Intel Threading Building Blocks] 		cluster:73 [2021/06/10 15:02]
hmeij07 [DeepChem]
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 \\
 +
 +====== DeepChem ======
 +
 +  * 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
 +
 +<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:$PATH"
 +    fi
 +fi
 +unset __conda_setup
 +# <<< conda initialize <<<
 +
 +</code>
 +
 +
 +<code>
 +Successfully installed absl-py-0.12.0 astunparse-1.6.3 
 +cachetools-4.2.2 flatbuffers-1.12 gast-0.4.0 google-auth-1.30.2 
 +google-auth-oauthlib-0.4.4 google-pasta-0.2.0 grpcio-1.34.1 
 +h5py-3.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 
 +markdown-3.3.4 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 
 +protobuf-3.17.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 requests-oauthlib-1.3.0 
 +rsa-4.7.2 tensorboard-2.5.0 tensorboard-data-server-0.6.1 
 +tensorboard-plugin-wit-1.8.0 tensorflow-2.5.0 tensorflow-estimator-2.5.0 
 +termcolor-1.1.0 typing-extensions-3.7.4.3 werkzeug-2.0.1 wrapt-1.12.1
 +</code>
 +
 +====== pytraj ======
 +
 +  * https://amber-md.github.io/pytraj/latest/installation.html#installation
 +  * From AMBER distribution (Linux, OSX)
 +  * pytraj is included in AMBER (version >= 16): ambermd.org
 +  * so below I opted for source code installation with python 3.8.3
 +  * git clone https://github.com/Amber-MD/pytraj; cd pytra
 +  * python ./setup.py install
 +  * requires CentOS7 so queues mwgpu, amber128 and exx96
 +  * /share/apps/CENTOS7/amber/pytraj
 +
 +
 +
 +<code>
 +
 + export PATH=/share/apps/CENTOS7/python/3.8.3/bin:$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 ======
 +
 +So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
 +
 +  * whitetail tar ball for centos7/warewulf (no slurm)
 +  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
 +  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
 +  * https://github.com/warewulf/warewulf3 (master git zip file)
  
 ====== OneAPI ====== ====== OneAPI ======
Line 1327: Line 1424:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** USER_QUIP **
 +
 +This is a version of lammps (29Oct20, last stable) that contains all packages with user-quip.
 +
 +It does compile with MPI (mpif90), not ifort, in CentOS7 ... was tricky, solution for MPI was the ''mpifort --showme:link'' answer
 +
 +  * Requires CentOS 7 so queues: mwgpu, amber128, exx96 for cpu-only binaries
 +  * Rwequires CentOS7 plus Cuda 10.2 so queue: exx96 for cpu+gpu binaries
 +
 +Read, if you wish  
 +
 +  * /share/apps/CENTOS7/lammps/QUIP-public.install 
 +  * /share/apps/CENTOS7/lammps/29Oct2020.install 
 +
 +**Environments**
 +
 +<code>
 +
 +# serial - cpu only (although quippy compiled, it refused to install)
 +# MPI STUBS is compiled in
 +
 +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
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_serial-with-quip.cpu -h
 +
 +# mpi - cpu only
 +# gfortran_openmpi
 +
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +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
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +
 +/share/apps/CENTOS7/lammps/29Oct2020/lmp_mpi-with-quip.cpu -h
 +
 +
 +# mpi - cpu+gpu
 +# gfortran_openmpi arch
 +
 +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
 +export QUIP_LIBRARY=/share/apps/CENTOS7/lammps/QUIP-public/9Apr2021/linux_x86_64_gfortran_openmpi
 +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
 +export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +export CUDA_HOME=/usr/local/cuda
 +export PATH=/usr/local/cuda/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
 +
 +# the "make" versions of lmp with quip do not work, deleted them
 +# 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
 +
 +# sample script: ~hmeij/k20redo/run.rtx.lammps2
 +
 +</code>
  
 ** CPU only ** -Centos6 ** CPU only ** -Centos6
Line 3042: Line 3206:
 ===== Intel  ===== ===== Intel  =====
  
-UPDATE, 2016 parallel studio cluster edition installed+UPDATE 2021 
 +latest version of icc/icx and ifort/ifx are inside OneAPI, search this page 
 + 
 +UPDATE 2016  
 +parallel studio cluster edition installed
  
   * 2 ifort and 2 icc float licenses   * 2 ifort and 2 icc float licenses
Line 3115: Line 3283:
 ====== 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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