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cluster:73 [2020/07/13 14:53]
hmeij07 [Gromacs] 		cluster:73 [2020/12/14 14:38]
hmeij07 [LAMMPS CPU/GPU]
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 ====== Software ====== ====== Software ======
 +
 +IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/home/apps'' **should be replaced with** ''/share/apps'' **which points to** ''/zfshomes/apps''
 +
 + --- //[[hmeij@wesleyan.edu|Henk]] 2020/07/31 15:08//  
  
 The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing). The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing).
Line 14: 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 \\
 +
 +====== DMTCP =====
 +
 +  * Installed as package ins OS on all nodes
 +  * v2.5.2
 +  * dmctp_launch ... etc
 +
 +====== EMBOSS ======
 +
 +  * /share/apps/CENTOS6/EMBOSS
 +  * /share/apps/CENTOS6/EMBOSS/6.6.0.install (read to setup env)
 +  * https://www.ebi.ac.uk/services
 +  * jfabry/kthayer
  
 ====== Sequencing Tools #2 ====== ====== Sequencing Tools #2 ======
Line 944: Line 961:
 ====== Gromacs ===== ====== Gromacs =====
  
-Gromacs-2018 for GPU (RTX2080)+Gromacs-2020.3 for GPU (RTX2080S) 
 +  * ''exx96'' queue 
 +  * see /share/apps/CENTOS7/gromacs/2020.3.install for env 
 +  * change env in script below 
 + 
 +Gromacs-2018 for GPU (RTX2080S)
   * ''exx96'' queue   * ''exx96'' queue
   * **/zfshomes/hmeij/k20redo/run.rtx sample script**   * **/zfshomes/hmeij/k20redo/run.rtx sample script**
Line 1054: Line 1076:
 [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]] [[https://dokuwiki.wesleyan.edu/doku.php?id=cluster:119|GPU version]]
  
-  * program: mcc, math, mathematica (v 11.0.1) +  * program: mcc, math, mathematica (v 12.1) 
-  * install dir: /share/apps/CENTOS6/mathematica/11.0.1+  * install dir: /share/apps/CENTOS6/mathematica/12.1
   * docs: on the web   * docs: on the web
   * www:  http://www.wolfram.com/mathematica/   * www:  http://www.wolfram.com/mathematica/
 +  * Campus wide license, use any queue.
  
   * Parallel kernels   * Parallel kernels
Line 1064: Line 1087:
     * http://reference.wolfram.com/mathematica/guide/ParallelComputing.html     * http://reference.wolfram.com/mathematica/guide/ParallelComputing.html
  
-Job submissions should go to queue //mathematica// which containes licensed nodes (all the hp12 nodes for now).+
  
 ====== Eigen ===== ====== Eigen =====
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 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +*** CPU only - CentOS6
 +
 +  *  /share/apps/CENTOS6/lammps/29Oct20.install
 +    * read for compilation env and packages installed: lmp_mpi
 +
 +** CPU only OR CPU+GPU**  for ''exx96'' queue - CentOS7
 +
 +  * 3Mar2020 added USER-REAXC
 +  * For KOKKOS MPI aware version  /share/apps/CENTOS7/openmpi/4.0.4-ucx with UCX
 +  * git download of latest did not work (lots of fortran errors?)
 +  * latest tarball is still 3Mar2020 (?)
 +  * added user-eaxc (but had to remove package python)
 +  * "kokkos" version includes GPU accelerator
 +  * please read **/share/apps/CENTOS7/lammps/3Mar2020.install **
 +
 +<code>
 +
 +# CPU
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_serial+user-omp+user-reaxc
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi+user-omp+user-reaxc
 +
 +# CPU+GPU
 +/share/apps/CENTOS7/lammps/3Mar2020/lmp_mpi-single-single_kokkos_cuda_mpi+user-omp+user-reaxc
 +
 +# env
 +
 + 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 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 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:$LD_LIBRARY_PATH
 +
 +</code>
 +
 +** CPU ONLY v2 CentOS7 **
 +
 +  * add user-opm on next compile ... done ... binaries with string +user-omp
 +  * /share/apps/CENTOS7/lammps/3Mar2020
 +    * lmp_serial, lmp_mpi
 +  * //latest// openmpi version as of today v4.0.4
 +  * consult this file for packages installed and compilations
 +    * /share/apps/CENTOS7/lammps/03Mar2020.install
 +    * should work only on exx96 and mwgpu queues
 +
 +<code>
 + export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH
 + export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH
 +</code>
  
 ** CPU ONLY ** ** CPU ONLY **
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 ** CPU or GPU ** ** CPU or GPU **
 +
 +  * added lmp_mpi-single-single+user-omp
  
   * /share/apps/CENTOS7/lammps/3Mar2020   * /share/apps/CENTOS7/lammps/3Mar2020
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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