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cluster:73 [2020/07/24 17:53]
hmeij07 [Gromacs] 		cluster:73 [2020/12/14 14:46]
hmeij07 [DMTCP]
Line 3: Line 3:
  
 ====== 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 =====
 +
 +  * /share/apps/CENTOS7/dmtcp/3.0.0
 +  * this came from the CRAC source, trying to install gpu checkpoint tool
 +  * [[cluster:198|GPU checkpoint/restart]]
 +  * but plugin will not compile, checking with developers 12 Dec 2020
 +
 +  * 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 1254: Line 1276:
  
 ====== LAMMPS CPU/GPU ====== ====== LAMMPS CPU/GPU ======
 +
 +** CPU only ** -Centos6
 +
 +  *  /share/apps/CENTOS6/lammps/29Oct20.install
 +  * read for env and compilation env: 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 ** ** CPU ONLY v2 CentOS7 **
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07

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