info specific to hood.math: Difference between revisions

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(Add details about OpenMPI, as well as how to set up for Intel compilers, and link to the page with login script info. --RBLanders)
(OS updated to 6.8. New version of NCL installed; describe NCL and mention various other math software.)
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== Software ==
== Software ==


* Hood currently runs [https://www.centos.org/ CentOS 6.7]
* Hood currently runs [https://www.centos.org/ CentOS 6.8]
* GCC 4.4.7 installed by default
* GCC 4.4.7 installed by default
* GCC 4.7.2 is also available, to use it, do '''one''' of the following:
* GCC 4.7.2 is also available, to use it, do '''one''' of the following:
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** the hood.sh set-up file in SPINS expects your environment to be set up to use Intel compilers, Intel MKL, and OpenMPI 1.10
** the hood.sh set-up file in SPINS expects your environment to be set up to use Intel compilers, Intel MKL, and OpenMPI 1.10
*** see the wiki page called [https://belize.math.uwaterloo.ca/mediawiki/index.php/Login_script Login Script] for details of that
*** see the wiki page called [https://belize.math.uwaterloo.ca/mediawiki/index.php/Login_script Login Script] for details of that
* NCL
** versions 6.2.1 and 6.3.0 are installed
** version 6.2.1 was prebuilt with gcc 4.4.7 and is in standard search rules for both commands and libraries
** version 6.3.0 was prebuilt with gcc 4.7.2 and is not in standard search rules
*** use the methods described above to select gcc 4.7.2
*** put the 6.3.0 package in your path by doing this for CSH shells:'''setenv PATH `showpath nclncarg-6.3.0 current`''' or this for SH shells: '''export PATH=`showpath nclncarg-6.3.0 current`'''
* Other mathematical software
** Maple, Matlab, R, Sage, CPLEX
** VisIT
** GSL, HTK, SuperLU
** TeX

Revision as of 11:40, 20 December 2016

Administration

  • hood.math is administered by MFCF
  • no root or sudo access for users
  • home directories on hood are served by NFS to winisk, kazan, and thelon

Hardware

Software

  • Hood currently runs CentOS 6.8
  • GCC 4.4.7 installed by default
  • GCC 4.7.2 is also available, to use it, do one of the following:
  1. Use SCL (Software Collection) to start a subshell with special environment, e.g.
    2. scl enable devtoolset-1.1 bash
    or if you prefer a CSH shell
    scl enable devtoolset-1.1 csh
  2. Set environment variables to refer to the optional versions, e.g.
    3. export CC=/opt/centos/devtoolset-1.1/root/usr/bin/gcc
  3. Set your $PATH to find the optional commands first, e.g.
    4. export PATH=`showpath /opt/centos/devtoolset-1.1/root/usr/bin current`
  • Intel Parallel Studio XE 2015 development suite (icc, ifort, MKL, etc.)
    • run the command source /opt/intel/bin/iccvars.sh intel64 (if you use bash login shell) or source /opt/intel/bin/iccvars.csh (if you use csh or tcsh login shell) to set up your environment for this
  • OpenMPI
    • we don't have Intel's MPI
    • there are three versions of OpenMPI installed
      • OpenMPI 1.8.1, from the OS, in a "module" called openmpi-1.8-x86_64
      • OpenMPI 1.8.4, built on hood using Intel compiler, installed in /usr/local/
      • OpenMPI 1.10, from the OS, in a "module" called openmpi-1.10-x86_64
    • run the command module load openmpi-1.10-x86_64 to set up your environment for OpenMPI 1.10
    • the hood.sh set-up file in SPINS expects your environment to be set up to use Intel compilers, Intel MKL, and OpenMPI 1.10
  • NCL
    • versions 6.2.1 and 6.3.0 are installed
    • version 6.2.1 was prebuilt with gcc 4.4.7 and is in standard search rules for both commands and libraries
    • version 6.3.0 was prebuilt with gcc 4.7.2 and is not in standard search rules
      • use the methods described above to select gcc 4.7.2
      • put the 6.3.0 package in your path by doing this for CSH shells:setenv PATH `showpath nclncarg-6.3.0 current` or this for SH shells: export PATH=`showpath nclncarg-6.3.0 current`
  • Other mathematical software
    • Maple, Matlab, R, Sage, CPLEX
    • VisIT
    • GSL, HTK, SuperLU
    • TeX
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