info specific to hood.math

Administration

• hood.math.private is administered by MFCF
• no root or sudo access for users
• home directories on hood are served by NFS to the "mountain lake" machines (bow, minnewanka, waterton)

Hardware

• SuperMicro 8047R-7JRFT
• Four Intel Xeon E5-4640 8-core 2.4 GHz CPUs (Sandy Bridge microarchitecture)
• 256 GiB RAM

File Systems

Hood.math.private has many file systems of different characteristics.

• /fsys1
  • applications and system management, no user files
• /u
  • home directories
  • shared by NFS to other machines
  • relatively small
  • do not run your large models while writing to files in your home directory
  • save copies of your source code or other important things here
  • backed up to MFCF's central file server
• /fsys2
  • higher speed for high I/O jobs run on hood
  • shared by NFS
• /fsys3, /fsys4, /fsys5, /fsys6, /fsys7
  • shared by NFS

Software

• Hood currently runs CentOS 6.10
• the recommended .cshrc and .profile files set up your environment automatically with recommended compilers, libraries, etc. mentioned below to work with the configuration files included with models such as SPINS, MITgcm, IGW
  • see the Login script wiki page and the Models section of the main page for details
• 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.

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.

export CC=/opt/centos/devtoolset-1.1/root/usr/bin/gcc

3. Set your $PATH to find the optional commands first, e.g.

export PATH=`showpath /opt/centos/devtoolset-1.1/root/usr/bin current`

• Similarly, GCC 9.1.1 is available as devtoolset-9

• 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

Network

Sometimes you might need access to the internet. You can use the following to use a proxy.

   # bash
   export http_proxy=http://calamar.uwaterloo.ca:3128
   export https_proxy=http://calamar.uwaterloo.ca:3128
   export HTTP_PROXY=http://calamar.uwaterloo.ca:3128
   export HTTPS_PROXY=http://calamar.uwaterloo.ca:3128

   # csh
   setenv http_proxy http://calamar.uwaterloo.ca:3128
   setenv https_proxy http://calamar.uwaterloo.ca:3128
   setenv HTTP_PROXY http://calamar.uwaterloo.ca:3128
   setenv HTTPS_PROXY http://calamar.uwaterloo.ca:3128

   # test
   wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh