Andes and Polaris Environments

Details

To connect to andes.dartmouth.edu (You need an ssh-client):

ssh netid@andes.dartmouth.edu

To connect to polaris.dartmouth.edu (You need an ssh-client):

ssh netid@polaris.dartmouth.edu

SSH clients

Macs come with an ssh client.  To use it open your Applications folder, then the Utilities folder, and then the Terminal application.

Windows users will need to download a SSH client.  We recommend either PuTTY www.putty.org or MobaXterm mobaxterm.mobatek.net.  Both are free (though MobaXterm does have a Pro version with additional features).

Andes and Polaris environment:
You have a HOME directory with 50 GB of space. This directory is housed in DartFS and can also be accessed from your laptop or desktop.  Both Andes and Polaris run Red Hat Enterprise Linux version 7 and from a software perspective should be identical.

Modules - Tailoring Your environment

  • Modules provides an easy mechanism for updating a user's environment especially the PATH, MANPATH, and LD_LIBRARY_PATH environment variables to name a few.
  • When you get an account on Andes or Polaris, your dot-files will be set up correctly to use modules.
  • You can modify your environment so that certain modules are loaded whenever you log in.
  • Use this command to have a module automatically loaded each time you log into the system:
    • module initadd modulename.
    • where modulename is the name of the module you want loaded.

Module commands

  • module help
    • Get a usage list of module options.
    • The listing has been abbreviated to only show those commands discussed in this page.

$ module help

Available Commands and Usage:

nbsp; add|load       modulefile [modulefile ...]
+  rm|unload      modulefile [modulefile ...]
+  switch         modulefile1 modulefile2
+  display        modulefile [modulefile ...]
+  avail          path [path]
+  list
+  initadd        modulefile [modulefile ...]
+  help           modulefile [modulefile ...]
+  initrm         modulefile [modulefile ...]
+  initswitch     modulefile1 modulefile2

  • module list
    • This lists all the modules which are currently loaded into the users environment on andes.

$ module list

Currently Loaded Modulefiles on andes

1) modules/3.2.65) totalview/8.8
2) matlab/2011b6) maple/14.0
3) intel-compilers/11.17) mathematica/8.0
4) pgi-compilers/10.58) mpich/1.2.7p1-intel

$ module avail

Use the module avail command to see the list of applications and libraries installed on the computer.

  • module help modulefile*
    • To retrieve more information about a module, use this command to display the help information contained within the given module file.

$ module avail

Use the module avail command to see the list of applications and libraries installed on the computer.

  • module help modulefile*
    • To retrieve more information about a module, use this command to display the help information contained within the given module file.

$ module help netcdf

----------- Module Specific Help for 'netcdf/4.0-gfortran4.1.2' ---------------

Sets up the environment to use the netCDf libraries
Sets up the netCDF libraries, include files, binaries and man pages.
Add $NETCDF_LIB to include the netcdf library when linking your program.
Example: ifort -o myprog myproc.f $NETCDF_LIB
Add $NETCDF_INCLUDE to include the netcdf include files when compiling.
Example: ifort $NETCDF_INCLUDE -c myproc.f

  • module display modulefile
    • Use this command to see exactly what a given modulefile will do to your environment, such as what will be added to the PATH, MANPATH, and other environment variables.

$ module display matlab

-------------------------------------------------------------------
/afs/northstar/common/apps/Modules/3.2.6/modulefiles/matlab/r2010a:

 

module-whatis    loads Matlab version R2011b
prepend-path    PATH /afs/northstar/common/apps/matlab/Matlab-R2011b/bin
-------------------------------------------------------------------

  • module load modulefile
    • This adds one or more modulefiles to the user's current environment.
    • It does so silently, unless there is a problem with a modulefile.
    • If you load the generic name of a module, you will get the default version.
    • To load a specific version, load the module using its full specification.

+ module load matlab/r2011a

  • module unload modulefile
    • This removes any listed modules from the user's current environment.
    • The modules can be removed in any order.

+ module unload matlab/r2011a

  • module switch old_modulefile new_modulefile
    • This command demonstrates the true advantages of modules.
    • Different versions of entire software packages can be replaced with a single module command.
  • module initadd modulefile
    • This command modifies your environment so the module is loaded automatically whenever you log in
  • module initrm modulefile
    • This command modifies your environment so the module will not be loaded automatically when you log into the system.
  • module initswitch modulefile1 modulefile2
    • This command modifies your environment so the modulefile2  will be loaded automatically instead of modulefile1.

Details

Article ID: 64641
Created
Tue 10/9/18 12:18 PM
Modified
Tue 2/12/19 10:51 AM