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Andes Environment

 

Connecting to Andes.Dartmouth.Edu (You need an ssh-client)
 

ssh username@andes.dartmouth.edu

Andes and Polaris environment:
You have a HOME directory with 20 GB of space.  This directory is housed on Dartmouth's AFS cell and can be accessed from anywhere if you have an AFS-client.

 
Introduction

• 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 should be set up correctly to use modules.  
  
  • If you delete or modify these files in such a way to make modules fail, contact research.computing@dartmouth.edu  for help.
• 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:

+  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.

$ module list

Currently Loaded Modulefiles:

1) modules/3.2.6	6) totalview/8.8
2) matlab/2010a	7) maple/14.0
3) intel-compilers/11.1	8) mathematica/7.0
4) pgi-compilers/10.5	9) opendx/4.4.0
5) mpich/1.2.7p1-intel	10) mkl/10.1

 

• module avail
  • This option lists all the modules which are available to be loaded.
  • Notice that many of them have version numbers associated with them.
  • Modules makes it easy to switch compiler application versions.
  • The default version is identified in the listing.

$module avail

---------------------- /afs/northstar/common/apps/Modules/3.2.6/modulefiles ---------------------------

dot	maple/14(default))	modules/3.2.6	pgi-compilers/6.2
ecce/6.0(default)	mathematica/6.0.2	mpich/1.2.7p1-gcc	pgi-compilers/8.0-2
gaussian/g03	mathematica/7.0(default)	mpich/1.2.7p1-gcc-p4	pgi-compilers/9.0-3
gaussian/g09(default)	matlab/2007b	mpich/1.2.7p1-intel(default)	totalview/8.04
idl/6.4(default)	matlab/2008a	netcdf/4.0-gfortran4.1.2(default)	totalview/8.6
idl/7.0	matlab/2008b	null	totalview/8.8(default)
intel-compilers/11.0	matlab/2010a(default)	opendx/4.4.0(default)	visit/2.0(default)
intel-compilers/11.1(default)	mkl/10.1(default)	paraview/3.2.1
intel-compilers/9.1	module-cvs	paraview/3.8(default)
maple/11.0	module-info	pgi-compilers/10.5(default)

 

•   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 R2010a
prepend-path     PATH /afs/northstar/common/apps/matlab/Matlab-R2010a/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/r2007b

• 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/r2007b

• 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.