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Modules and available third party software


“Modules” makes it easier for users to run a standard or customized application and/or system environment.

“Modules” allows users to set environmental variables that are specific to their compilation, parallel programming, and/or application requirements. “Modules” makes it convenient to select different compiler, parallel programming, or applications versions. “Modules” can adjust the environment in an orderly way, altering or setting environmental variables as such PATH, MANPATH, LD_LIBRARY_PATH, etc.

Modules is available on ANDY, KARLE, PENZIAS, and SALK.

Modules for the novice user

The “Module” help facility provides basic descriptive information about the application version and purpose of the modules file.

To load a module enter:

module load <module_name>

For documentation on “Modules”:

man module

For help enter:

module help

To see a list of currently loaded “Modules” run:

module list

To see a complete list of all modules available on the system run:

module avail

To show content of a module enter:

module show <module_name>

Modules for the advanced user

A “Modules” example for advanced users who need to change their environment.

The HPC Center supports a number of different compilers, libraries, and utilities. In addition, at any given time different versions of the software may be installed. “Modules” is employed to define a default environment, which generally satisfies the needs of most users and eliminates the need for the user to create the environment. From time to time, a user may have a specific requirement that differs from the default environment.

In this example, the user wishes to use a version of the NETCDF library on the HPC Center’s Cray Xe6 (SALK) that is compiled with the Portland Group, Inc. (PGI) compiler instead of the installed default version, which was compiled with the Cray compiler. The approach to do this is:

• Run module list to see what modules are loaded by default.
• Determine what modules should be unloaded.
• Determine what modules should be loaded.
• Add the needed modules, i.e., module load

The first step, see what modules are loaded, is shown below.

user@SALK:~> module list
Currently Loaded Modulefiles:

  1) modules/
  2) nodestat/2.2-1.0400.31264.2.5.gem
  3) sdb/1.0-1.0400.32124.7.19.gem
  4) MySQL/5.0.64-1.0000.5053.22.1
  5) lustre-cray_gem_s/1.8.6_2.6.32.45_0.3.2_1.0400.6453.5.1-1.0400.32127.1.90
  6) udreg/2.3.1-1.0400.4264.3.1.gem
  7) ugni/2.3-1.0400.4374.4.88.gem
  8) gni-headers/2.1-1.0400.4351.3.1.gem
  9) dmapp/3.2.1-1.0400.4255.2.159.gem
 10) xpmem/0.1-2.0400.31280.3.1.gem
 11) hss-llm/6.0.0
 12) Base-opts/1.0.2-1.0400.31284.2.2.gem
 13) xtpe-network-gemini
 14) cce/8.0.7
 15) acml/5.1.0
 16) xt-libsci/11.1.00
 17) pmi/3.0.0-1.0000.8661.28.2807.gem
 18) rca/1.0.0-2.0400.31553.3.58.gem
 19) xt-asyncpe/5.13
 20) atp/1.5.1
 21) PrgEnv-cray/4.0.46
 22) xtpe-mc8
 23) cray-mpich2/5.5.3
 24) pbs/

From the list, we see that the Cray Programming Environment (PrgEnv-cray/4.0.46) and the Cray Compiler environment are loaded (cce/8.0.7) by default. To unload these Cray modules and load in the PGI equivalents we need to know the names of the PGI modules. The module avail command shows this.

 user@SALK:~> module avail

We see that there are several versions of the PGI compilers and two versions of the PGI Programming Environment installed. For this example, we are interested in loading PGI's 12.10 release (not the default, which is pgi/12.6) and the most current release of the PGI programming environment (PrgEnv-pgi/4.0.46), which is the default.

The following module commands will unload the Cray defaults, load the PGI modules mentioned, and load version 4.2.0 of NETCDF compiled with the PGI compilers.

user@SALK:~> module unload PrgEnv-cray
user@SALK:~> module load PrgEnv-pgi
user@SALK:~> module unload pgi
user@SALK:~> module load pgi/12.10
user@SALK:~> module load netcdf/4.2.0
user@SALK;~> cc -V

/opt/cray/xt-asyncpe/5.13/bin/cc: INFO: Compiling with CRAYPE_COMPILE_TARGET=native.

pgcc 12.10-0 64-bit target on x86-64 Linux 
Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
Copyright 2000-2012, STMicroelectronics, Inc.  All Rights Reserved.

A few additional comments:

• The first three commands do not include version numbers and will therefore load or unload the current default versions.
• In the third line, we unload the default version of the PGI compiler (version 12.6), which is loaded with the rest of the PGI Programming Environment in the second line. We then load the non-default and more recent release from PGI, version 12.10 in the fourth line.
• Later, we load NETCDF version 4.2.0 which, because we have already loaded the PGI Programming Environment, will load the version of NETCDF 4.2.0 compiled with the PGI compilers.
• Finally, we check to see which compiler the Cray "cc" compiler wrapper actually invokes after this sequence of module commands by again entering module list.