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 1. You can view help on the module (and you should before loading) with the following command
  {{{
module help <module_name>
}}}
  There may or may not be important information you need before loading a specific module.

Linux Software Notes

  1. Contact us is you have a question regarding installation of software on the PMC linux systems.

  2. Were feasible, we install requested software directly on linux machines using yum repositories.
  3. In the case of commercial software or software were there is no yum repository we install on the software server and you can find these in the directory "/soft".
  4. For software released with a distro, we only support the version of the software released with the distro. This is to prevent distro dependency issues. If you want a more recent version of a specific distro installed software you will need to install in your own in your home directory. (Examples: firefox, thunderbird). If you have difficulty installing in your home directory contact us for help and and in some cases we can install different versions in the "/soft" directory that you can use to override the distro versions.

  5. The globally installed packages can be viewed by:
    • module avail
  6. You can view help on the module (and you should before loading) with the following command
    • module help <module_name>
      There may or may not be important information you need before loading a specific module.
  7. You can configure your environment to use one of these packages by including the line:
    • module load <module_name>
    in your .cshrc file.
  8. You can list your currently loaded software:
    • module list
  9. You can see the environment changes that will be made by a module:
    • module show <module_name>
  10. If one module conflicts with another you will get a conflict message. As an example there are several modules which load their own python environments (anaconda, antelope, passcal, qiime, scipy). You can't have more than one of these loaded at a time. The solution is to unload the conflicting module:
    • module unload <conflicting_module>
      module load <new_module>
  11. Some modules have multiple versions available. These will show in the "module avail" list in a format like this:
    • <module>/<version1>
      <module>/<version2>
      <module>/<version3>
      etc

      The highest version number will be loaded by default if you issue a "module load <module>" command. If you want a specific version issue a "module load <module>/<version>" command.

  12. Some packages in "/soft" are not for normal use because there are standard versions already installed on each machine. These duplicate versions in "/soft" are for special purposes and are often old and out of date (examples: gcc).
  13. Some packages in "/soft" are only licensed to specific individuals and you should not use without obtaining the license holders permission. (Currently these are the pgi compilers, lahey compilers, intel compilers, totalview, and mathematica). Please contact us for specific license status for all commercial packages.

  14. In some cases you may find software in "/soft" that was compiled for specific OS versions/architectures, but not others. If you find a software package that does not have a version for your OS version/architecture contact us and we can compile a version for your OS version/architecture. In some case,s the software may have been installed globally to fill in gaps where the software did not exist in an older OS distro and may be already be installed via yum on your machine.

  15. You can always contact us directly about software availability, where to find it on our system, or to have new software installed.