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If your job does not use the system openmpi, or does not use MPI, then any desired core binding will need to be set up with whatever mechanism the software uses. Otherwise, there will be no core binding. Again, that may not be a major issue. If your job does not work well with HT then run on a number of cores equal to half of the number of slots requested and the OS scheduler will minimize contention.
new SGE utilities
While SoGE is very similar to previous versions of SGE there are some new utilities that people may find of interest. There are manual pages for each of these.
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While there are many software applications installed from RPM packages, many commonly used packages, and their dependencies, are built from source. See the Argon Software List to view the packages and versions installed. Note that this list does not include all of the dependencies that are installed, which will consist of newer versions than those installed via RPM. Use of these packages is facilitated through the use of environment modules, which will set up the appropriate environment for the application, including loading required dependencies. Some packages like Perl, Ruby, R and Python, are extendable. We build a set of extensions based on commonly used and requested extensions so loading modules for those will load all of the extensions, and dependencies needed for the core package as well as the extensions. The number of extensions installed, particularly for Python and R is too large to list here. You can use the standard tools of those packages to determine what extensions are installed.
Environment Modules
Like previous generation UI HPC systems, Argon uses environment modules for managing the shell environment needed by software packages. Argon uses LMod rather than the TCL modules used in previous generation UI HPC systems. More information about Lmod can be found in the Lmod: A New Environment Module System. Briefly, Lmod provides improvements over TCL modules in some key ways. One is that Lmod will automatically load and/or swap dependent environment modules when higher level modules are changed in the environment. It can also temporarily deactivate modules if a suitable alternative is not found, and can reactivate those modules when the environment changes back. We are not using all of the features that Lmod is capable of so the modules behavior should be very close to previous systems but with a more robust way of handling dependencies.
Lmod provides a mechanism to save a set of modules that can then be restored. For those who wish to load modules at shell startup this provides a better mechanism than calling individual module files. The reasons are that
- Only one command is needed
- The same command can be used at any time
- Restoring a module set runs a
module purgewhich will ensure that the environment, at least the part controlled by modules, is predictable.
To use this, simply load the modules that you want to have loaded as a set. Then run the following command.
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module save |
That will save the loaded modules as the default set. To restore that run
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module restore |
That command could then be put in your shell initialization file. In addition to saving/restoring a default set you can also assign a name to the collection.
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module save mymodules
module restore mymodules |
There is also a technical reason to use the module save/restore feature as opposed to individual modules that involves how the LD_LIBRARY_PATH environment variable is handled at shell initialization.
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One of the things that environment modules sets up is the |
Other than the above items, and some other additional features, the environment modules controlled by Lmod should behave very similarly to the TCL modules on previous UI HPC systems.
Setting default shell
Unix attributes are now available in the campus wide Active Directory Service and Argon makes use of those. One of those attributes is the default Unix shell. This can be set via the following tool: Set Login Shell - Conch. Most people will want the shell set to /bin/bash so that would be a good choice if you are not sure. For reference, previous generation UI HPC systems set the shell to /bin/bash for everyone, unless requested otherwise. We recommend that you check your shell setting via the Set Login Shell - Conch tool and set it as desired before logging in the first time. Note that changes to the shell setting may take up to 24 hours to become effective on Argon.
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