Many popular software packages are installed and available as modules. There may be several versions of a package available.
On Ocelote, many libraries like FFTW and MPICH came with the Cluster Manager. As a consequence, they have different naming from the other clusters. For example, module load blas on the older clusters will need to be module load blas/gcc/64. There are frequently versions of these libraries that have several compilation options, for example, blas was created with four different compilers on Ocelote.
|actionTitle||Request Software Install|
Software packages are available as modules and are accessible from the compute nodes of any of our three clusters. They are not available on the login nodes so you will need to be in an interactive session to access them. A list of installed software can be seen by clicking the link below, but may not be as current as using the
module avail command (more information under Module Commands).
|title||Click here to view a list of all software modules|
If multiple versions of software are available on the system, the newest is made the default. This means loading a module without specifying the version will select the most recent. We strongly recommend including version information in your module statements. This ensures that you maintain a consistent environment for your analyses in the event of a software upgrade.
To see, access, and get information on individual software packages available on the system, use the module commands detailed below. If you have trouble accessing the module command, see our FAQ section.
$ module avail
| Display all the software and versions installed on the system| module load modulename
$ module avail module_name
|Display all installed versions of the software "module_name" |
|Display the software you have loaded in your environment|
$ module what-is module_name
|Displays some descriptive information about a specific module|
$ module load module_name
|Load a software module in your environment|| module purge Unload all the software modules Unload a specific software package |
$ module unload module_name
|Unload a specific software package from your environment|| module unload modulename| module GCC is available without loading a module. gcc --version shows that it is 5.2.0. If you also need the GNU Scientific Libraries (gsl), that is available using module load gsl which will get you version 2.1The Intel Compiler suite 2016 is available in both 32 and 64 bit versions. The math kernel libraries (mkl) are provided as separate modules, also in 32 and 64 bit versions.MPI compilers. There are more choices now so pay attention.
| Unload all the software modules from your environment|
AVX2 The new cluster has Intel V3 Haswell processors. A key feature of these is AVX2. Read this Intel document.
- There are standard Red Hat versions of mpich, mvapich, mvapich2 and openmpi. Some extra options are invoked when you load one - use module avail to see the specific name.
- The same four compilers are available with more detailed options for gcc, intel and open64. Again use module avail for the appropriate choices.
For AVX2 support, compile with the -xHOST option. Note that -xHOST alone does not enable aggressive optimization, so compilation with -O3 is also suggested. The -fast flag invokes -xHOST, but should be avoided since it also turns on interprocedural optimization (-ipo), which may cause problems in some instances.
For GNU compilers, AVX support is only available in version 4.6 or later. For AVX support, compile with -mavx
| Display a help menu for the module command|
Example for Using Modules
To display a list of the available packages when your logged in to one of the HPC login nodes:
To load the latest installed version of the "Trinity" software:
module load trinity
To list the software you currently have loaded:
To unload all modules if you want to start over. Logging out will also unload modules.
Installing Your Own Software
Follow this link for detailed information on how to install your own software
Using and Installing Python
Follow this link for more information on using Python.
There are several compilers available for your use. Remember when you run your code and you need to do a module load, that you use the same version of compiler that the code was originally compiled with.GCC is available by default. gcc --version shows that it is 4.4.4 That version was installed at cluster installation and has not been updated to maintain consistency between compiling software and subsequently running it. If you also need the GNU Scientific Libraries (gsl), that is available using module load gsl which will get you version 1.15The Intel 2012 compiler suite is available as a module. module load intel will load the 2012 suite. It is the default for the same reason as gcc. The math kernel libraries (mkl) are provided when you module load intel (any version) - no separate step is required.The Intel 2013 compiler suite is also available as an optional module. module load intel/2013.5.192 will provide that version if needed.The latest Intel suite is now available with module load intel/xe.2016.u2. Unlike earlier versions, you do not need to separately load the MPI capable compiler. For detailed information, refer to the Intel documentation:
MPI compilersintel-mpi/2012.0.032 is the default version which matches the non-mpi version. Use module load intel-mpiintel-mpi/2013.5.192 is available by specifying module load intel-mpi/2013.5.192openmpi version 1.4.4 is available by specifying module load openmpimpich2 is available at version 1.4.1p1 by default or you can get version 3.1.4 with module load mpich2/3.1.4
The principles are similar for ElGato except that the intel and intel-mpi compilers are only available for the 2013 versions.
openmpi is available both for version 1.6.5 and version 1.8.1
El Gato has a separate web site with easy to follow instructions.
Puma, Ocelote, and El Gato all run CentOS7 and have the following compilers available:
$ module load intel/2020.1
$ module load intel/2020.4
$ module load gnu/5.4.0
$ module load gnu7/7.3.0
$ module load gnu8/8.3.0
This one is loaded by default
Common Software Packages
Installing additional software
To submit a request to have software installed on the UArizona HPC systems, use our HPC Software Install Request form. There is no expected time frame for how long it takes to install software, there are many variables that determine this. If you haven't heard back in a week, it is reasonable for you to follow up with a support ticket
You may also install software packages into the space that is allocated to you with your HPC account. However, you cannot install software that requires root permission or use a method like "yum install" that accesses system paths. For information on installing software locally, see our online guide for an example.