Software and Modules

Software and Modules

Q. Are any software modules loaded by default?

Yes, when you start an interactive terminal session or submit a batch script, the modules ohpc, gnu8, openmpi3, and cmake are automatically loaded. If your code uses Intel compilers, you will want to manually unload gnu8 and openmpi3 to prevent conflicts.

The exception: If you are working in a terminal in an Open OnDemand interactive desktop session, nothing is loaded by default and you will need to manually load any necessary modules.

Q. How do I install this R package/Why can't I install this R package?

R installations can sometimes be frustrating. We have instructions for how to set up a usable R environment, how to diagnose and troubleshoot problems, and steps to help with known troublesome packages documented in in our Using and Customizing R Packages section.

Q. How do I install Python packages?

You can install python packages locally using either a virtual environment or a local conda environment. See our documentation on using Python for instructions on how to set these up.

Q. I've been using an older version of Singularity, why isn't available anymore?

The current version of Singularity is 3.7.4. Prior versions have been removed, only the latest one is considered secure. Notify the consultants if you need help with transition to the current version. Singularity is installed on the operating systems of all compute nodes so does not need to be loaded with a module.

Q. What executables are available when I load a module?

Load the module, find the path to the executable by checking the $PATH variable, then list the contents. For example:

module load lammps
echo $PATH
ls /opt/ohpc/pub/apps/lammps/3Mar20/bin
lmp_mpi

Q. Why am I getting "command: module not found"?

There are a few different possibilities:

You are not in an interactive session. Modules are not available on the login nodes. You may request an interactive session by using the command interactive.
Your shell is not set to bash. If this is the case, contact our consultants so that they can reset it for you.
You have modified or deleted your ~/.bashrc. If this is the case, open (if the file exists) or create and open (if the file is missing) the file .bashrc in your home directory and add the lines:
```
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi
```

Q. How can I maximize my software performance on Puma?

If you are able to compile your software you can take advantage of most of the AMD Zen architecture.

Compiler	Arch-Specific	Arch-Favorable
GCC 9	-march=znver2	-mtune=znver2
LLVM 9	-march=znver2	-mtune=znver2

Neither of these compiler versions (GCC 9 or LLVM 9) is available on Puma so you will have to build that first. If you use GCC 8.3 you can set znver1 instead.

Q. I have an application that runs on Windows and uses GPUs, where can I run it?

Windows applications can't be run on HPC, however, AWS has been used successfully for Windows software with GPU needs. It’s easy to set up, cost effective, and very scalable. Amazon also has a cloud credit for research program available
https://aws.amazon.com/government-education/research-and-technical-computing/cloud-credit-for-research/ [aws.amazon.com]

You may also consider trying Jetstream2, a national resource where you can create and use virtual machines. More information can be found here: https://jetstream-cloud.org/

Q. Is the Intel compiler faster than GCC on Puma?

Intel compilers are optimized for Intel processors. There is some debate around the concept of unfair CPU dispatching in Intel compilers. By default, software on the HPC clusters is built with GCC (on Puma it is GCC 8.3). This is in keeping with our preference for community software.

Q. How do I access Gaussian or Gaussview?

You need to belong to a special group called g03. You can request to be added by submitting a help ticket. This is a constraint in Gaussian that other modules do not have.

Q. How do I take advantage of the Distributed capability of Ansys?

Ansys has the Distributed capability built in to increase performance. Ansys uses the Intel compiler and so uses Intel MPI. By default, we load OpenMPI, so you will need to do this:

module unload gnu8 openmpi3
module load intel
module load ansys

Q. How do I access custom Python packages from an OOD Jupyter session?

Instructions on accessing custom packages are under Accessing Custom Packages from a Jupyter Session in our documentation on Using and Installing Python.