Applications FAQ

Open OnDemand¶

Why is my Open OnDemand session failing?

If you're encountering issues while using OOD, please visit our Open OnDemand Troubleshooting page.

How do I fix "Failed to execute default Web Browser." on OOD Desktop?

When you see the above message on a Desktop session after trying to launch the default Web Browser application from the Applications menu follow these steps:

Go to Settings > Default Applications
Click on the "Web Browser" drop-down menu under the "Internet" tab
If you see another browser selected, change the selection to "Google Chrome"
Launch Google Chrome and open OOD

Python¶

Installed a python package via pip install PACKAGEX, but import PACKAGEX results in an error.

A pip install you performed puts the resulting package into your personal directory tree located in the ~/.local/lib/pythonX.Y/site-packages directory tree. A personal pip install can often result in an installation of a python package from a binary archive (wheel) that was built on a system against software libraries that are not compatible with HiPerGator. A typical error message in such case complains about the lack of a particular GLIBC version or some other missing library. Note that the issue can be exacerbated by an incompatible interaction between an environment loaded via an environment module ('module load something') and a personal python package install. To avoid this issue the python package must be installed into an isolated environment. Our approach for creating such environments depends on many factors, but usually results in a Conda or containerized environment.

Custom Installation¶

I want to have a custom install of an application or python modules.

We recommend creating a Conda environment and installing needed packages with the mamba tool from the conda environment module. It is possible to mix conda and pip installed packages inside a conda environment as conda/mamba is aware of packages installed via pip, but not vice versa.

You can also visit our: Managing Conda Environments page for more information.

R¶

How do I install R packages?

Users can install R packages in their local directory. The default directory is /home/my.username/R/x86_64-pc-linux-gnu-library/X.X/. (X.X = version number)

From a standard repository (such as CRAN-R):

$ module load R/X.X
$ R
> install.packages("PACKAGE")

From GitHub:

$ module load R/X.X
$ R
> devtools::install_github("author/software")
or
> remotes::install_github("author/software")

From a Tarball:

$ module load R/X.X
$ R CMD INSTALL /path/package.tar.gz

When I submit a job using 'parallel' package all threads seem to share a single CPU core instead of running on the separate cores I requested.

On SLURM you need to use --cpus-per-task to specify the number of available cores. E.g.

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12

will allow mcapply or other function from the 'parallel' package to run on all requested cores

Jupyter¶

Why do I see the following error message? (kernel).ipynb appears to have died. It will restart automatically.

This is typically caused by the kernel using more RAM than what was requested when starting the session. Increase your memory request.

Why am I not able to spawn a Jupyter session?

One common cause for being unable to login to a Jupyter (JupyterHub or Jupyter Notebook) session is running out of home space quota. See the FAQ item above for "No Space Left".

Another reason is packages conflicting while loading the session. In this case, it is necessary to look for errors in the output and check for packages from the user's local environment listed.

MATLAB¶

How do I run MATLAB programs?

You may use the interactive MATLAB interpreter on the test nodes. However, in order to run MATLAB programs through the batch system, you must compile your MATLAB source code into a standalone executable. This is required because there are not enough MATLAB licenses available to run the programs directly. To learn how to compile your MATLAB program please see our MATLAB docs page.

How do I compile a MATLAB program?

Generally speaking, you will load the MATLAB module and then use the MATLAB compiler, mcc, to compile your MATLAB program(s). See our MATLAB docs page for more detailed instructions.

Why can't I check out a MATLAB compiler license?

If you tried to use the MATLAB compiler, mcc, and received the message Could not check out a compiler license it is because Research Computing does not have its own MATLAB licenses but relies on the UF campus license. There are a limited number of MATLAB compiler licenses shared by the whole campus. When the license is checked out during an interactive MATLAB session, it does not get checked back in until the MATLAB session is terminated, which could take a long time depending on what the user is doing. Unfortunately, you will not be able to run mcc until a license becomes available.

Galaxy¶

How can I add large datasets to the Galaxy?

Create your Galaxy upload directory as '/data/apps/galaxy/incoming/' and copy your datasets there. Note, it may take up to 15 minutes for Galaxy to fix the permissions before uploaded files will become available in a list at the bottom of the Galaxy 'Get Data > Upload File' tool. Please see our Galaxy docs page for more detailed information.

How do I report a Galaxy problem?

If you run into an issue using Galaxy, please be sure to report it via a support ticket. Our knowledgeable RC support staff will do their best to solve the issue.

I'd like to use a particular tool, but I can't find it in the Galaxy. What should I do?

Please submit a support request. The tool in question could already be wrapped by someone and available in the Galaxy Tool Shed. If it’s in the Tool Shed we can usually make it available in the UF Galaxy instance almost immediately. If the tool is not available in the Galaxy Tool Shed, we can look at the tool to determine if we can “wrap” it into the Galaxy interface and what the timeline for the project may be.