Storage

Navigating Blue and Orange Storage

If you are listing /blue or /orange you won't see your group's directory tree. It's automatically connected (mounted) when you try to access it in any way e.g. by using an 'ls' or 'cd' command. E.g. if your group name is 'mygroup' you should list or cd into /blue/mygroup or /orange/mygroup. See also this short video: https://web.microsoftstream.com/video/87698fe6-84df-40dc-9d22-c3a6c63820fa

No Space Left

If you see a 'No Space Left' or a similar message (no quota remaining, etc) check the path(s) in the error message closely to look for 'home', 'orange', 'blue', or 'red' and check the respective quota for that filesystem. All quota commands are in the 'ufrc' environment module and include 'home_quota', 'blue_quota', 'orange_quota'. See Getting Started and Storage for more help.

A convenient interactive tool to see what's taking up the storage quota is 'ncdu' in the 'ufrc' env. module.

In case you consider purchasing more storage, please visit the Purchase Allocation portal.

Applications

Custom Installation

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

A: 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.

Python

Q: Installed a python package via 'pip install something', but 'import something' results in an error.

A: 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.

R

Q: 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.
A: 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

Q: How do I install R packages?
A: 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

$ 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 non-standard repository (tarball available)

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

Scheduling

Running Jobs

Q: Why is my job still pending?

A: According to SLURM documentation, when a job cannot be started a reason is immediately found and recorded in the job's "reason" field in the squeue output and the scheduler moves on to the next job to consider. Please refer to "Why is my job not running" for a list of reasons.

Performance

Q: Why is HiPerGator running so slow?

A: There are many reasons why users may experience unusually low performance while using HPG. First, users should ensure that performance issues are not originated from their Internet service provider, home network, or personal devices.

Once the possible causes above are discarded, users should report the issue as soon as possible via the RC Support Ticketing System. When reporting the issue, please include detailed information such as:

Time when the issue occurred
JobID
Nodes being used, i.e. username@hpg-node$. Note: Login nodes are not considered high performance nodes and intense jobs should not be executed from them.
Paths, file names, etc.
Operating system
Method for accessing HPG: Jupyterhub, Open OnDemand, or Terminal interface used.

In case you consider purchasing more resources, please visit the Purchase Allocation portal.

FAQ

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