Software#
The general ECCO landing page at BIOHPC (https://biohpc.cornell.edu/lab/ecco.htm) for the general overview.
Available software#
MATLAB (various versions)
Stata (various versions)
OxMetrics
In addition, all regular BioHPC-maintained software is available, see the full list. You search through the list with ctrl-f or cmd-f in your browser.
You can also run
Tip
Always read the BioHPC-specific instructions on how to run the software!
Using module#
When multiple versions of a software exist, you must decide which version to use. For BioHPC-maintained software, you can use the module command to load the desired version.
BioHPC-managed modules#
You can find out the available versions of software “managed” through module by using the module avail command.
module avail
which will list out the available configurations:
$ module avail
------------------------------------------------------ /usr/share/modulefiles -------------------------------------------------------
mpi/openmpi-x86_64
-------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------
gcc/10.2.0 java/1.7.0 java/13.0.2 perl/5.16.3 python/2.7.5 python/3.6.15-r9 R/4.0.5-r9 R/4.2.1-r9
gcc/10.4.0 java/1.8.0 java/21.0.1 perl/5.22.0 python/2.7.15 python/3.10.6-r9 R/4.1.3-r9 R/4.3.2
(default versions may be underlined).
For instance, to load the default version of R, use:
module load R
To load a specific version of R, use:
module load R/4.3.2
Customizing modules#
BioHPC only maintains modules for common software. For ECCO-specific software, you may need to create your own module files, or use a pre-configured set maintained by Lars.
Getting additional module configurations#
The easiest way to get started is to copy the module files from Lars’s Github repository:
git clone https://github.com/labordynamicsinstitute/biohpc-modules $HOME/.modulefiles.d
You can refresh this at any time using
cd $HOME/.modulefiles.d
git pull
Not all modules listed are actually installed!
The modules listed in the repository will work on the specific nodes that the software is installed. Not all nodes have all software installed. The module command only allows the shell to find the software if it is installed, but does not actually install the software.
Creating your own module files#
You can suggest additional module files, or create your own. If you create your own, create a fork from Lars’ repository, and create additional ones there. If you want to contribute back, issue a pull request.
Additional software#
You can use additional software via docker or singularity (apptainer). If you need software installed, contact BioHPC, or install in your own home directory.