The ECCO high-performance computing system is deployed as a part of BioHPC. All the resources available at BioHPC are available on ECCO servers, including networked storage and software .
Each ECCO user must have BioHPC account (it can be requested online) and belong to one of ECCO user groups:
|ecco01||general group for all ECCO users that do not belong to any of the groups below|
|ecco_sl2448||Shanjun Li Lab|
|ecco_lv39||Lars Vilhuber Lab|
|ecco_faculty||Group for ECCO Faculty|
BioHPC machines are divided into two groups: rental (pay-per-use) and hosted (owned by a group who has continuous access). The machines in the ECCO HPC cluster are operated as rental machines, however they are a bit special: reservations are restricted to ECCO group members, and there is no cost per use. This system ensures that the ECCO machines can be effectively shared among the group members.
Importantly, as with all BioHPC rental machines, your files stored on the rental machine are subject to deletion when your reservation ends. Therefore, you must transfer files out of /workdir/$USER/ before your reservation ends! For more information about the file deletion policy on rental machines, see the section "Local storage" here.
To use an ECCO server, a user has to create a reservation on BioHPC website (login first, then go to "Reservations" and choose category "Restricted"), or a user can be added to an existing reservation (the reservation owner can do this through the webpage, in the My Reservations section).
Once your reservation begins, you can access the machine through ssh or VNC. More documentation about access can be found here.
Each group has its own access priorities summarized in the table below. L (low) priority means maximum single reservation length of 1 day (24 hours), M (medium) 3 days (72 hours), H (high) 7 days (168 hours).
|Machine name||previous name (CAC)||ecco01||ecco_sl2448||ecco_faculty||ecco_lv39|
In addition to BioHPC software (including GCC set, R, Julia, Python, Perl) there are several customized software titles installed on the ECCO machines. Not all software is available on all servers; the availability on each server is shown in the table below. Also, note that tmux and vim versions on ECCO machines are different than on the rest of BioHPC servers.
|Machine name||previous name (CAC)||tmux||vim||Matlab||STATA||OXMetrics||SAS||Intel Compilers||NAG Fortran Lib||NAG Fortran Compiler|
* - installed but user-supplied license (in home directory) is required to use it
NOTE about MATLAB versions: The goal is to have the latest 'a' version installed on all machines, and additionally up to two previous 'a' versions available on cbsuecco02-06.
At present, the default MATLAB version is R2022a on all machines. To use a specific non-default version of MATLAB (available only on cbsuecco02-06), modify your search PATH by running
replacing 'XXXX' with the desired year. You can add the export command above to your .bashrc file to have the PATH modified automatically upon login.