Quick start#
Command line#
You need command line access to submit. You do not need a reservation to access a command line, you can connect to the BioHPC Login (head) node cbsulogin?.biohpc.cornell.edu.
One-time setup#
Note
Setting up SLURM-specific settings
From a command line, run the following lines, logout, then back in, and henceforth you can skip the --cluster cbsueccosl01 option:
echo 'export SLURM_CLUSTERS="cbsueccosl01"' >> $HOME/.bash_profile
In the following, replace netid with your actual NetID.
echo netid@cornell.edu >> $HOME/.forward
Enabling software via module
git clone https://github.com/labordynamicsinstitute/biohpc-modules $HOME/.modulefiles.d
See Customizing modules for more details.
Submitting jobs#
You can submit from the command line (SSH) at the login nodes cbsulogin?.biohpc.cornell.edu (see access description. All commands (sbatch, squeue, sinfo, etc) have to be run with option --cluster cbsueccosl01 (but see one-time setup).
There is only one partition (queue) containing all nodes, default parameters (changeable through SLURM options at submission, see below) are:
1 core and 4 GB RAM per job
infinite run time.
Interactive shell#
Interactive shell can be requested with command
srun --cluster cbsueccosl01 --pty bash -l
or if you ran the above TIP:
srun --pty bash -l
If you need a specific node, use
srun -w cbsueccoXX --pty bash -l
You can use all valid SLURM command line options (the same as are listed in a sbatch file) as well. In their absence, you will get default values (limitations).[1] For instance, the above invocations get unlimited memory, but are limited to 1 task on 1 CPU. If you needed to use more within your interactive shell, you might want to specify
srun -w cbsueccoXX --nprocs 8 --pty bash -l
Interactive GUI jobs#
You should be able to get interactive GUI jobs (Stata, MATLAB) to work as follows:
srun -n 2 -N1 --mem=8G --x11 --pty bash -l
/usr/local/stata18/xstata
or
srun -n 2 -N1 --mem=8G --x11 --pty bash -l
/local/opt/MATLAB/R2023a/bin/matlab
When done, type exit to exit the interactive session. Note that you must align the requested CPU count (-n 2) with the expected usage of the MATLAB and Stata/MP. While just opening them will not cause a problem, our Stata/MP version will use up to 8 cores, and MATLAB, unless specifically configured not to do so, will utilize the amount of physical cores on the system. For any serious computing, please use non-interactive mode, or adjust the number of cores you request accordingly.
Warning
It is technically feasible to login to each node without using SLURM. However, this confuses the job scheduler. Do not abuse this, exclusion from use of the cluster may be the consequence.
Running RStudio#
See the BioHPC Software site (search for Rstudio, then click on the link) for instructions on how to run Rstudio on the cluster. In a nutshell,
salloc -N 1
srun /programs/rstudio_server/rstudio_start 4.4.0
will run an instance of RStudio Server on the node you were allocated (if it isn’t already running). You can then connect to it using a web browser, using port 8016. The output of the srun command will tell you which node to connect to. For instance,
Nov 18 08:37:44 cbsueccosl03.biohpc.cornell.edu systemd[1]: Starting RStudio Server...
Nov 18 08:37:44 cbsueccosl03.biohpc.cornell.edu systemd[1]: Started RStudio Server.
means you would connect to http://cbsueccosl03.biohpc.cornell.edu:8016. If you are connected to the VPC, you can connect to it from your laptop, otherwise use the browser within the VNC session.
Warning
If you see
[lv39@cbsueccosl01 ~]$ srun /programs/rstudio_server/rstudio_start 4.4.0
Rserver is already running - no need to start it
If you want to restart it please stop it first using
/programs/rstudio_server/rstudio_stop
then somebody else may already have started an instance there. DO NOT STOP IT. You can still connect to your own session on that server.
To see running jobs#
squeue
To cancel a running job#
Use
scancel (ID)
where the ID can be gleaned from the squeue command.