There are some limited access clusters managed by SICE that are using the slurm job scheduler. These systems have a head node that you can log into and, from there, you use slurm commands to allocate and run jobs on the compute nodes. This page provides a very quick introduction to using slurm on these SICE-managed clusters. Please see the SLURM Homepage for more detailed information about using SLURM and see the Storage System Notes below for cluster-specific storage information.
Head Nodes and Compute Nodes
The SICE clusters have what is called a head node that you can just log into and compute nodes that you can use by allocating them via SLURM.
|Cluster||Head Node||Compute Nodes|
Bio SGX Cluster
bio-sgx01.soic.indiana.edu through bio-sgx12.cs.indiana.edu
dagger01.sice.indiana.edu through dagger16.sice.indiana.edu
tatooine1.sice.indiana.edu through tatooine8.sice.indiana.edu
From the head node, you can then run your jobs on the compute nodes. You should NOT do your compute processing on the head node. Rather, you will need to use SLURM from the head node to allocate compute nodes and run your jobs there.
In some cases, you will just want to allocate a compute node (or nodes) so you can ssh login and use the system interactively. Note that you are not allowed to just ssh login to a node without first allocating the resource. If you just want an interactive shell on one note you can easily do that as follows using srun:
You can also allocate a single node or multiple notes for ssh logins using the salloc command and then see which node(s) you were allocated using the squeue command. For example, you can ssh into the head node and allocate a node in the cluster as follows:
In this example (and those that follow) the command prompt is displayed as the host name in brackets followed by a dollar sign (eg. "[odin]$") to indicate which system you are logged into.
Be sure to exit the shell created by the salloc to relinquish your allocation, thereby making the modes available to others. If you need to allocate multiple nodes for interactive ssh logins, you can just give the desired number of nodes using the -N argument to salloc.
There may be a limit on the time you can allocate a node and you will loose your allocation and be logged out of the nodes if you hit this limit.
Running Jobs Interactively
If you have a program that you just want to run interactively on a number of compute nodes, one way to do this is using the SLURM srun command. For example, let's create a simple executable script called hostname.sh that just prints the hostname:
Then, we can run this script on 4 compute nodes as follows:
In this example you can see that we were allocated 4 different nodes and the output of running the test.sh script on each of them is displayed. This was run in parallel so the ordering of the output is indeterminate and may well vary each time you run this.
Running Batch Jobs
In many cases your job will have to run for a long time, you will have multiple jobs to run, and/or the resources needed to run your job will not be immediately available. In such cases, rather than using srun interactively and waiting around for the output you will want to use batch mode. This is specified using sbatch and, when your job completes, the output is then written to a file rather to the terminal. For example:
At this point you are probably asking yourself why the output didn't show the hostname of 4 systems since we allocated 4 nodes? It is important to note that sbatch allocates 4 nodes but then only runs your script on the first node in the allocation (odin006 in the above example). Typically, your program will be taking care of managing the nodes that are allocated so sbatch doesn't run the same program on all 4 nodes.
Here is an example script called batchtest.sh that will run our simple hostname.sh script on all allocated nodes:
We can then run batchtest.sh via sbatch to run hostname.sh on all allocated nodes:
Our simple batchtest.sh script doesn't have to tell srun how many nodes to use. The SLURM system sets up environment variables defining which nodes we have allocated and srun then uses all allocated nodes.
The above examples provide a very simple introduction to SLURM. You should see the slurm man pages and on-line documentation for further information. The SLURM commands you are likely to be interested in include srun, sbatch, sinfo, squeue, scancel, and scontrol.
Storage System Notes
Each of the cluster are configured differently regarding data storage space. This table gives a summary of the storage space available on each cluster.
|Bio SGX||$HOME||No backups|
No disk redundancy
No disk redundancy on sigma
No disk redundancy