If you are new to cluster computing, you You may be wondering why you can't simply run your applications in the same way that you do on your laptop or desktop. First, as a shared resource we need a method of coordinating the work of many researchers simultaneously so that users aren't stepping on each others' toes.
Second, when you first log into Talapas you will be connected to one of our "login nodes". These nodes are essentially a lobby in which users can do file management, write scripts, and submit jobs. They
| Info |
|---|
login nodes are not an appropriate place to run applications or conduct simulations. A good rule of thumb is: If it takes more than one second to complete, it's not appropriate for a login node. |
...
Instead Instead, these tasks should be conducted on a "compute node." These are purpose-built for running intensive computations and can only be accessed via the SLURM Slurm job scheduler. SLURM Slurm will ensure that the compute nodes are allocated in a fair and equitable manner that prevents resource conflicts. The primary method by which you will run simulations on Talapas will be to "submit a job."
Step-by-step guide
...
Components of a job
...
Slurm job script
The Shell
| Code Block |
|---|
#!/bin/bash |
...
Slurm resource requests
See Slurm sbatch documentation for more information.
| Code Block |
|---|
#SBATCH -- |
...
account= |
...
<myPIRG> #SBATCH --job-name=HiWorld |
...
#SBATCH --output=Hi.out |
...
|
...
#SBATCH --error=Hi.err
|
...
#SBATCH --partition=computelong #SBATCH --time=0-00:01:00 |
...
#SBATCH --ntasks=1 #SBATCH --cpus-per- |
...
task=1 #SBATCH --mem-per-cpu=500M |
Program dependencies
Load all software your job requires, for example python
| Code Block |
|---|
module load python3/3.11.4 |
Call the program or job steps
| Code Block |
|---|
./a.out |
Slurm job script
Example of a job script:
hello.sbatch
Code Block language bash #!/bin/bash #SBATCH --account=<myPIRG> #SBATCH --job-name=hiworld #SBATCH --output=hi.out #SBATCH --error=hi.err #SBATCH
...
--partition=compute #SBATCH --time=0-00:01:00 #SBATCH --ntasks=1 #SBATCH --
...
cpus-per-
...
task=1
...
#SBATCH --
...
mem-per-cpu=500M module
...
load python3/3.11.4 ./a.out
...
Above we see the contents of our SLURM script (aka job script) called
hello.
...
sbatch(
...
script name and suffix is arbitrary–use whatever name you like).
...
Notice that the script begins with
#!/bin/bash. This line tells Linux which shell interpreter to use when executing the script.
...
We used
bash(the Bourne Again Shell) and it's by far the most common choice
...
.
Next, we see a collection of specially formatted comments, each beginning with#SBATCHfollowed by option definitions. These are used by thesbatchcommand to set job options.
...
This allows us to describe our job to the scheduler and ensure that we reserve the appropriate resources (cores, memory,
...
time) for an appropriate amount of time.
...
Submit your job
o the scheduler using the sbatch command.
| Code Block | ||
|---|---|---|
|
...
$ sbatch hello. |
...
sbatch Submitted batch job 20190 |
...
The job has been submitted and is assigned the job number 20190 which will serve as its primary identifier.
Check
...
job
...
status
Use the squeue command.
| Code Block | ||
|---|---|---|
|
...
$ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 20190 computelo |
...
HiWorld duckID CG 1:09 1 n074
|
...
|
...
... |
Here we see that our job, number 20190, is in the CG (completing state).
...
Jobs in the system
...
may be R (running) or PD (pending
...
).
Jobs are pending when there are insufficient resources available to accommodate the request as specified in the job script.
...
To view only your jobs
...
:
| Code Block |
|---|
$ squeue -u duckid |
If necessary, cancel your job using the scancel command followed by the job number of the job you wish to cancel.
Code Block language text
...
$ scancel 20190
...
Related articles
| Filter by label (Content by label) | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| Page Properties | ||
|---|---|---|
| ||
|