# Running scripts on Rivanna at UVA

A tutorial on how to run scripts on Rivanna (SLURM in general) cluster at UVA, along with some tricks.

Image credit: uvarc/rc-website (GitHub)

# Overview

Our department has a nice collection of 16 servers, each with 4 GPUs. While this may sound like a lot, the servers are shared across the department and thus fill out pretty fast. We do have a SLURM cluster too, but it’s not as fast (or big enough to run GPU-based jobs via SLURM) as the servers. I recently looked into Rivanna after my advisor suggested it. I did write some sbatch scripts during my internship at Oracle Research Labs, so that definitely came in handy while trying to write wrapper scripts for the Rivanna cluster.

# Settings things up

The structure for these environments here is pretty similar to what we have for the CS servers. You can load up specific modules using module load. Since sbatch files get passed onto in a new bash environment, it’s always a good idea to have all your module load and other related commands (like conda activate) in your .bashrc file so that you don’t have to worry about adding all of them to every sbatch file.

For referencem, here’s what I added to my .bashrc:

module load singularity

#Identify whether using Rivanna version (load data accordingly)
export ISRIVANNA=1

# Conda-init related stuff that is auto-populated
conda activate phd # phd is the name of my environment


The only downside here is that storage is not shared with the other CS servers: you must either commit to using only Rivanna or only CS servers, or make sure you regularly sync your generated code (which is straightforward, thanks to Git) and data (not so trivial).

There are two storage directories: /home and /scratch. The former has a 50GB quota limit with weekly snapshots for backup, while the /scratch directory has a quota of 10TB/350,000 files (whichever is more). As mentioned on the Rivanna Storage page:

Slurm jobs run against /home will be slower than those run against /scratch

Thus, it is advisable to have all your scripts and data in the /scratch directory, even your Anaconda environment. You can specify a location for your Conda environment with the --prefix <PATH> flag while running conda create.

# Writing SBATCH scripts

Okay, enough talk! Let’s start with a basic wrapper script- let’s call it test.sbatch. If you are already familiar with these options and/or just want to use the defaults and get started, feel free to use the template here.

#!/bin/bash

#SBATCH -A uvasrg
#SBATCH --mem=32G
#SBATCH -p gpu
#SBATCH --gres=gpu:rtx2080:1
#SBATCH --time=3-00:00:00
#SBATCH --output=logs/%x-%j.out
#SBATCH --error=logs/%x-%j.err

echo "Parameters were $PARAM1 and$PARAM2"


Wait, wait, wait! Aren’t the #SBATCH commands going to get ignored (starts with #, so it’s got to be a comment, duh?). Well, not really- #SBATCH are treated differently by sbatch.

### #SBATCH --ntasks=1

This argument specifies the number of tasks you want to run with the given script. In most cases, this will be 1 unless you want parallel execution and will utilize it explicitly via your script.

For instance, you could specify --ntasks=2 to run two tasks in parallel:

 echo "Hello there" &
echo "General Kenobi" &
wait


This can be particularly useful when you have some form of caching, utilize the same file across different scripts, or just like the idea of having all your experiments run on the same physical machine.

### #SBATCH -A uvasrg

This option specifies which “allocation” you want to use. As a user at UVA (or SLURM clusters in general), you may be part of one or more allocation groups, which all have their compute budgets. This option ensures that your scripts run on the allocation group you specify. If you happen to be in UVASRG, this is the option for you!

If you’re curious about the compute budget used up/left in your allocation, you can run:

allocations


Furthermore, if you’re curious about other members in the same allocation group, you can run:

allocations -a <your_group_name>


### #SBATCH --mem=32G

This is pretty straightforward and lets you specify the total memory (in GBs) you want to allocate to your job. In most cases, 32 or 64 GBs is enough.

### #SBATCH -p gpu

This option here specifies which partition you want your scripts to run on. For most users (at least with machine learning), this will be ‘gpu’. You can have a look at all the available partitions here.

### #SBATCH --gres=gpu:rtx2080:1

This option here (the --gres in general) allows you to specify configurations of the nodes you want to run your scripts on. In this case, the rtx2080 is the name of the GPU card, and 1 is the number of cards you want to use. In terms of speed, you might want to prefer v100 over 2080.

One thing to note here: there may be times when machines with one type of GPU card are free while others are in use. It might be better to specify the other GPU in such cases instead of waiting for the busy GPU machines to clear up. But how exactly would you know which machines are free and which ones are not?

sinfo -o "%20N %10R %10e %25f %25G %t %C" -t IDLE,MIX


This provides information on the status of all machines, their GPU cards (and how many they have), free memory, and free/busy CPU cores. Pretty useful, huh!

### #SBATCH --cpus-per-task=10

This option lets you specify the number of CPUs you require per task in your script. From what I know, Rivanna has an upper limit of 10 per job for the GPU servers, but I’m not too sure about it.

### #SBATCH --time=3-00:00:00

This option here lets you specify an upper limit for your job. SLURM will terminate any jobs after this given time limit (set to a default value much lower than 3 days for Rivanna, from what I remember). We have an upper limit of 3 days, so this pretty much tells SLURM to run the job for as long as possible. If you want to run your job for longer, make sure you cache results so that the re-run can pick up from where the previous job left off.

### #SBATCH --output=logs/%x-%j.out

These two formats (this and #SBATCH --error=logs/%x-%j.err) specify the filenames for error and log files. The %x is the script’s name, and %j is the job ID.

## Submitting a job

There you go! Now that you know what each flag here means, let’s get to submitting the job:

 sbatch --export=ALL,PARAM1='no',PARAM2=42 --job-name=try test.sbatch


Note how we have two additional parameters, PARAM1 and PARAM2. This is a way for you to pass parameters to your job, which can then be used in your script. Make sure you leave the ALL in there since this passes on your environment’s predefined variables to the job.

# Job Arrays

Sometimes you might want to run the same commands inside but with different parameters- maybe you want to run a grid search or generate results for multiple datasets. Instead of creating new sbatch scripts in this case, you can utilize job arrays. This is a way to run multiple jobs with the same configuration but with different parameters.

For instance, you could run a job array with the following command:

sbatch --job-name=try test.sbatch --array=0-6


Note the additional --array=0-6 option. This specifies that you want to run 7 jobs, starting from 0 until 6 (all-inclusive). You could then modify the sbatch script to use different parameters based on the job index:

...
RATIOS=(0.2 0.3 0.4 0.5 0.6 0.7 0.8)
echo "Running for ratio ${RATIOS[$SLURM_ARRAY_TASK_ID]}"
...


# Tips and Tricks

## Start-Time Estimate

Submitted a job, but it’s stuck in (Priority) or (Resources)? If you see it’s way too much, you can always default back to some other servers (or change the configuration of your job so that it gets accepted). In cases like these, getting a rough estimate for the start time for your job can be helpful.

 squeue -u <your_username> --start


If you skip the --start above, you can view all your jobs and relevant information: how long they’ve been running for, their status, etc.

## Opening interactive sessions

Sometimes you may want to test your code out for smaller cases and/or debug, and going to and fro with log files may not be very convenient. You can open an interactive session with your job using the following command:

 ijob -A uvasrg -p gpu --time=0-00:30:00 --gres=gpu:rtx2080:1 --mem=8G


This command here would open an interactive session (capped at 30 minutes, so that you don’t accidentally leave it on and get charged for it) with your job, run on a machine with the RTX2080 GPU card and an allocation of 8GB memory.

## Adjuting resources based on job efficiency

It may so happen that you over-estimate the resources needed for your job, which can lead to higher allocation consumption as well as your scripts running at a later time (because of busy resources). A good starting point is to look at runs of your completed scripts:

you@machine:~$sacct --starttime=2022-02-04 --endtime=2022-02-11 --state COMPLETED -u <your_username> JobID JobName Partition Account AllocCPUS State ExitCode ------------ ---------- ---------- ---------- ---------- ---------- -------- 32259190 job1 gpu <acc_name> 16 COMPLETED 0:0 32259191 job2 gpu <acc_name> 16 COMPLETED 0:0  This command here, for instance, will give you a list of all completed jobs that started and finished between 4th and 11th February, 2022. You can then pick any jobID that you like and look at its CPU and memory usage efficiency: you@machine:~$ seff 32259190
Job ID: 32259190
Cluster: shen
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 16
CPU Utilized: 1-20:54:32
CPU Efficiency: 21.72% of 8-14:47:28 core-walltime
Job Wall-clock time: 12:55:28
Memory Utilized: 5.72 GB
Memory Efficiency: 17.86% of 32.00 GB


## Running GPU-based scripts

It’s good practice to specify the GPU card you want to use for your job. Most users might be familiar with CUDA_VISIBLE_DEVICES and setting this value before their experiments, or via code (in PyTorch, for instance). However, the machines that SLURM runs scripts on have shared GPUs that are visible to each job for some reason. As a result, even if you request one GPU and your job is run on a machine with 8 GPUs, using export CUDA_VISIBLE_DEVICES=0 will, instead of doing nothng (since you’d expecte the visible compute environment to have only one GPU), the job will run on the 1st GPU, even if it’s not the one that’s free.

I found this out the hard way (not mentioned on the website documentation, but the support staff were nice enough to tell me about it)- I submitted 8-10 jobs and they were all really slow, since they all got assigned the same machine and the CUDA_VISIBLE_DEVICES made them run on the same GPU.

##### Anshuman Suri
###### PhD Student

My research interests include privacy and security in machine learning.