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Hello attendees

slurm

This repository contains materials introducing the campus compute clusters with R.

The directories contain the following minimal working examples of jobs:

  • bash: Process data in bash
  • R: One single R script
  • arrayR: Array job with R

Each has their own submit.sh script. Run them from a cluster with:

sbatch ./submit.sh

Lecture

Given Tue Feb 5 11:41:23 PST 2019 for STA 141C class

Demo video 1 Demo video 2

Cluster Resources:

UC Davis Specific:

Draw picture of architecture. Mention the 10 or so clusters on campus. This lesson applies to all of them, notably peloton which the statistics department now has more nodes on. It also applies to other supercomputers, and other types of clusters more generally.

The goal today is to convey the concepts, because this will make it much easier if you're reading the documentation later. I'm going to show you one conventional way to do things. There are many variations, for example, there are at least 4 ways to run an R script from the command line.

Vocabulary:

  • client: your laptop or desktop
  • server: a computer that is not right in front of you
  • node: a single computer
  • head node: the computer that everyone logs into.
  • hostname: a name that resolves to an IP address part of domain naming system, like google.com

Points:

  1. head node manages a queue of jobs and contention for resources
  2. this class has a reserved partition
  3. interactive versus batch jobs
  4. run your jobs on the worker nodes
  5. job can either be waiting in the queue to start, running, or finished
  6. network file system is an abstraction that makes all the files seem like they're on the same computer

I open up a terminal and login to the cluster Gauss with s141c-76 as follows:

$ ssh [email protected]

ssh means 'secure shell'.

If you don't have your SSH keys set up it will prompt you for a password, but no letters appear as you type. This is normal (otherwise you would see how long my password is! GASP!) I type it in and press enter, and then I see this:

$ ssh [email protected]
[email protected]'s password:

No backups of home directories are available for this cluster. Copy important files to another location.

NOTICE! Biannual generator test is scheduled for Friday April 5th 5am. The gauss cluser will shut down Thursday for system maintenance.

Last login: Sun Feb  3 09:16:27 2019 from resnet-122-161.ucdavis.edu
Module slurm/2.6.2 loaded
s141c-76@gauss:~$

Now I have a terminal in front of me that looks similar my local one, but I'm using a remote machine. I can verify this:

s141c-76@gauss:~$ whoami
s141c-76
s141c-76@gauss:~$ hostname
gauss.cse.ucdavis.edu

This says, I am the user s141c-76 on the machine gauss.cse.ucdavis.edu. To logout, I just type exit.

partitions

The partition staclass consists of two nodes, c0-10 and c0-19. We own these nodes for the duration of the quarter, so nobody else can use them.

The sta141c-XX student accounts have access to the entire cluster resources. It's possible for you to request a job that uses the entire cluster for 3 months. Do not do this. Use the staclass partition.

We have two nodes, each with 32 processors, so we should all be able to run jobs simultaneously if we use one core. I will give you specific guidance for each assignment.

moving your code and data

We're logged into the cluster, and now we need to put our code on the cluster so that we can run it. I have some example code in a git repository that I will pull from Github.

git clone https://github.com/clarkfitzg/slurm-example.git

Typically you'll write some file fancy_analysis.R on your laptop, and get it working so that you can call Rscript fancy_analysis.R locally.

You'll probably use some specific analysis software. It may be tricky to configure everything in exactly the way you want it, so that it runs the same way next time you try it. That's what the module command on the cluster is for.

Let's see what open source software is available and ready to use.

module avail

We've got installs for julia 1.0.2, numpy 1.7.0, R 3.3.2. If you would like any free software installed then email [email protected], they can add more.

running batch jobs

I have a script called analysis.R that I would like to run:

$ cd slurm-example/R
$ cat analysis.R

Here we see a script, and it even has a secret message in it.

# Your R script
x = 1:10

message("Adding messages like this is an easy way to add logging to your program.
This will help you debug things that run in batch mode.
Look for it in a file that ends with .out.")

Besides my actual data analysis script I need a submission script to make it work.

s141c-76@gauss:~/slurm-example/R$ cat submit.sh
#!/bin/bash -l

# All of these SBATCH options below are optional.

# Use the staclass partition. Only applies if you are in STA141C
#SBATCH --partition=staclass

# Email me a result
#SBATCH --mail-type=ALL
#SBATCH [email protected]

# Specify which version of the software you want to use, and make it available
module load R/3.3.2

Rscript analysis.R

I can put it into the queue and have it run as follows:

sbatch ./submit.sh

It tells me that I submitted the job and brings me back to the head node.

checking status

Suppose I do something dumb.

echo "
n = 0
while(n != Inf) n = n + 1
print(n)
" >> analysis.R

cat analysis.R

Question: Will analysis.R ever finish? No, check in R: 1e100 == 1e100 + 1.

Oh well, I'm just going to try it anyways.

sbatch ./submit.sh

Let's look at the queue and see who is running what:

$ squeue

It shows the job that I'm currently running:

     JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
   2065112  staclass    Rtest s141c-76  R       6:15      1 c0-10

Another way is to check the job through the online monitoring: http://stats.cse.ucdavis.edu/ganglia/

We can also examine the output file as it runs:

$ cat slurm-2065112.out

At some point I realize that I did something unwise, and I decide to kill my job with scancel 2065112. If this is the only job that I'm runnning then I can cancel all jobs for my user.

$ scancel --user=s141c-76

Examining the queue again we see that my job is gone.

array jobs

One way to submit a bunch of jobs is to just use a bunch of sbatch commands. If we do this, then it's good etiquette to pause for ~1 second between submissions so that we don't overwhelm the scheduler. source

If we're doing a bunch of simulations, then a better way is to use an array job.

We specify that it's an array job by adding this to our submission script:

SBATCH --array=1-10

This says that 10 jobs will be run. Inside each individual job, the bash environment variable SLURM_ARRAY_TASK_ID will vary between 1 and 10.

Our submission script also contains the line:

srun Rscript analysis.R ${SLURM_ARRAY_TASK_ID}

Our analysis.R takes in this variable and can do something different based on the value. One typical example is to use it to specify the state of the random number generator so that simulation results are independent. This is a nice way to do things, because then we can do local runs to make sure things go as planned:

$ Rscript analysis.R 3

transferring data

If I need to move small results or data back and forth between my local machine and the cluster then I can use git. The last I checket, Github.com supports up to 250 MB, but you want to stay way under this, less than 1 MB is fine.

Demo?

If I need to move large data sets, say greater than 1 MB, I can use sftp or scp from my local machine.

clark@local $ sftp [email protected]

Commands:

  • ls shows the files available in the current remote directory
  • cd navigates to a different remote directory
  • get downloads a file from the remote to the local
  • lls shows the files available in the current remote directory
  • put uploads a file from the local to the remote
  • exit quits the sftp program

interactive mode

Interactive mode is useful for developing and experimenting. It is not useful for running a large job that takes hours, because when you close your laptop your interactive job will be killed.

Lets get on a worker node.

srun --partition staclass --pty bash -i
  • srun is the SLURM command
  • --partition staclass specifies that we are running a job on the partition assigned to this class
  • --pty is a flag for 'pseudo terminal mode'
  • bash is the main argument, an executable to run
  • -i, and anything else following the main argument bash, are arguments to the bash executable. -i means interactive mode.

Now I have an interactive terminal on a worker node, and I can enter whatever commands I like.

s141c-76@c0-10:~$ hostname
c0-10

exit brings me back to the head node.

With the defaults on this system I get 1 core and unlimited memory on this machine.

Detailed notes are in the file lecture.md