A short tutorial on using ACCRE aimed at Biostatistician needs.
Vanderbilt University Medical Center Department of Biostatistics
A short intro to ACCRE is provided by Jeffrey Liang. This is designed to be a useable template and example of a recommended solution design using R. It is executable and modifiable, with clear instructions on what modifications should be made. Please fork this repository and use as a seed for your own ACCRE simulation project. Two key goals: reproducibility and simplicity.
Parallel computing is required to numerically evaluate large simulations involving spatial and time information. The Parallel Pipeline Computation Model at Northwestern demonstrates this numerical analytic design.
These kinds of problems are common in solving large partial differential equations, ultra high dimensional spectral analysis, and nuclear simulations. ACCRE provides resources for solving such problems, and it involves having a high number of CPUs and nodes with high speed communication buses allocated all at once. A problem of this type quickly burns through fair share and can leave ones smaller shared group account depleted with just a couple requests. It also leads to long delays in a job getting executed. The proper configuration and solution design of such problems is complex and requires dedicated study.
Biostatistics problems typically consist of simulations involving multiple
runs that are independent and do not communicate or share information with
other runs. These types of problems are known as batch array jobs. Note the
lack of coordination or communication between the nodes. The
relevant slurm parameter is array.
This runs multiple jobs independently and fits them in as possible, likely
using less resources than a parallel job request.
Important: A batch array should slurm look something like this:
...
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --array=1-250
...
The advice going around that 'the more nodes the faster the job' is not true. In fact it's the opposite. This snippet says we don't need complex coordination across nodes and tasks with multiple cpus running for a task. We just need 1 job run 250 times. In other words each independent simulation needs a single node for a single task with a single CPU. It requests this configuration 250 times independently, and doesn't ask for any special parallel needs.
With a large parallel setup, ACCRE has to plan and wait for all those resources to be available at once. With independent batch arrays it can fit in the cracks between all the other jobs running. Array jobs will get queued faster and turn around will generally be quicker, and depending on fair share weighting takes fewer resources from the group pool than a parallel request.
One could submit more batches later and give them a different range of numbers.
...
#SBATCH --array=251-500
...
When slurm executes the job, this array number is important. It can control the associated design from a data.frame, it can seed the random number generator for repeatability. It can be used to identify failures. Understanding the propagation of the array batch number from the slurm file through the R and how it's used is a key concept of this tutorial.
What is required is some simple scripts that allow one to quickly identify a failed job and to reproduce that behavior locally. For example, batch array number 123 might fail, and in a local development environment one would wish to reproduce that exact failure to determine what set of conditions led to that failure. These scripts should also require no modification running locally or on ACCRE.
Make sure one has taken the required training courses for using ACCRE. If one has not done this and opens a support request or consumes too many resources, access may be denied. This will also help get your account setup.
One also needs to understand the command line using a terminal or shell. Various references exist on the web of the most common commands.
This is a tricky bit. Two pieces of unknown information are required. Time to execute and memory used.
> source('simulation.R')
> system.time(simulation(1))
user system elapsed
0.021 0.000 0.020
> sum(.Internal(gc(FALSE, FALSE, TRUE))[13:14])
[1] 44.3
Running the job locally and tracking simulation time and total memory used tells us that we need 0.02 seconds of time and 44.3 MB. These are then used to inform the slurm requirements. In general modern laptops are more powerful that the nodes on ACCRE, but with ACCRE you get access to 1000's. Modify your slurm jobs parameters to be twice the time and about 50% or more of the memory required for some margin of safety.
If one overspecifies, it penalizes placement in the queue. If one underspecifies the job is terminated before completion.
In the example case, we went a bit over this as these values are quite low.
#SBATCH --time=00:01:00
#SBATCH --mem=100M
This asks for a 1 minute of time with 100M available.
The slurm line
#SBATCH --output=status/job%a.out
Tells ACCRE that all output from cat, message, print, and stop be
written into the directory status, and give a title like job12.out via substitution of the array number. There is a lot of freedom in naming,
See filename pattern in slurm
help files. Most the other possible information is great for tracking a
running job, but not very helpful for reproducibilty of results. The
array number allows to identify what succeeded and what failed from our
requested jobs.
design.R
: This contains or creates a data.frame simulation_design that provides parameters associated with the array number. This should be heavily modified by the end user for their target problem.
sim-accre.R
: This requires no modification and takes the ARRAY number from the command line when executed and sets the random seed and calls simulation(x) where x is the array number.
sim-local.R : This is for local testing using multiple cores. Generally good for trying a few array batches to make sure the code is ready for ACCRE. It has a couple modification points for your local configuration or array goals.
simulation.R : This is the R code that demonstrates a simulation, that pulls the design, provides that to a function and saves the output. It is a template that requires modification for your project and research. It should remain about as simple as it is now, and complex simulation code should be sourced into it. It has a cohesive clear purpose and outline. Putting a lot of simulation custom code here would reduce the cohesion.
simulation.slurm : An example slurm file that runs this example simulation, "add it up".
The Array Task ID propagates through the code in the following manner:
Slurm (${SLURM_ARRAY_TASK_ID}) ->
sim-accre.R (command line) ->
set.seed(array_task_id) ->
simulation(array_task_id) ->
simulation_design[array_task_id,] ->
save( part of output file name )
The setting of the random seed allows one to reproduce any given job run in another setting. Thus a failed job, one can debug locally.
vunetid:~$ ssh vunetid@login.accre.vanderbilt.edu
vunetid@login.accre.vanderbilt.edu's password: *****
Last login: Thu Sep 1 13:50:59 2022 from 10.151.20.117
Vanderbilt University - Advanced Computing Center for Research and Education
_ ____ ____ ____ _____ ____ _ _
/ \ / ___/ ___| _ \| ____| / ___| |_ _ ___| |_ ___ _ __
/ _ \| | | | | |_) | _| | | | | | | / __| __/ _ \ |__|
/ ___ \ |__| |___| _ <| |___ | |___| | |_| \__ \ || __/ |
/_/ \_\____\____|_| \_\_____| \____|_|\__,_|___/\__\___|_|
===============================================================
Go forth and compute!
This is a shared gateway node designed for interactive use and small test jobs.
Please restrict your total system memory usage to less than 31 GB,
and do not run individual processes exceeding 20 minutes of CPU-time.
To list useful cluster commands type: accre_help
To view your current storage type: accre_storage
To list basic Linux commands type: commands101
Once logged in it's good (but not required) to set up a ssh key with github to allowed easy editing from ACCRE. See github docs.
[vunetid@gw346 ~]$ ssh-keygen -t ed25519 -C "your_email@example.com"
Generating public/private ed25519 key pair.
Enter file in which to save the key (/home/vunetid/.ssh/id_ed25519):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/vunetid/.ssh/id_ed25519.
Your public key has been saved in /home/vunetid/.ssh/id_ed25519.pub.
The key fingerprint is:
SHA256:QfgECwi18rmohyLD/8lJ/ASDFASDFOvP7Ajof/g your_email@example.com
The key's randomart image is:
+--[ED25519 256]--+
|.oo.. .o. |
|. o .o.o |
| .. ..o. |
| o . o =.. |
| ...o + + + |
| o o +S= |
|oo...= . = |
|B...=.O . |
|++oo+EoB |
+----[SHA256]-----+
[vunetid@gw346 ~]$ cat ~/.ssh/
id_ed25519 id_ed25519.pub known_hosts
[vunetid@gw346 ~]$ cat ~/.ssh/id_ed25519.pub
ssh-ed25519 AAAAC3ASDFASDFASDFASDFASDFASDFASDFsXRQwPG2kQLdeV your_email@example.com
Copy the resulting public key id_ed25519.pub to your github account. It's on the github.com website, click your icon in the upper right and then select "Settings". On that pack select the left hand side option "SSH and GPG keys". Click the green button "New SSH Key" and name it so you know the associated system it came from and past the above crypto string (from the cat results starting with ssh-ed25519 above) as the key. The associated
id_ed25519 is the private key that is equivalent to a password and
should be treated with great care.
[vunetid@gw346 ~]$ git clone git@github.com:vubiostat/accre_tutorial.git
Cloning into 'accre_tutorial'...
Warning: Permanently added the ECDSA host key for IP address '140.82.112.3' to the list of known hosts.
remote: Enumerating objects: 29, done.
remote: Counting objects: 100% (29/29), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 29 (delta 12), reused 23 (delta 9), pack-reused 0
Receiving objects: 100% (29/29), 7.39 KiB | 0 bytes/s, done.
Resolving deltas: 100% (12/12), done.
[vunetid@gw346 ~]$ cd accre_tutorial
This has cloned the project and pulled the source in from github to the local ACCRE gateway. If one uses github, coordinating source code between a local device and accre is relatively easy. One could edit code on ACCRE, commit to get and push centrally. Then pull locally. As well as edit locally and pull modified code onto ACCRE. The purpose of git is to keep all copies and edits of source code and synchronize them between devices. Note, the clone would need to use the ssh link for the project and keys from ACCRE loaded to github.
[vunetid@gw346 accre_tutorial]$ git pull
Already up-to-date.
Now one can submit this example job for execution using slurm commands and check on it's status. It's design to use few resources so feel free to give it a try.
[vunetid@gw346 accre_tutorial]$ sbatch simulation.slurm
Submitted batch job 61567954
[vunetid@gw346 accre_tutorial]$ squeue -u vunetid
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
61567954_10 productio simulati vunetid CG 0:05 1 cn1345
61567954_1 productio simulati vunetid R 0:05 1 cn1275
61567954_2 productio simulati vunetid R 0:05 1 cn1284
61567954_3 productio simulati vunetid R 0:05 1 cn1348
61567954_4 productio simulati vunetid R 0:05 1 cn1352
61567954_5 productio simulati vunetid R 0:05 1 cn1369
61567954_8 productio simulati vunetid R 0:05 1 cn1333
61567954_9 productio simulati vunetid R 0:05 1 cn1333
61567954_11 productio simulati vunetid R 0:05 1 cn1345
61567954_12 productio simulati vunetid R 0:05 1 cn1367
61567954_13 productio simulati vunetid R 0:05 1 cn1367
61567954_14 productio simulati vunetid R 0:05 1 cn1399
61567954_15 productio simulati vunetid R 0:05 1 cn1399
61567954_16 productio simulati vunetid R 0:05 1 cn1307
61567954_17 productio simulati vunetid R 0:05 1 cn1308
61567954_18 productio simulati vunetid R 0:05 1 cn1308
After waiting a few minutes, most of the jobs will be done.
[vunetid@gw346 accre_tutorial]$ squeue -u vunetid
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
Now we can check to see how successful this was.
[vunetid@gw346 accre_tutorial]$ cd status
[vunetid@gw346 status]$ grep -i error *
job12.out:Error in simulation(x) : SOMETHING WENT HORRIBLY WRONG!
[vunetid@gw346 status]$ less job12.out # examines full log
Sure enough one of the jobs contained an error. Let's run that locally and see if we can recreate it. Jumping back to a local terminal.
[vunetid@gw346 status]$ exit
logout
Connection to login.accre.vanderbilt.edu closed.
vunetid:~/Projects/accre_tutorial$
Then editing sim-local.R, this line:
mclapply(12:13, # <=== MODIFY HERE Batch Array numbers to run locally
mc.cores=8,
This says we will rerun 12 and 13 locally. But this is for doing multiple batches. A better direct debug session would be as follows:
vunetid:~/Projects/accre_tutorial$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source('simulation.R')
> set.seed(12)
> simulation(12)
Error in simulation(12) : SOMETHING WENT HORRIBLY WRONG!
Locally we've reproduced the failure and can move towards getting that
fixed. After some work, the problem is found in simulation.R on this
line:
if(array_task_id == 12) stop("SOMETHING WENT HORRIBLY WRONG!")
If one deletes that line, locally commits and saves to git. One can jump back over to ACCRE and do a git pull in the project and the changes will be ready to rerun job 12.
We just need to edit the simulation.slurm and change the request batch to rerun the fixed job.
...
#SBATCH --array=12
...
Now when we submit this slurm job it will only run the single job that has task array id 12.
[vunetid@gw344 accre_tutorial]$ sbatch simulation.slurm
... Wait and check for job to complete and check for errors
[vunetid@gw344 accre_tutorial]$ grep -i error status/*
With that clean bill of health, let's pull the data locally for analysis. The
scp command stands for 'secure copy' and can move files between environments.
Be sure to always include a ':' in a url of a remote device, otherwise it
will just work locally and lead to confusion.
vunetid:~/Projects/accre_tutorial$ scp -r login.accre.vanderbilt.edu:accre_tutorial/output .
vunetid@login.accre.vanderbilt.edu's password:
result-0001.Rdata 100% 85 2.7KB/s 00:00
result-0002.Rdata 100% 85 2.9KB/s 00:00
result-0004.Rdata 100% 85 2.8KB/s 00:00
result-0003.Rdata 100% 85 2.7KB/s 00:00
result-0015.Rdata 100% 86 2.9KB/s 00:00
result-0014.Rdata 100% 86 1.8KB/s 00:00
result-0016.Rdata 100% 86 2.9KB/s 00:00
result-0017.Rdata 100% 86 2.8KB/s 00:00
result-0007.Rdata 100% 85 2.3KB/s 00:00
result-0008.Rdata 100% 85 2.9KB/s 00:00
result-0018.Rdata 100% 86 2.7KB/s 00:00
result-0006.Rdata 100% 85 3.0KB/s 00:00
result-0005.Rdata 100% 85 2.8KB/s 00:00
result-0010.Rdata 100% 86 2.9KB/s 00:00
result-0009.Rdata 100% 85 2.7KB/s 00:00
result-0013.Rdata 100% 86 2.8KB/s 00:00
result-0011.Rdata 100% 86 2.7KB/s 00:00
result-0019.Rdata 100% 86 2.9KB/s 00:00
result-0020.Rdata 100% 86 2.6KB/s 00:00
result-0012.Rdata 100% 132 3.4KB/s 00:00
vunetid:~/Projects/accre_tutorial$ ls output
result-0001.Rdata result-0006.Rdata result-0011.Rdata result-0016.Rdata
result-0002.Rdata result-0007.Rdata result-0012.Rdata result-0017.Rdata
result-0003.Rdata result-0008.Rdata result-0013.Rdata result-0018.Rdata
result-0004.Rdata result-0009.Rdata result-0014.Rdata result-0019.Rdata
result-0005.Rdata result-0010.Rdata result-0015.Rdata result-0020.Rdata
Let's aggregate results for reporting now that they are pulled local.
> results <- do.call(rbind, lapply(list.files('output'), function(x) {
load(file.path('output',x))
n <- nchar(x)
result <- as.data.frame(result)
result$batch <- as.numeric(substr(x, n-9, n-6))
result
}))
> results
result batch
1 3 1
2 4 2
3 5 3
4 6 4
5 7 5
6 4 6
7 5 7
8 6 8
9 7 9
10 8 10
11 4 11
12 5 12
13 6 13
14 7 14
15 8 15
16 5 16
17 6 17
18 7 18
19 8 19
20 9 20
There it is, the results of our batch runs. One can now proceed to produce spectacular reports of the findings. This ends the main tutorial of running jobs on ACCRE for Biostatistics.
Installing packages in the ACCRE environment can be challenging.
The following if placed in ~/.Rprofile will set quit to always not save the
environment and set the CRAN mirror to nearby Oak Ridge.
utils::assignInNamespace(
"q",
function(save="no", status=0, runLast=TRUE)
{
.Internal(quit(save, status, runLast))
},
"base"
)
options(repos=c(CRAN="https://mirrors.nics.utk.edu/cran/"))
One can now proceed to install R packages from source by loading the latest R modules into the environment.
module purge
module load GCC/11.3.0
module load OpenMPI/4.1.4
module load R/4.2.1
With R loaded one can proceed to install packages. Chose local library when asked.
[vunetid@gw344 accre_tutorial]$ R
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('cli')
Warning in install.packages("cli") :
'lib = "/cvmfs/oasis.opensciencegrid.org/accre/mirror/optimized/sandy_bridge/easybuild/software/MPI/GCC/11.3.0/OpenMPI/4.1.4/R/4.2.1/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘/panfs/accrepfs.vampire/home/vunetid/R/x86_64-pc-linux-gnu-library/4.2’
to install packages into? (yes/No/cancel) yes
trying URL 'https://mirrors.nics.utk.edu/cran/src/contrib/cli_3.6.2.tar.gz'
Content type 'application/x-gzip' length 569771 bytes (556 KB)
==================================================
downloaded 556 KB
* installing *source* package ‘cli’ ...
...
installing to /panfs/accrepfs.vampire/home/vunetid/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-cli/00new/cli/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
The downloaded source packages are in
‘/tmp/RtmpeV14yC/downloaded_packages’
>
The R versions hosted by ACCRE are usually out of date, as the speed of R versions changes rapidly. This can cause issues with getting all the packages installed, since CRAN has no support for older versions of R or the packages compiled for them. The recommended solution is Docker. It allows one to create a binary bundle that contains all the installed packages required and is a lightweight virtual computer. Let's explore the steps required to create a docker image of our Add It Up example.
Jeffrey has a tutorial on building a Docker image using Singularity, which is the version of Docker supported by ACCRE.
This tutorial demonstrated a strategy to properly configure array jobs for ACCRE that corresponds to general needs of statisicians. This helps prevent excessive fairshare usage by misconfigured jobs. It does not ensure that fairshare priority is adequate for one's group. In practical terms, this means that a job one day can be immediately executed when there is fairshare and take 3 days when there is no fairshare left. Fairshare is paid for by your department, and once exhausted ones jobs have to age into being executed. This tutorial helps one not exhaust fairshare carelessly, but the usage rate and how long till it runs out is based on what your group has paid for and how many jobs one's group is running. If there is remaining fairshare for one's group ACCRE adds this to the priority of the job and deducts the group pool. Each job not run gets it's priority incremented per some timestamp.
A completely made up example with made up numbers would be as follows:
Group A with remaining fairshare submits a large array job. These jobs get bumped in priority by +100 by using fairshare (and theirs goes down), and thus have a rating of 100.
Group B with no remaining fairshare in the time cycle submits a large array job. These jobs get no bump in priority and start at 0.
The ACCRE scheduler picks Group A's jobs to run. As time marches forward, Group B's jobs get incremented for every time step they wait. Let's say they wait 24 hours, the jobs now have priority 24. If A doesn't submit another group using fairshare then B's will get picked. Otherwise, as long as group A keeps submitting they will have priority over till B's jobs are over 100 hours old or the next round of fairshare gets released into accounts (I think it's monthly).
While these numbers are completely made up, my personal experience is that once my groups fair share has been spent it takes about 3 days before my jobs are executed.
Using commercial cloud services is an alternative for immediate execution, but the expense involved requires much more funding. ACCRE is very cost effective in comparison, but jobs will take a few days to start up when fairshare is exhausted.