Optimising workflow performance

Overview

Questions

• What compute resources are available on my system?
• How do I define jobs with more than one thread?
• How do I measure the compute resources being used by a workflow?
• How do I run my workflow steps in parallel?

Objectives

• Understand CPU, RAM and I/O bottlenecks
• Understand the threads declaration
• Use standard Linux tools to look at resource usage

For reference, this is the final Snakefile from episodes 1 to 7 you may use to start this episode.

Processes, threads and processors

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Some definitions:

• Process - A running program (in our case, each Snakemake job can be considered one process)
• Threads - Each process has one or more threads which run in parallel
• Processor - Your computer has multiple CPU cores or processors, each of which can run one thread at a time

These definitions are a little simplified, but fine for our needs. The operating system kernel shares out threads among processors:

• Having fewer threads than processors means you are not fully using all your CPU cores
• Having more threads than processors means threads have to “timeslice” on a core which is generally suboptimal

If you tell Snakemake how many threads each rule will use, and how many cores you have available, it will start jobs in parallel to use all your cores. In the diagram below, five jobs are ready to run and there are four system cores.

Listing the resources your Linux machine

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Find out how many CPU cores you have on your machine with the lscpu command.

BASH

$ lscpu

Likewise find out the amount of RAM available:

BASH

$ free -h

And finally disk space, on the current partition:

BASH

$ df -h .

(or df -h without the . to show all partitions)

Parallel jobs in Snakemake

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You may want to see the relevant part of the Snakemake documentation.

We’ll force all the trimming and kallisto steps to re-run by using the -F flag to Snakemake and time the whole run using the standard /usr/bin/time -v command. You have to type the command like this because time is a built-in command in BASH which takes precedence, so eg:

BASH

$ /usr/bin/time -v snakemake -j1 -F -- kallisto.{ref,temp33,etoh60}_{1,2,3}

Measuring how concurrency affects execution time

What is the wallclock time reported by the above command? We’ll work out the average for the whole class, or if you are working through the material on your own repeat the measurement three times to get your own average.

Now change the Snakemake concurrency option to -j2 and then -j4.

• How does the total execution time change?
• What factors do you think limit the power of this setting to reduce the execution time?

Show me the solution

The time will vary depending on the system configuration but somewhere around 30 seconds is expected, and this should reduce to around 25 secs with -j2 but higher -j will produce diminishing returns.

Things that may limit the effectiveness of parallel execution include:

• The number of processors in the machine
• The number of jobs in the DAG which are independent and can therefore be run in parallel
• The existence of single long-running jobs like kallisto_index
• The amount of RAM in the machine
• The speed at which data can be read from and written to disk

There are a few gotchas to bear in mind when using parallel execution:

1. Parallel jobs will use more RAM. If you run out then either your OS will swap data to disk, or a process will crash
2. Parallel jobs may trip over each other if they try to write to the same filename at the same time (this can happen with temporary files, and in fact is a problem with our current fastqc rule definition)
3. The on-screen output from parallel jobs will be jumbled, so save any output to log files instead

Multi-thread rules in Snakemake

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In the diagram at the top, we showed jobs with 2 and 8 threads. These are defined by adding a threads: part to the rule definition. We could do this for the kallisto_quant rule:

rule kallisto_quant:
    output:
        outdir = directory("kallisto.{sample}"),
    input:
        index = "Saccharomyces_cerevisiae.R64-1-1.kallisto_index",
        fq1   = "trimmed/{sample}_1.fq",
        fq2   = "trimmed/{sample}_2.fq",
    threads: 4
    shell:
        "kallisto quant -t {threads} -i {input.index} -o {output.outdir} {input.fq1} {input.fq2}"

You should explicitly use threads: 4 rather than params: threads = "4" because Snakemake considers the number of threads when scheduling jobs. Also, if the number of threads requested for a rule is less than the number of available processors then Snakemake will use the lower number.

We also added -t {threads} to the shell command. This only works for programs which allow you to specify the number of threads as a command-line option, but this applies to a lot of different bioinformatics tools.

Getting other programs to run with multiple threads

Find out how to set the number of threads for our salmon_quant and fastqc jobs. Which of the options below would need to be added to the shell command in each case?

1. -t {threads}
2. -p {threads}
3. -num_threads {threads}
4. multi-threaded mode is not supported

Hint: use salmon quant --help-alignment and fastqc --help, or search the online documentation.

Make the corresponding changes to the Snakefile.

Show me the solution

For salmon_quant, -p {threads} or equivalently --threads {threads} will work.

For fastqc, it may look like -t {threads} is good but this only sets “the number of files which can be processed simultaneously”, and the rule we have only processes a single file per job. So in fact the answer is that, for our purposes, multi-threading is unsupported.

Fine-grained profiling

Rather than timing the entire workflow, we can ask Snakemake to benchmark an individual rule.

For example, to benchmark the kallisto_quant step we could add this to the rule definition:

rule kallisto_quant:
    benchmark:
        "benchmarks/kallisto_quant.{sample}.txt"
    ...

The dataset here is so small that the numbers are tiny, but for real data this can be very useful as it shows time, memory usage and IO load for all jobs.

Running jobs on a cluster

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Learning about clusters is beyond the scope of this course, but for modern bioinformatics they are an essential tool because many analysis jobs would take too long on a single computer. Learning to run jobs on clusters normally means writing batch scripts and re-organising your code to be cluster-aware. But if your workflow is written in Snakemake, it will run on a cluster will little to no modification. Snakemake turns the individual jobs into cluster jobs, then submits and monitors them for you.

• The Snakemake manual explains how to set this up
• We have some specific suggestions for Eddie, the University of Edinburgh cluster

Cluster demo

A this point in the course there may be a cluster demo…

{% comment %} Photo credit: Cskiran Sourced from Wikimedia Commons CC-BY-SA-4.0 {% endcomment %}

For reference, this is a Snakefile incorporating the changes made in this episode.

Key Points

• To make your workflow run as fast as possible, try to match the number of threads to the number of cores you have
• You also need to consider RAM, disk, and network bottlenecks
• Profile your jobs to see what is taking most resources
• Snakemake is great for running workflows on compute clusters