Arvados

h1. Pipeline Optimization

h2. Crunchstat Summary

Crunchstat-summary is an arvados tool to help choose optimal configurations for arvados jobs and pipeline instances. It helps you choose "runtime_constraints":http://doc.arvados.org/api/schema/Job.html specified in the pipeline template under each job, as well as graph general statistics for the job, for example, CPU usage, RAM, and Keep network traffic across the duration of a job.

h3. How to install crunchstat-summary

<pre>

$ git clone https://github.com/curoverse/arvados.git

$ cd arvados/tools/crunchstat-summary/

$ python setup.py build

$ python setup.py install --user

</pre>

h3. How to use crunchstat-summary

<pre>

$ ./bin/crunchstat-summary --help

usage: crunchstat-summary [-h]

                          [--job UUID | --pipeline-instance UUID | --log-file LOG_FILE]

                          [--skip-child-jobs] [--format {html,text}]

                          [--verbose]

Summarize resource usage of an Arvados Crunch job

optional arguments:

  -h, --help            show this help message and exit

  --job UUID            Look up the specified job and read its log data from

                        Keep (or from the Arvados event log, if the job is

                        still running)

  --pipeline-instance UUID

                        Summarize each component of the given pipeline

                        instance

  --log-file LOG_FILE   Read log data from a regular file

  --skip-child-jobs     Do not include stats from child jobs

  --format {html,text}  Report format

  --verbose, -v         Log more information (once for progress, twice for

                        debug)

</pre>

Example job: bwa-aln + samtools -Sb

<pre>

category        metric  task_max        task_max_rate   job_total

blkio:202:0     read    310334464       -       913853440

blkio:202:0     write   2567127040      -       7693406208

blkio:202:16    read    8036201472      155118884.01    4538585088

blkio:202:16    write   55502038016     0       0

blkio:202:32    read    2756608 100760.59       6717440

blkio:202:32    write   53570560        0       99514368

cpu     cpus    8       -       -

cpu     sys     1592.34 1.17    805.32

cpu     user    11061.28        7.98    4620.17

cpu     user+sys        12653.62        8.00    5425.49

mem     cache   7454289920      -       -

mem     pgmajfault      1859    -       830

mem     rss     7965265920      -       -

mem     swap    5537792 -       -

net:docker0     rx      2023609029      -       2093089079

net:docker0     tx      21404100070     -       49909181906

net:docker0     tx+rx   23427709099     -       52002270985

net:eth0        rx      44750669842     67466325.07     14233805360

net:eth0        tx      2126085781      20171074.09     3670464917

net:eth0        tx+rx   46876755623     67673532.73     17904270277

time    elapsed 949     -       1899

# Number of tasks: 3

# Max CPU time spent by a single task: 12653.62s

# Max CPU usage in a single interval: 799.88%

# Overall CPU usage: 285.70%

# Max memory used by a single task: 7.97GB

# Max network traffic in a single task: 46.88GB

# Max network speed in a single interval: 67.67MB/s

# Keep cache miss rate 0.00%

# Keep cache utilization 0.00%

#!! qr1hi-8i9sb-bzn6hzttfu9cetv max CPU usage was 800% -- try runtime_constraints "min_cores_per_node":8

#!! qr1hi-8i9sb-bzn6hzttfu9cetv max RSS was 7597 MiB -- try runtime_constraints "min_ram_mb_per_node":7782

</pre>

!86538baca4ecef099d9fad76ad9c7180.png!

Here, you can see the distinct computation between the bwa-aln and the samtools step. I can sort of see a plateau on CPU, so it would be worth trying a bigger node, maybe 16 threads to see if the plateau is actually at 8 cpus or if it can scale well.

h3. When to pipe and when to write to keep

in general writing straight to keep will reap benefits. If you run crunchstat-summary --html and you see keep io stopping once in a while, then youre cpu bound. If you're seeing cpu level off and keep-read or keep-write taking too long, then you're io bound.

That being said, it's very safe for a job to write to a temporary directory then spending time to write the file to keep. On the other hand, writing straight to keep would save all the compute time of writing to keep. If you have time, it's worth trying both and seeing how much time you save by doing both. Most of the time, writing straight to keep using TaskOutputDir will be the right option, but using a tmpdir is always the safe alternative.

Choosing usually depends on how your tool works with an output directory. If its reading/writing from it a lot, then it might be worth using a tmpdir (SSD) rather than going through the network. If it's just treating the output directory as a space for stdout then using TaskOutputDir should work.

h3. choosing the right number of jobs

each job must output a collection, so if you don't want to output a file, then you should combine commands with each other.

h2. Job Optimization

h3. How to optimize the number of tasks when you don't have native multithreading

tools like gatk have native multithreading where you pass a -t. Here, you usually want to use that threading, and choose the min_cores_per_node. You can use any number of min_tasks_per_node making sure that your tool_threading*min_tasks_per_node is <= min_cores_per_node.

tools like varscan/freebayes blah blah don't have native multithreading so you need to find a workaround. generally, some tools have a -L --intervals to pass in certain loci to work on. If you have a bed file you can split reads on, then you can create a new task per interval. If 

h3. piping between tools or writing to a tmpdir.

Creating pipes between tools has shown to sometimes be faster than writing/reading from disk. Feel free to pipe your tools together, for example using subprocess.PIPE in the "python subprocess module":https://docs.python.org/2/library/subprocess.html