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README.md
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README.md

The vr-runner package provides a lightweight pipeline framework. Check these short motivation slides with examples to see how it works.

Runner pipelines

The runner pipelines are usually named as run-something. This document uses run-bt-mpileup as an example, but the usage is the same for all runners. Check the run-test-simple example to learn how to write your own pipelines.

For the impatient

The minimum commands sufficient to install and run the pipelines is:

# Get the code
git clone git://github.com/VertebrateResequencing/vr-runner.git

# Create a config file, edit, and run
run-bt-mpileup +sampleconf > my.conf
vim my.conf
run-bt-mpileup +config my.conf +loop 600 -o outdir

Important: see also the section about setting environment variables below!

In more detail

The Runner.pm pipelines have two types of options. The options prefixed by + are common to all runners, the options prefixed by - are pipeline specific. For a complete list of the options run with -h, the output of which is shown at the bottom of this page

run-bt-mpileup -h

The pipelines can be run in a daemon mode (turned on by giving the +loop option) or they can do one iteration only and stop (+loop option not given). The latter is suitable for execution from cron. Because the runner script itself consumes close to zero CPU time and memory, it can be run on farm head nodes. In this mode, it is convenient to run it from screen. For details about how to use screen see the manual pages (man screen), but generally knowing the following is enough:

  • Launch a new screen by executing the command screen
  • Type enter and run whatever commands you like. (In our case it will be the run-st-mpileup command.)
  • Detach from the screen by pressing ctrl+a followed by d
  • At any time one can reattach to a running screen by executing screen -r

If the farm has multiple head nodes, note that the screen lives on a concrete computer and therefore one has to log into the exact same machine to access it. One can simultaneously run as many screens as necessary.

Note that it is not necessary (nor recommended) to submit the runner scripts to the farm as they take little CPU and memory. Nonetheless, if the pipeline is run this way, the exit status is 111 when successfully completed.

Setting environment variables

The vr-wrapper script can be used to set environment variables without having to change user's profile. It may look like this:

#!/bin/bash
export PATH="$HOME/git/vr-runner/scripts:$PATH"
export PERL5LIB="$HOME/git/vr-runner/modules:$PERL5LIB"

Save the config in the file, say ~/.vrw/runners and use like this:

vr-wrapper ~/.vrw/runners run-bt-mpileup +config my.conf +loop 600 -o outdir

Chaining multiple runners

Read here if you need to chain multiple runners

Runner options

+help                   Summary of commands
+config <file>          Configuration file
+debug <file1> <file2>  Run the freezed object <file1> overriding with keys from <file2>
+js <platform>          Job scheduler (lowercase allowed): LSF (bswitch), LSFCR (BLCR) [LSF]
+kill                   Kill all running jobs
+local                  Do not submit jobs to LSF, but run serially
+lock <file>            Exit if another instance is already running
+loop <int>             Run in daemon mode with <int> seconds sleep intervals
+mail <address>         Email when the runner finishes
+maxjobs <int>          Maximum number of simultaneously running jobs
+nocache                When checking for finished files, do not rely on cached database and 
                           check again
+retries <int>          Maximum number of retries. When negative, the runner eventually skips
                           the task rather than exiting completely. [1]
+run <file> <id>        Run the freezed object created by spawn
+sampleconf             Print a working configuration example
+show <file>            Print the content of the freezed object created by spawn
+silent                 Decrease verbosity of the Runner module

Frequently (and not so frequently) asked questions

How to rerun a task
The pipelines know that a task finished by checking the existence of checkpoint files. In order to reduce the number of stat calls, the pipeline keeps a cache of finished tasks. Therefore, to rerun a task, it is not enough to remove the specific checkpoint file, one has to tell the pipeline to ignore the cached status: run the pipeline as usual, but add the +nocache option. Note however, that pipeline's logic can be complex: it can be deleting intermediate checkpoint files and relying on information not available to the runner framework.
Performance: the runner daemon takes too long to submit a job!
By default, the pipeline runs at most 100 jobs in parallel. This limit can be increased by providing the +maxjobs option. For example, if the computing farm typically lets you run 500 jobs in parallel, running with +maxjobs 500 tells the pipeline to submit the jobs in batches up to 500. Note that if the limit is set too high (tens of thousands of jobs) and most tasks are pending, the runner daemon can spend a long time by checking the status of the pending tasks; therefore it is better to set the number to a realistic value.
How to skip a job
If a task keeps failing, the pipeline can be told to skip the offending task by setting negative value of the +retries option. With negative value of +retries, a skip file with the ".s" suffix is created and the job is reported as finished. The skip files are cleaned automatically when +retries is set to a positive value. A non cleanable variant is a force skip ".fs" file which is never cleaned by the pipeline and is created/removed manually by the user. When .fs is cleaned by the user, the pipeline must be run with +nocache in order to notice the change.
Kill all running jobs
When something goes wrong and all running jobs must be killed, use the +kill option.
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