runjob

Summary

runjob is a program for managing a group of related jobs running on a compute cluster localhost, Sun Grid Engine, BatchCompute, slurm . It provides a convenient method for specifying dependencies between jobs and the resource requirements for each job (e.g. memory, CPU cores). It monitors the status of the jobs so you can tell when the whole group is done. Litter cpu or memory resource is used in the login compute node.

OSCS

Software Requirements

python >=3.5

Installation

The development version can be installed with (for recommend)

pip install git+https://github.com/yodeng/runjob.git

The stable release (maybe not latest) can be installed with

pypi:

pip install runjob -U

conda:

conda install -c bioconda runjob

User Guide

All manual can be found here.

Usage

You can get the quick help like this:

runjob/runflow：

$ runjob --help
Usage: runjob [-h] [-v] [-j [<jobfile>]] [-n <int>] [-s <int>] [-e <int>] [-w <workdir>] [-d] [-l <file>] [-f]
              [-M {local,localhost,sge,slurm}] [--config <configfile>] [--dag] [--dag-extend] [--strict] [--quiet] [--show-config]
              [-r <int>] [-R <int>] [--max-check <float>] [--max-submit <float>] [--max-queue-time <float/str>]
              [--max-run-time <float/str>] [--max-wait-time <float/str>] [--max-timeout-retry <int>]
              [--local | --localhost | --sge | --slurm] [-i [<str> ...]] [-L <logdir>] [-q [<queue> ...]] [-c <int>] [-m <int>]
              [--node [<node> ...]] [--round-node]

runjob is a tool for managing parallel tasks from a specific job file running in localhost, sge, slurm.

Optional Arguments:
  -h, --help            show this help message and exit
  --local               submit your jobs to local, same as '--mode local'.
  --localhost           submit your jobs to localhost, same as '--mode localhost'.
  --sge                 submit your jobs to sge, same as '--mode sge'.
  --slurm               submit your jobs to slurm, same as '--mode slurm'.
  -i, --injname [<str> ...]
                        job names you need to run. (default: all job names of the jobfile)
  -L, --logdir <logdir>
                        the output log dir. (default: join(workdir, "logs"))

Base Arguments:
  -v, --version         show program's version number and exit
  -j, --jobfile [<jobfile>]
                        input jobfile, if empty, stdin is used. (required)
  -n, --num <int>       the max job number runing at the same time. (default: all of the jobfile, max 1000)
  -s, --start <int>     which line number(1-base) be used for the first job. (default: 1)
  -e, --end <int>       which line number (include) be used for the last job. (default: last line of the jobfile)
  -w, --workdir <workdir>
                        work directory. (default: /home/dengyong/soft/git/runjob)
  -d, --debug           log debug info.
  -l, --log <file>      append log info to file. (default: stdout)
  -f, --force           force to submit jobs even already successed.
  -M, --mode {local,localhost,sge,slurm}
                        the mode to submit your jobs, if no sge installed, always localhost. (default: sge)
  --config <configfile>
                        input configfile for configurations search.
  --dag                 do not execute anything and print the directed acyclic graph of jobs in the dot language.
  --dag-extend          do not execute anything and print the extend directed acyclic graph of jobs in the dot language.
  --strict              use strict to run, means if any errors, clean all jobs and exit.
  --quiet               suppress all output and logging.
  --show-config         show configurations and exit.

Rate Arguments:
  -r, --retry <int>     retry N times of the error job, 0 or minus means do not re-submit. (default: 0)
  -R, --retry-sec <int>
                        retry the error job after N seconds. (default: 2)
  --max-check <float>   maximal number of job status checks per second, fractions allowed. (default: 5)
  --max-submit <float>  maximal number of jobs submited per second, fractions allowed. (default: 20)

Time Arguments:
  --max-queue-time <float/str>
                        maximal time (d/h/m/s) between submit and running per job. (default: no-limiting)
  --max-run-time <float/str>
                        maximal time (d/h/m/s) start from running per job. (default: no-limiting)
  --max-wait-time <float/str>
                        maximal time (d/h/m/s) start from submit per job. (default: no-limiting)
  --max-timeout-retry <int>
                        retry N times for the timeout error job, 0 or minus means do not re-submit. (default: 0)

Resource Arguments:
  -q, --queue [<queue> ...]
                        queue/partition for running, multi-queue can be sepreated by whitespace. (default: all accessed)
  -c, --cpu <int>       max cpu number used. (default: 1)
  -m, --memory <int>    max memory used (GB). (default: 1)
  --node [<node> ...]   node for running, multi-node can be sepreated by whitespace. (default: all accessed)
  --round-node          round all define node per job for load balance

runsge/runshell/runbatch:

$ runsge --help
Usage: runsge [-h] [-v] [-j [<jobfile>]] [-n <int>] [-s <int>] [-e <int>] [-w <workdir>] [-d] [-l <file>] [-f]
              [-M {local,localhost,sge,slurm}] [--config <configfile>] [--dag] [--dag-extend] [--strict] [--quiet] [--show-config]
              [-r <int>] [-R <int>] [--max-check <float>] [--max-submit <float>] [--max-queue-time <float/str>]
              [--max-run-time <float/str>] [--max-wait-time <float/str>] [--max-timeout-retry <int>]
              [--local | --localhost | --sge | --slurm] [-N <jobname>] [-L <logdir>] [-g <int>] [--init <cmd>] [--call-back <cmd>]
              [-q [<queue> ...]] [-c <int>] [-m <int>] [--node [<node> ...]] [--round-node]

runsge is a tool for managing parallel tasks from a specific shell file runing in localhost, sge, slurm.

Optional Arguments:
  -h, --help            show this help message and exit
  --local               submit your jobs to local, same as '--mode local'.
  --localhost           submit your jobs to localhost, same as '--mode localhost'.
  --sge                 submit your jobs to sge, same as '--mode sge'.
  --slurm               submit your jobs to slurm, same as '--mode slurm'.
  -N, --jobname <jobname>
                        job name. (default: basename of the jobfile)
  -L, --logdir <logdir>
                        the output log dir. (default: "/home/dengyong/soft/git/runjob/runsge_*_log_dir")
  -g, --groups <int>    N lines to consume a new job group. (default: 1)
  --init <cmd>          command before all jobs, will be running in localhost.
  --call-back <cmd>     command after all jobs finished, will be running in localhost.

Base Arguments:
  -v, --version         show program's version number and exit
  -j, --jobfile [<jobfile>]
                        input jobfile, if empty, stdin is used. (required)
  -n, --num <int>       the max job number runing at the same time. (default: all of the jobfile, max 1000)
  -s, --start <int>     which line number(1-base) be used for the first job. (default: 1)
  -e, --end <int>       which line number (include) be used for the last job. (default: last line of the jobfile)
  -w, --workdir <workdir>
                        work directory. (default: /home/dengyong/soft/git/runjob)
  -d, --debug           log debug info.
  -l, --log <file>      append log info to file. (default: stdout)
  -f, --force           force to submit jobs even already successed.
  -M, --mode {local,localhost,sge,slurm}
                        the mode to submit your jobs, if no sge installed, always localhost. (default: sge)
  --config <configfile>
                        input configfile for configurations search.
  --dag                 do not execute anything and print the directed acyclic graph of jobs in the dot language.
  --dag-extend          do not execute anything and print the extend directed acyclic graph of jobs in the dot language.
  --strict              use strict to run, means if any errors, clean all jobs and exit.
  --quiet               suppress all output and logging.
  --show-config         show configurations and exit.

Rate Arguments:
  -r, --retry <int>     retry N times of the error job, 0 or minus means do not re-submit. (default: 0)
  -R, --retry-sec <int>
                        retry the error job after N seconds. (default: 2)
  --max-check <float>   maximal number of job status checks per second, fractions allowed. (default: 5)
  --max-submit <float>  maximal number of jobs submited per second, fractions allowed. (default: 20)

Time Arguments:
  --max-queue-time <float/str>
                        maximal time (d/h/m/s) between submit and running per job. (default: no-limiting)
  --max-run-time <float/str>
                        maximal time (d/h/m/s) start from running per job. (default: no-limiting)
  --max-wait-time <float/str>
                        maximal time (d/h/m/s) start from submit per job. (default: no-limiting)
  --max-timeout-retry <int>
                        retry N times for the timeout error job, 0 or minus means do not re-submit. (default: 0)

Resource Arguments:
  -q, --queue [<queue> ...]
                        queue/partition for running, multi-queue can be sepreated by whitespace. (default: all accessed)
  -c, --cpu <int>       max cpu number used. (default: 1)
  -m, --memory <int>    max memory used (GB). (default: 1)
  --node [<node> ...]   node for running, multi-node can be sepreated by whitespace. (default: all accessed)
  --round-node          round all define node per job for load balance

qs/qcs:

$ qs --help 
For summary jobs
Usage: qs [jobfile|logdir|logfile]
       qcs --help
       qslurm

License

runjob is distributed under the MIT license.

Contact

Please send comments, suggestions, bug reports and bug fixes to yodeng@tju.edu.cn.

Example

$ cat test.flow

logs: ./logs
envs:
    samples: A B C

qc:
    echo "qc $samples"
bwa:
    echo "bwa $samples"
    depends: qc.samples   ## each sample-bwa depends each sample-qc
    # depends: qc   ## each sample-bwa depends all sample-qc
sort:
    echo "sort $samples"
    depends: bwa.samples
index:
    echo "index $samples"
    depends: sort.samples
calling:
    echo "calling allsample"
    depends: index
stats:
    echo "stats allsample"
    depends: calling

command runflow -j test.flow --dag | dot -Tsvg > test.svg will get the job graph:

Todo

More functions will be improved in the future.