.. note::
    :class: sphx-glr-download-link-note

    Click :ref:`here <sphx_glr_download_auto_examples_batch_qtohdf5.py>` to download the full example code
.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_batch_qtohdf5.py:


======================================
Convert ROOT to HDF5 on the Batch Farm
======================================

Convert ROOT files to HDF5 on the SGE.

The ``IRODS_PATH`` will be scanned recursively and if ``-s`` is specified, a
substring will be used to filter the files. You can for example convert
all numu CC files in ``/in2p3/km3net/mc/prod/v4/JTE_r2356`` if you call
the script with ``-s numuCC``.

Before constructing the job scripts, the ``OUTPUT_PATH`` will be traversed
to find files which have already been converted to avoid multiple conversions.

.. code-block:: console

    Usage:
        qtohdf5.py IRODS_PATH OUTPUT_PATH [options]
        qtohdf5.py (-h | --help)

    Options:
        IRODS_PATH     Path the the files on iRODS.
        OUTPUT_PATH    Path to store the converted HDF5 files.
        -s SUBSTRING   String to match on filenames.
        -n N_FILES     Number of files to process per job [default: 10].
        -e ET          Estimated walltime per file in minutes [default: 15].
        -m VMEM        Estimated vmem for a job [default: 8G].
        -j JOBNAME     The name of the submitted jobs [default: tohdf5].
        -l LOG_PATH    Path of the job log files [default: qlogs].
        -q             Dryrun: don't submit jobs, just print the first job script.
        -h --help      Show this screen.




.. code-block:: python

    from __future__ import absolute_import, print_function, division

    from glob import glob
    import os
    from os.path import basename, join
    import time
    import km3pipe as kp
    from km3pipe.tools import chunks

    __author__ = "Tamas Gal"
    __email__ = "tgal@km3net.de"
    __version__ = "1.0"


    def mkdir(path):
        """Create folder if it does not exist."""
        if not os.path.exists(path):
            os.makedirs(path)


    def main():
        from docopt import docopt
        args = docopt(__doc__, version=__version__)

        CWD = os.getcwd()
        IRODS_PATH = args['IRODS_PATH']
        OUTPUT_PATH = join(CWD, args['OUTPUT_PATH'])
        SUBSTRING = '' if args['-s'] is None else args['-s']
        ET_PER_FILE = int(args['-e']) * 60    # [s]
        FILES_PER_JOB = int(args['-n'])
        VMEM = args['-m']
        LOG_PATH = args['-l']
        JOB_NAME = args['-j']
        DRYRUN = args['-q']

        mkdir(OUTPUT_PATH)

        mupage_files = kp.tools.ifiles(args['IRODS_PATH'])
        files = [basename(f) for f in mupage_files if SUBSTRING in f]
        conv_files = [basename(f)[:-3] for f in glob(join(OUTPUT_PATH, '*.h5'))]
        rem_files = list(set(files) - set(conv_files))

        print("{} MUPAGE files on iRODS".format(len(files)))
        print("{} files to be converted.".format(len(rem_files)))

        s = kp.shell.Script()

        for job_id, file_chunk in enumerate(chunks(rem_files, FILES_PER_JOB)):
            n_files = len(file_chunk)
            s.add("echo A job to convert {} files to HDF5".format(n_files))
            s.add("cd $TMPDIR; mkdir -p $USER; cd $USER")
            s.add("echo")

            for fname in file_chunk:
                ipath = join(IRODS_PATH, fname)
                s.separator('=')
                s.echo("Processing {}:".format(fname))
                s.iget(ipath)
                h5_fname = fname + '.h5'
                lock_fname = join(OUTPUT_PATH, h5_fname + '.copying')
                s.add("tohdf5 {} -o {}".format(fname, h5_fname))
                s.add("touch {}".format(lock_fname))
                s.cp(h5_fname, OUTPUT_PATH)
                s.add("rm -f {}".format(lock_fname))
                s.add("rm -f {}".format(h5_fname))
                s.echo("File '{}' converted.".format(fname))
                s.separator('-')

            walltime = time.strftime(
                '%H:%M:%S', time.gmtime(ET_PER_FILE * n_files)
            )

            kp.shell.qsub(
                s,
                '{}_{}'.format(JOB_NAME, job_id),
                walltime=walltime,
                vmem=VMEM,
                log_path=LOG_PATH,
                irods=True,
                dryrun=DRYRUN
            )

            if DRYRUN:
                break

            s.clear()


    if __name__ == "__main__":
        main()

**Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_batch_qtohdf5.py:


.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-example



  .. container:: sphx-glr-download

     :download:`Download Python source code: qtohdf5.py <qtohdf5.py>`



  .. container:: sphx-glr-download

     :download:`Download Jupyter notebook: qtohdf5.ipynb <qtohdf5.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_