|

cwb_condor
~~~~~~~~~~~~

This page provides a description of the cwb_condor command.

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| **Usage**
|
|  This command prepares and submits the analysis jobs on the considered computing cluster by using the condor batch system.
|
| **Syntax**
|

 - ``cwb_condor`` (without arguments)
    Prints help
 - ``cwb_condor benchmark``
    Prints help in the benchmark type
 - ``cwb_condor action [dag_file/cwb_stage] [input_dir]``
    Prepares and submits the jobs

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| **Further informations**
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 The following options can be passed to cwb_condor:

 .. code-block:: bash

    action =     create    : it creates the dag and sub files under the condor directory

                 submit    : it submits the jobs to the considered computing cluster

                 recovery  : it compares the list of jobs in the dag file and checks the number of jobs 
                             completed (from history). It produces the dag file data_label.dag.recovery.x 
                             (x = recovery version).

                 resume    : same as recovery but is done only if previous cwb_stage is present 
                             in the output dir
                 status    : it shows the jobs status.

                 remove    : (R/H/I) it remove the jobs with status (Running/Held/Idle).

                 check     : it checks which jobs have been completed. 
                             (by reading the history reported in the output root files).

                 list      : it lists the jobs reported in the dag file.

                 benchmark : it shows the computation load and related statistics 
                             (see cwb_condor benchmark).

                 cleanup   : remove broken symbolic links in the condor log dir (avoid init condor failure)
                             to be used when jobs are in held status.

                 sdag      : read the standard \*.dag file produced with cwb_condor create and produced
                             a new dag file \*.sdag
                             The \*.sdag permits to submit in each node N jobs in sequential mode

                 mtpe      : used to generate the multitask mode for the Parameter Estimation analysis 
                             (see How to do the Parameter Estimation Analysis).


 .. code-block:: bash

    dag_file/cwb_stage (optional) =  


                 dag_file  : path to the dag file dag_file to be submitted 
                             (used as cwb_condor submit dag_file).

                 cwb_stage : used in the 2G analysis
                             [FULL(default)/INIT/STRAIN/CSTRAIN/COHERENCE/SUPERCLUSTER/LIKELIHOOD]


 .. code-block:: bash

    input_dir (optional)  : it is used with the recovery option. The default input directory is the 
                            output_dir directory defined in cwb_parameters.C

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| **Examples**
| 

 -  The following command lines launch a **full stage analysis**:

  - ``cwb_condor create``
  - ``cwb_condor submit``

 -  The following command lines launch a **two-stage analysis**:

  -  ``cwb_condor create SUPERCLUSTER``
  -  ``cwb_condor submit``
  -  ``cwb_condor recovery LIKELIHOOD outpu``
  -  ``cwb_condor submit condor/XXX.dag.recovery.x``

 -  The following command line creates the **condor/data_label.sub** and **condor/data_label.dag** condor files:

  -  ``cwb_condor create``

 -  The following command lines submit the analysis jobs to the considered computing cluster:

  -  ``cwb_condor submit``
  -  ``cwb_condor submit condor_data/data_label.dag``

 -  The following command line recovers the analysis which did not get completed and creates the file **condor/data_label.dag.recovery.1**:

  -  ``cwb_condor recovery``

 -  The following command line submits the dag files listing the recovered files:

  -  ``cwb_condor submit condor/data_label.dag.recovery.1``

 -  The following command line creates the condor files for the **SUPERCLUSTER stage** of the 2G analysis:

  -  ``cwb_condor create SUPERCLUSTER``

    The intermediate jobs are stored in the node's temporary directory.  Symbolic links to the remote job files are created in the output directory.

 -  The following command lines complete an analysis conducted with the 2G cWB pipeline starting from an intermediate stage:

  -  ``cwb_condor recovery LIKELIHOOD`` 
  -  ``cwb_condor submit condor/data_label.dag.recovery.1``

 -  The following command line creates the condor/file.sdag file from the condor/file.dag (it defines 10 sequential jobs per node):

  -  ``cwb_condor sdag 10 condor/file.dag``