From 1d39ab31c8e5f5aa269d0b4d7a307541806dc251 Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Sat, 27 Jul 2019 15:05:04 +0200 Subject: [PATCH] Add Pbs Pro execution documentation --- README.md | 2 +- docs/executor.rst | 33 ++++++++++++++++++++++++++++----- docs/process.rst | 1 + 3 files changed, 30 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 58f2fc3be5..c4952b7d29 100644 --- a/README.md +++ b/README.md @@ -104,7 +104,7 @@ Currently the following clusters are supported: + [LSF](https://www.nextflow.io/docs/latest/executor.html#lsf) + [SLURM](https://www.nextflow.io/docs/latest/executor.html#slurm) + [PBS/Torque](https://www.nextflow.io/docs/latest/executor.html#pbs-torque) - + [HTCondor (experimental)](https://www.nextflow.io/docs/latest/executor.html#htcondor) + + [HTCondor (beta)](https://www.nextflow.io/docs/latest/executor.html#htcondor) + [Moab (beta)](https://www.nextflow.io/docs/latest/executor.html#moab) For example to submit the execution to a SGE cluster create a file named `nextflow.config`, in the directory diff --git a/docs/executor.rst b/docs/executor.rst index 74f9b4979e..d11629309a 100644 --- a/docs/executor.rst +++ b/docs/executor.rst @@ -136,12 +136,12 @@ The amount of resources requested by each job submission is defined by the follo * :ref:`process-memory` * :ref:`process-clusterOptions` -.. _nqsii-executor: +.. _pbspro-executor: -NQSII -===== +PBS Pro +======= -The `NQSII` executor allows you to run your pipeline script by using the `NQSII `_ resource manager. +The `PBS Pro` executor allows you to run your pipeline script by using the `PBS Pro `_ resource manager. Nextflow manages each process as a separate job that is submitted to the cluster by using the ``qsub`` command provided by the scheduler. @@ -149,7 +149,7 @@ by the scheduler. Being so, the pipeline must be launched from a node where the ``qsub`` command is available, that is, in a common usage scenario, the cluster `login` node. -To enable the NQSII executor simply set the property ``process.executor = 'nqsii'`` in the ``nextflow.config`` file. +To enable the PBS Pro executor simply set the property ``process.executor = 'pbspro'`` in the ``nextflow.config`` file. The amount of resources requested by each job submission is defined by the following process directives: @@ -186,6 +186,29 @@ The amount of resources requested by each job submission is defined by the follo * :ref:`process-memory` * :ref:`process-clusterOptions` +.. _nqsii-executor: + +NQSII +===== + +The `NQSII` executor allows you to run your pipeline script by using the `NQSII `_ resource manager. + +Nextflow manages each process as a separate job that is submitted to the cluster by using the ``qsub`` command provided +by the scheduler. + +Being so, the pipeline must be launched from a node where the ``qsub`` command is available, that is, in a common usage +scenario, the cluster `login` node. + +To enable the NQSII executor simply set the property ``process.executor = 'nqsii'`` in the ``nextflow.config`` file. + +The amount of resources requested by each job submission is defined by the following process directives: + +* :ref:`process-cpus` +* :ref:`process-queue` +* :ref:`process-time` +* :ref:`process-memory` +* :ref:`process-clusterOptions` + .. _condor-executor: HTCondor diff --git a/docs/process.rst b/docs/process.rst index ce050cce48..60829ab28c 100644 --- a/docs/process.rst +++ b/docs/process.rst @@ -1506,6 +1506,7 @@ Name Executor ``lsf`` The process is executed using the `Platform LSF `_ job scheduler. ``slurm`` The process is executed using the SLURM job scheduler. ``pbs`` The process is executed using the `PBS/Torque `_ job scheduler. +``pbspro`` The process is executed using the `PBS Pro `_ job scheduler. ``moab`` The process is executed using the `Moab `_ job scheduler. ``condor`` The process is executed using the `HTCondor `_ job scheduler. ``nqsii`` The process is executed using the `NQSII `_ job scheduler.