A simple-to-use program for quickly batch creating job tasks based on the PBS job scheduling system (including OpenPBS, PBS Pro, and TORQUE) based on a command list.
Project description
Pbstool
Introduction
A simple-to-use program for quickly batch creating job tasks based on the PBS job scheduling system (including OpenPBS, PBS Pro, and TORQUE) based on a command list.
This application consists of two parts, pbstool is used to quickly create pbs job scripts, and qsubs is used to submit job scripts in batches.
Install
From source code
git clone https://github.com/interestingcn/pbstool.git
cd pbstool
pip install .
From Pypi
pip install pbstool
Usages
Quick start
# Create job script
pbstool -c cmd.txt -n job_name -q cu
# Submit them all!
qsubs
pbstool: help information
Useage: pbstool <command> [options]
Commands:
-c / --cmd Set job command list path.
-n / --name Job name prefix.
-e / --env If the software you are using is in a conda environment,
define the conda environment name here.
-q / --queue Target queue name.
-- / --node Set the number of nodes required for the job.Default 1.
-- / --ppn Set the number of CPU cores that can be used by each node.Default 1.
-o / --output Output path to generate job script.Default current path
--walltime Set the maximum wallclock time required for the job.Default 1000hours.
--log_info_output Job standard log output path.Default current path.
--log_error_output Job error log output path.Default current path.
-s / --sample Create a sample pbs script.
-h / --help Display this help message.
-v / --version Detailed version information.
qsubs
qsubs has no parameters. It will submit all pbs job scripts in the current path by default. You only need to execute qsubs
under the path to be submitted.
qsubs
License
Copyright [2023] [wangzt]
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
About
Author: Wangzt (interestingcn01@gmail.com)
Bioinformatics Laboratory of South China Agricultural University
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