GoSub: Automatically Submit PBS Files to Free Your Hands

# GoSub: Automatically Submit PBS Files to Free Your Hands This program helps submit PBS files in file/directory format one by one or generate a work pbs to parallelly run all PBS files. If an error is encountered, the program will re-submit in 5 minutes. ## Download and Install Pick the latest version of `gosub` and install it, e.g.: ```bash wget -c https://github.com/ShixiangWang/gosub/releases/download/v1.4/gosub_1.4_Linux_x86_64.tar.gz tar zxvf gosub_1.4_Linux_x86_64.tar.gz chmod u+x gosub ./gosub -h ``` ## Usage ### Simple mode ```bash ./gosub <path_to_PBS> ``` > Both file path and directory path are supported. A better way is to use it with nohup and `&`. ```bash nohup ./gosub <path_to_PBS> & ``` So you can free your terminal. Just remember to record the PID in case you want to kill it. ### Parallel mode In parallel mode, `gosub` will generate a new work PBS file and use [`rush`](https://github.com/shenwei356/rush) to parallelly run your all PBS files. ```sh ./gosub -h Usage of ./gosub: -abs render and use PBS absolute path. -hold set it if you want to check and qsub by your own. Only work when -p enabled. -jobs int run n jobs in parallel, at default will use nodes*ppn. Only work when -p enabled. -mem string memory size, e.g. 5gb. Only work when -p enabled. (default "auto") -name string an file prefix for generating output PBS file. Only work when -p enabled. (default "pwork") -nodes int an int to specify node number to use. Only work when -p enabled. (default 1) -p enable parallel processing. -ppn int an int to specify cpu number per node. Only work when -p enabled. (default 1) -walltime string walltime setting. Only work when -p enabled. (default "24:00:00") ``` For example: ```sh ./gosub -p -nodes 3 -ppn 5 -mem 5gb testp ``` ## Tests I tested it in a HPC account. ```bash $ biosoft/gosub test_gosub/ gosub version: 0.3.1 Starting... Submitted file list will be save to success_submitted_list.txt ==================================== 2020/03/30 22:20:35 Submitting test_gosub/test.pbs 2020/03/30 22:20:35 Submitting test_gosub/test_1.pbs 2020/03/30 22:20:35 Submitting test_gosub/test_10.pbs 2020/03/30 22:20:35 Submitting test_gosub/test_100.pbs 2020/03/30 22:20:35 Submitting test_gosub/test_100.pbs failed with error: 2020/03/30 22:20:35 exit status 200 2020/03/30 22:20:35 Waiting for 5 minutes.. 2020/03/30 22:25:35 Calling back to submit... 2020/03/30 22:25:35 Submitting test_gosub/test_100.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_11.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_12.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_13.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_14.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_15.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_16.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_17.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_18.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_19.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_2.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_20.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_21.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_22.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_23.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_24.pbs 2020/03/30 22:25:35 Submitting test_gosub/test_24.pbs failed with error: 2020/03/30 22:25:35 exit status 200 2020/03/30 22:25:35 Waiting for 5 minutes.. 2020/03/30 22:30:36 Calling back to submit... 2020/03/30 22:30:36 Submitting test_gosub/test_24.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_25.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_26.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_27.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_28.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_29.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_3.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_30.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_31.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_32.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_33.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_34.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_35.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_36.pbs 2020/03/30 22:30:36 Submitting test_gosub/test_37.pbs 2020/03/30 22:30:37 Submitting test_gosub/test_38.pbs 2020/03/30 22:30:37 Submitting test_gosub/test_39.pbs 2020/03/30 22:30:37 Submitting test_gosub/test_39.pbs failed with error: 2020/03/30 22:30:37 exit status 200 2020/03/30 22:30:37 Waiting for 5 minutes.. ``` ## LICENSE MIT@ShixiangWang, 2020.