Xhpc

Convert of .sh script into Torque's .pbs or Slurm's script for use on a computer cluster with intel or gpu nodes

Description

Working on computer cluster necessitates the querying of nodes, cpus-per-node and memory resources that is conveniently done using directives in a script for job schedulers such as Slurm or Torque.

This package allows one to pass on a bash/sh script and get a copy of the script, but expanded with Slurm (or Torque) directives and other file system operations in order to get the scripts to run as requested and for it to take care of moving files to (local)scratch location for more efficiency.

From the user is only needed an email address (to get notified if a job crashes or completes... and for nothing else!)

Install

git clone https://github.com/FranckLejzerowicz/Xhpc.git
cd Xhpc
pip install -e .

*Note that python should be python3

Requisite

Attention:

1. upon first use, the user is asked for and email address, that will be written in Xhpc/config.txt. This file can be edited afterwards if you want to change your email address.
2. please consider setting up a temporary directory using the environment variable $TMPDIR (for example in your .bash_profile dotfile), if you want the temporary files of some jobs to be written somewhere convenient and removed before the job completes, e.g.: export $TMPDIR="/Users/edith/temporary_dir"".

Input

Two types of inputs can be passed to -i or --i-script:

1. A path to a file containing sh/bash command line(s) (the file extension needs not to be .sh)
2. A command directly (double quoted, e.g. -i "tar xz archive.tar.gz folder")

It might be of great convenience for you to use the option -e to give the name of a conda environment within which you have installed a software and that the job activate before running the script.

Outputs

A Slurm (or Torque) script including directives for resources querying, which by default have the extension .slm (or .pbs).

The user would then need to:

1. Check the output .slm (or .pbs) script for modified paths or errors (strongly advised - this is tested, but I'm a human too).
   • especially if option --scratch or --localscratch is used (copies input files and execute on the job's $LOCALSCRATCH folder), as in this case some existing path may be copied that should not be (e.g. the executables of piped programs)
   • attention: if option --run is used, the output script will be run immediately (use --run with caution!)
2. Run sbatch <outputname>.slm (Slurm) or qsub <outputname>.pbs (for Torque)

Options

One key aspect of this package is that it takes care of moving to the scratch folder the existing input files and folders that are passed in command lines. This can be cumbersome to track and therefore, for this be done in the resulting .slm or .pbs script, one just need to set the ´--move´ option. By default, the files will be moved to the folder defined in the TMPDIR environment variable, but it is strongly advised to change this default location to a scratch folder, using at least one of:

• --scratch
• --userscratch
• --localscratch

If --scratch or --userscratch is activated for the first time, you will be queried to enter the absolute paths to these locations. You can choose to enter a path or an environment variable. For example, on the NRIS's machine "SAGA", these two scratch locations already exist, under variables "SCRATCH" and "USERWORK" (feel free to input these variables instead). see here You can always change this path using option --config-scratch.

If --localscratch is used, then you just need to give an integer corresponding to an amount of memory (in GB) that will be allocated to the --gres=localscratch:<MEM> option (in Slurm).

Note that it is possible to prevent some files and folders to be moved to scratch bz providing their relative path within the input folder, using option --exclude. This can be very useful if you run a command that takes as input a folder that not only contains some the files/folders you need, but also many, many other files/folders. For example, say you have such a folder called "input_dir" with some path in the command lines:

.
└── input_dir
    ├── useful.dat            # file in command lines
    ├── useful                # folder in command lines
    │   ├── useful_too.dat    # file in command lines
    │   ├── useless.dat
    │   ├── useless
    │   └── ...
    └── partly_useful
        ├── huge_useless
        │   └── ...
        └── useful_too        # folder in command lines
            └── ...

In there, you may only need to move:

• ./input_dir/useful.dat
• ./input_dir/useful
• ./input_dir/useful/useful_too.dat
• ./input_dir/partly_useful/useful_too

But the basic command to move these to scratch (using rsync) will include folder ./input_dir/useful, and thus all what if contains. To avoid these useless files/folder, just specify using option --exclude relative to the input folders:

--exclude useless.dat --exclude useless --exclude partly_useful/huge_useless

Think of wildcards:

--exclude *useless* --exclude */*useless

Usage

Xhpc -i </path/to/file.sh> -o </path/to/output.slm> -j <job_name> ... 

Options

  -i, --i-script TEXT             Input script path (or double-quoted command)
                                  [required]
  -o, --o-script TEXT             Output script path (default to
                                  <input>_<YYYY-MM-DD-HH-MM-SS>.slm)
  -j, --i-job TEXT                Job name  [required]
  -a, --p-account TEXT            Name of the account
  -p, --p-partition [normal|bigmem|accel|optimist]
                                  Partition name
  -n, --p-nnodes INTEGER          Number of nodes  [default: 1]
  -c, --p-cpus INTEGER            Number of CPUs  [default: 1]
  -t, --p-time INTEGER            Wall time limit (in hours)  [default: 1]
  -M, --p-mem TEXT...             Requested memory as two space-separated
                                  entries: an integer and either 'MB' or 'GB'.
                                  (Default: '500 MB')
  -m, --p-mem-per-cpu TEXT...     Requested memory per cpu as two space-
                                  separated entries: an integer and either
                                  'MB' or 'GB'. (Default: '500 MB')
  -N, --p-nodes TEXT              Node names, e.g. `-N c1-4 -N c6-10 -N c7-1`
                                  (overrides option `-n`)
  -e, --p-env TEXT                Conda environment to run the job
  -d, --p-dir TEXT                Output directory  [default: .]
  -T, --p-tmp TEXT                Alternative temp folder to the one defined
                                  in $TMPDIR (if not defined: will be set to
                                  $USERWORK, or to $SCRATCH if any scratch
                                  option is activated)
  -w, --p-workdir TEXT            Working directory to use instead of
                                  $SLURM_SUBMIT_DIR
  -y, --p-include TEXT            Folder to not move to and from scratch using
                                  rsync (must exist)
  -x, --p-exclude TEXT            Relative path(s) within input folder(s) to
                                  not move in scratch
  --move / --no-move              Move files/folders to chosen scratch
                                  location  [default: no-move]
  -l, --localscratch INTEGER      Use localscratch with the provided memory
                                  amount (in GB)
  --scratch / --no-scratch        Use the scratch folder to move files and
                                  compute  [default: no-scratch]
  --userscratch / --no-userscratch
                                  Use the userscratch folder to move files and
                                  compute  [default: no-userscratch]
  --clear-scratch / --no-clear-scratch
                                  Whether to cleat the scratch area at the end
                                  of the job or not  [default: clear-scratch]
  --stdout / --no-stdout          Rename stdout (and stderr) with job name and
                                  ID  [default: stdout]
  --email / --no-email            Send email at job completion (always if
                                  fail)  [default: no-email]
  --run / --no-run                Run the job before exiting (subprocess)
                                  [default: no-run]
  --stat / --no-stat              Whether to prepend `/usr/bin/time -v` to
                                  every script command  [default: stat]
  --verif / --no-verif            Print script to stdout and ask for 'y/n'
                                  user input to sanity check  [default: no-
                                  verif]
  --gpu / --no-gpu                Query a gpu (experimental)  [default: no-
                                  gpu]
  --torque / --no-torque          Adapt to Torque  [default: no-torque]
  --config-email / --no-config-email
                                  Show current email and/or edit it  [default:
                                  no-config-email]
  --config-scratch / --no-config-scratch
                                  Show current scratch folders and/or edit
                                  them  [default: no-config-scratch]
  --sinfo / --no-sinfo            Print sinfo in stdout (and update
                                  `~/.sinfo`)  [default: no-sinfo]
  --allocate / --no-allocate      Get current machine usage (sinfo) to
                                  allocate suitable nodes/memory  [default:
                                  no-allocate]
  --version                       Show the version and exit.
  --help                          Show this message and exit.

Bug Reports

contact [email protected]

Acknowledgments

Tomasz Kosciolek had been the one providing me with a first example of PBS script that collect nice job info (temp path, setup) - Thanks Tomek!