condorize

A command-line tool that monitors a program's resource usage and generates an HTCondor submit file. Designed for NMRbox users who want to run jobs on the HTCondor pool without writing submit files by hand.

Usage

condorize [--timeout SECONDS] [--output FILE] -- command [arguments...]

Prepend condorize -- to the command you would normally run:

condorize -- voronota-voromqa --input structure.pdb

To change the monitoring duration from the default of 60 seconds:

condorize --timeout 120 -- my_slow_program arg1 arg2

To specify the output submit file path:

condorize --output myjob.sub -- myprogram arg1

What it does

1. Monitors your program

Condorize launches your command and monitors it for the specified duration (default 60 seconds), sampling every 0.5 seconds. It tracks:

• Memory (RSS) across the entire process tree (parent and all child processes), read directly from /proc.
• CPU/thread count across the process tree, to determine how many CPUs your job needs.
• GPU usage using two methods: checking /proc/PID/fd for open /dev/nvidia* file descriptors, and querying nvidia-smi for active compute processes.

After the timeout, the process is terminated with SIGTERM (and SIGKILL if it doesn't exit within 5 seconds). If the process exits on its own before the timeout, monitoring stops early.

A live status line shows progress during monitoring:

  [15s/60s] Peak RSS: 245.3 MB | CPUs: 4 | GPU: No

If memory usage is still increasing when monitoring stops, condorize will warn you that the observed values may be underestimates and suggest running with a longer --timeout.

If the program exits quickly with a non-zero exit code (e.g., bad arguments or a missing input file), condorize will warn you and ask whether to continue, since the monitored resource usage likely doesn't reflect the program's real needs.

2. Inspects the package (in parallel)

While the program is being monitored, condorize looks up the executable's package in the background:

• Resolves the binary path using which and follows symlinks.
• Runs dpkg -S to find which package owns the binary.
• Checks the package for Nmrbox-Software and Nmrbox-Version metadata using dpkg-query. If found, it formats an HTCondor requirement to ensure the job runs on a node with the correct software version installed (e.g., requirements = VORONOTA == "v121").

3. Asks you to confirm

After monitoring, condorize displays a summary of what it detected and prompts you to confirm or adjust each value. Press Enter to accept the suggested default (shown in brackets), or type a new value:

============================================================
  Condorize - Detected Settings
============================================================
  Peak memory (RSS):  245.3 MB
  Suggested request:  320 MB (with 25% headroom)
  Peak CPUs/threads:  4
  GPU used:           No
  NMRBox requirement: VORONOTA == "v121"
============================================================

  Review the settings below. Press Enter to accept the
  suggested value shown in [brackets], or type a new value.

  Memory to request in MB [320]:
  CPUs to request [4]:
  Request a GPU? [y/N]:
  Include NMRBox requirement 'VORONOTA == "v121"'? [Y/n]:

Memory suggestions include 25% headroom over the observed peak, rounded up to the nearest 64 MB.

If an NMRBox requirement is included, condorize will query condor_status to check whether any machines in the pool currently match. If none do, it will print a warning so you can investigate before submitting.

4. Writes the submit file

Condorize writes a .sub file named after the executable (e.g., voronota-voromqa.sub) in the current directory, ready to submit. If a file with that name already exists, you will be asked whether to overwrite it or choose a different name.

condor_submit voronota-voromqa.sub

The generated submit file includes:

• executable and arguments (properly quoted for HTCondor)
• initialdir set to the directory where you ran condorize
• request_memory, request_cpus, request_disk (default 2 GB), request_gpus, and require_gpus with minimum GPU memory (if needed)
• requirements for NMRBox software version (if applicable)
• +Production = True to target production NMRbox machines
• output, error, and log files named with cluster and process IDs
• getenv = True to preserve your shell environment
• should_transfer_files = NO for the shared filesystem (automatically switches to IF_NEEDED if paths on /tmp or /scratch are detected)

File transfer detection

Condorize checks the executable path, current working directory, and all command arguments that look like file paths. If any of them are located under /tmp or /scratch (which are local to each machine and not shared), it sets should_transfer_files = IF_NEEDED so HTCondor will handle file transfers. Otherwise it uses should_transfer_files = NO to rely on the shared filesystem.

Requirements

• Python 3.6+
• Linux (uses /proc filesystem for monitoring)
• dpkg and dpkg-query (for package inspection; gracefully skipped if unavailable)
• nvidia-smi (for GPU detection; gracefully skipped if unavailable)
• condor_status (for pool validation; gracefully skipped if unavailable)