Bonus tips

🎱 Some extra features to maximize your isabl journey!"

🌈 Colored Logs with Batch Systems

Default: No colored logs

Colored unbuffered logs

When running jobs using batch systems like LSF or Slurm, many programs detect whether their output is being sent to a terminal (TTY) or a file and may disable features like color formatting or progress bars if they detect non-interactive output.

One workaround, using it carefully, is to use the unbuffer utility from the expect package. unbuffer simulates a terminal by running the program in a pseudo-terminal (PTY), tricking the program into thinking it is running interactively in a terminal, so it continues to produce colored output.

Requirements:

• Have unbuffer available. See tips on how to install on an HPC.

• unbuffer: True, in your isabl_clis SUBMIT_CONFIGURATION.

• >=0.3.28 version of @papaemmelab/isabl_web

• 8c8ad75 commit of isabl_cli

Unbuffered output will redirect both stdout/stderr to the samehead_job.logfile, causing the file head_job.err output to be empty from errors of the running application.

By simulating a pseudo-PTY, you can gain desired colored outputs, but some outputs like progress bars print undesired characters that can clutter your logs. Be aware to disable those if possible (i.e. toil ... --disableProgress),or for specific applications add a dummy envTERM=dumb to tell the program there's no effective terminal attached.

➕ Bonus tip: Install unbuffer in an HPC with miniconda.

conda create -n myenv
conda activate myenv
conda install -c conda-forge expect

Having $OPT_DIR where you install your packages and $BIN_DIR where you add your executable binaries, create a runnable script called unbuffer, where you add your miniconda env's unbuffer executable and add its shared libraries:

${BIN_DIR}/unbuffer

#!/bin/bash

OPT_DIR=<your-installation-dir>
export LD_LIBRARY_PATH="${OPT_DIR}/miniconda3/envs/myenv/lib:$LD_LIBRARY_PATH"
${OPT_DIR}/miniconda3/envs/myenv/bin/unbuffer "$@"

Test it works:

$ unbuffer echo "Hello World!" 
Hello World