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General guidance for YH Huang lab

Welcome aboard. Here are some general guidelines for using the school server for members of YH Huang Lab.

Top note: Please backup your codes or important data, as this server is not back upped.

  • Codes: we suggest backup with GitHub private repo, and commit/push regularly
  • Data: always back up raw / precious files, e.g. on another server or local external hard disk. For intermediate files, keep your analysis scripts and make sure you can reproduce the results easily.

Personal / small projects / scripts

  • User specific data and script: use the home directory
  • Ideally home directory is not more than 10 GB
  • Still, please prioritise using lab folders (see below) for easier potential collaboration!!

Project data

Before you start using the lab folder (or any folder that others may have write permission): think if you want others to over-write your files (generally not)!!! If so, please check the default file permission setting. Here is the school server the default is (775 / 664), YH suggests changing it to (755/644) by adding the codes in .bashrc or .bash_profile:

# Set default file/folder permission to 644/755
umask 022

Ideally project data should be stored in the lab directory for easier collaboration / navigation

  • Data for your projects in lab: /storage/yhhuang/users/$YOUR_USER_NAME
  • Large projects for collaboration: /storage/yhhuang/research/$PROJECT_NAME
  • Shared common software or systems settings: /storage/yhhuang/systems
  • Shared common tools and packages: /storage/yhhuang/tools

Computing usage

The school server hasn't introduce any queuing system to keep higher flexibility, so always keep an eye on your jobs and being nice. You can using top [-u YOUR_USER_NAME] to check the CPU and memory used.

  • CPUs: ideally not more than 4000% (namely 40 CPUs out of 800)
  • Memory: ideally not more than 50% in total and not more than 30% for a single job. Otherwise, make sure it finishes in a short period time.