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TACC Setup

Accessing TACC and Basic Commands

Multi-Factor Authentication Pairing

Set up multi-factor authentication using a token app or SMS.

TACC Account Portal (TAP)

Visit www.tap.tacc.utexas.edu and use the following information:

  • System: Lonestar6
  • Application: DCV remote desktop
  • Project: IBN22012
  • Queue: vm-small, development, normal, gpu, gpu-development
  • Time limit: 48:0:0 (Small and normal queues have time limits of 48h, development queue has a time limit of 2h)
  • Click submit and connect once you’re off the queue
  • Use Utilities to link scratch work here

Mac Terminal

  • Type: ssh [email protected]
  • Confirm with: yes
  • Enter your TACC password
  • Enter your duo mobile key code
  • Get idev node before doing anything here
  • Type: idev -p NODETYPE -t TIME(h:m:s)

Lonestar6

  • Put all working files in /scratch, there's no space limit
    • BUT it purges files if you don't access them for 10 days. Always back up files to /work or /corral.
  • /work has a limit of 1024 GB. If work is full then transfer to /corral. See corral_guide.
  • Type cd for $HOME, cdw for $WORK, cds for $SCRATCH.
    • In shell, type $HOME/ and press tab, it will show you the absolute path. You need the absolute path instead of $SCRATCH to access directories when you transfer files from and to local computer and when you use jupyter notebook.

Rsync for File Transfer

  • rsync -avz SOURCE DESTINATION
  • SOURCE is where you’re sending the file from
  • DESTINATION is where you’re sending the file to

Other Instructions

  • No sudo, yum, apt-get or anything similar.

Working with Anaconda in Lonestar6

Bash File

  • The bash file is located in the home1 folder. Use ls -a to see it in the directory, nano to edit it.
    • There should be this command in the last line of the file: conda deactivate
  • Include the Anaconda installation in the bash.
  • Add directories to the PATH: export PATH=.:$WORK/YOUR/ANACONDA/PATH:$PATH. Do this every time you install/compile a new thing.
  • Source the bashrc when you added a new path: source ./bashrc.

Anaconda Installation

  • Download through the web browser, making sure it’s installed under $WORK not $HOME.

libmamba

  • Install libmamba in the base environment and set it as solver. More information can be found here.

conda-forge

  • Add conda-forge in the environment channels. More information can be found here.

Creating Environments and Installing minian

  • Other environments: Sklearn (optional)
  • Add minian and other environments as jupyter kernel: python -m ipykernel install --user --name=EnvName. More information can be found here.

Possible Issues running minian

  • Update GCC in minian environment: conda install -c conda-forge gcc=12.1.0
  • Downgrade pyviz: conda install pyviz_comms==2.2.0
  • Use new version of pipeline from minian github (minian-install --notebooks), but remember to change the custom codes for slicing and parameter defining.
  • Add to PATH"/work/09117/xz6783/ls6/Anaconda/envs/minian/bin".
  • Need to install ffmpeg, which requires nasm and other things
  • You might need to get a new load after these steps since jupyter only use the $PATH when it started and can’t be updated during running.

General Downloading and Compiling Instructions

From browser: Change firefox download file to work or scratch first!!

From wget or Curl(need to compile): cd to target folder first

Unzip:

  1. First download the Unzip package to work. Then compile it in the terminal (at the downloaded folder) following the instruction here
  2. After installation, unzip the file in the terminal by running “unzip filename”
  3. You can also use 7zip which might be better

Other Resources

https://wikis.utexas.edu/display/CoreNGSTools/Linux+fundamentals

https://issm.ess.uci.edu/trac/issm/wiki/lonestar

https://filezilla-project.org/download.php?type=client

https://www.linux.com/training-tutorials/get-know-rsync/

https://wikis.utexas.edu/display/bioiteam/GVA2022+-+Class+Review#GVA2022ClassReview-Anaconda/Miniconda

https://wikis.utexas.edu/display/CoreNGSTools/Day+1%3A+Intro+to+NGS%2C+Linux+and+TACC

denisecailab/minian#195

https://tacc.github.io/ctls2017/docs/intro_to_linux/intro_to_linux_05.html

https://tacc.github.io/ctls2017/docs/intro_to_linux/intro_to_linux_01.html

https://sites.google.com/site/tacchadoop/home/upload-your-data-to-tacc-computer