search

EpiModel / EpiModeling

Tutorials for Using the EpiModel Software Platform for Research
4 stars 2 forks source link

Notes from Kristin H #1

Closed smjenness closed 2 years ago

smjenness commented 2 years ago
  1. Registering for and logging in to HPC a. Remember that you have to let them know when your VPN is ready to go once Sam has requested access for you to the cluster b. *don’t forget to have the VPN on* when you are first trying to log on
  2. Setting up your HPC environment a. Be cognizant about what ‘space’ you are working in and supposed to be working in (own computer vs. HPC environment) i. I first made the key on the HPC side, but you need to be making it on your own computer in the hidden ssh folder and then copy it over to the HPC b. Know what functions you can use to create files in folders. I ended up using ‘nano’, but can use ‘touch’ also i. This is relevant for creating the config file in your hidden ssh folder
  3. Follow directions at bottom for how to ‘write’ (?) or save file (I think on a mac it is control+O, maybe twice) c. Where to put aliases in your bashrc file i. Do not put them in the potentially already existing ‘if’ chunk of code under ‘# User specific aliases and functions’ (the code chunk ends with ‘fi’  so write your alias under this line
  4. Did it both ways and it only worked this way (did not work if I put it in the ‘if’ chunk above the ‘fi’ line  put it below the ‘fi’ line!
  5. Using git on command line to access Github repositories (typo in title on wiki) a. If you have a github PAT, you might not have this .Renviron file (and would need to make it yourself like I did, would need to have your Github PAT on file to copy and paste, however) b. When you modify your config file in the hidden ssh folder, the linked Github tutorial states to add extra lines into this file i. Where it says ‘Host …’ – put all of these lines written beneath actually under your own ‘Host sph’ line. I created an extra line that literally was ‘Host *’ to put these lines under and that was incorrect and didn’t work. c. In one of the linked Github tutorials, it says to use ‘pbcopy’ at some point, but that never worked on my machine. I just printed out on a line what it wanted me to copy and copied it over myself manually.
smjenness commented 2 years ago

These points are now incorporated into the Wiki.