Quick Start:
- main website: https://www.sherlock.stanford.edu/docs/#what-to-expect
- Join their sherlock slack & follow their instructions (basically join the two channels they recommend by searching the channels in the slack app, they don't have a workspace it seems): https://www.sherlock.stanford.edu/docs/#user-community
- Support email, read this: https://www.sherlock.stanford.edu/docs/#email-recommended
High level plan
- ssh into the login/head node
ssh your_sunetid@login.sherlock.stanford.edue.g.,ssh brando9@login.sherlock.stanford.edu(see https://www.sherlock.stanford.edu/docs/#quick-start) - git clone the repo so it's accessible in any node when using the slurm resource manger, to do that you need to put the public ssh key on sherlock
- set up the conda env so it's accesible in any node and learn to use pip install -e .
- test the code by running with interactive job (srun) and background jon (sbatch)
- modify the code, test again, and learn to push to repo
- learn to vscode into sherlcok (either ssh or push file on save)
- then do new experiment repeat
- and request an optional pull rquest
note: you should understand (roughly) what everything means in here to be effective. Google, gpt4/claude it etc. Tips:
- use
manto understand bash command or if you want to chat with it use LLMs/GPT4/Claude.
List of thinks to know about:
- git, ssh, bash,
- basic unix commands, ls, ls -lah, cd, pwd, which,
ssh your_sunetid@login.sherlock.stanford.eduget the git clone command from your fork (create your fork in github! To fork go to github our project's webpage and click fork on the top right) and do with your own specific ssh url clone text (gotten from the topish left green button called "code", copy the ssh flag):
git clone git@github.com:brando90/evals-for-autoformalization.gitGoal: add the public key you created on sherlock's login node to your github so you can clone your fork. For that follow the instructions here https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account or the outline from bellow that was inspired from the official github link in this sentence.
First create ssh public key on sherlock
ssh your_sunetid@login.sherlock.stanford.edu
[brando9@sh03-ln06 login ~/.ssh]$ ssh-keygen -t ed25519 -C "brandojazz@gmail.com"
Generating public/private ed25519 key pair.
Enter file in which to save the key (/home/users/brando9/.ssh/id_ed25519):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/users/brando9/.ssh/id_ed25519.
Your public key has been saved in /home/users/brando9/.ssh/id_ed25519.pub.
The key fingerprint is:
...
The key's randomart image is:
+--[ED25519 256]--+
...
+----[SHA256]-----+
# press the enter key to not change file name
# press the enter key or a passphase to use this keyNow run ssh agent in sherlock
[brando9@sh03-ln06 login ~/.ssh]$ eval "$(ssh-agent -s)"
Agent pid 50895
Now configure your .ssh if you've never done it on this server. Concretely, if ~.ssh/config doesn't exist create it with (or vim):
touch ~/.ssh/config
# or
[brando9@sh03-ln06 login ~/.ssh]$ vim .config
put the contets of for hithub (i.e., copy the bellow into your clip board, read it) with the vim:
Host github.com
AddKeysToAgent yes
UseKeychain yes
IdentityFile ~/.ssh/id_ed25519
i.e. use vim editor in sherlock(read about vim, it's just an edit) in the server i.e. do
[brando9@sh03-ln06 login ~/.ssh]$ cat ~/.ssh/config
cat: /home/users/brando9/.ssh/config: No such file or directory
vim ~/.ssh/config
# press i in the new black window,
#copy paste the contents above after pressing i,
#then press escape esc
# then safe the file and exist with :x or :w followed by :q
# then do
cat .config
# confirms you copied it correctly
[brando9@sh03-ln06 login ~/.ssh]$ cat .config
Host github.com
AddKeysToAgent yes
UseKeychain yes
IdentityFile ~/.ssh/id_ed25519
Then add the key to your github using https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account . For a summary of what I did do:
# in the sherlock login/head node do:
[brando9@sh03-ln06 login ~/.ssh]$ cat ~/.ssh/id_ed25519.pub
# then copy paste the output, very carefully, do not share this stuff publicly wide web
Then go to setting in your github e.g., https://github.com/settings/keys and create a new key by copy pasting the contents of the previous cat command.
Then git clone on your fork should work, e.g.,:
[brando9@sh03-ln06 login ~/.ssh]$ git clone git@github.com:brando90/evals-for-autoformalization.git
Cloning into 'evals-for-autoformalization'...
remote: Enumerating objects: 270, done.
remote: Counting objects: 100% (264/264), done.
remote: Compressing objects: 100% (163/163), done.
remote: Total 270 (delta 150), reused 175 (delta 90), pack-reused 6
Receiving objects: 100% (270/270), 78.74 KiB | 0 bytes/s, done.
Resolving deltas: 100% (151/151), done.
- create the
setup.pyfile - Make sure your setup.py file has the following
package_dir={'': 'src'},
packages=find_packages('src'),so that pip install -e . knows were the python modules are when installing the python library.
Anything outside src`` won't be found for this libraries pip -e install. Read the comments for those lines in setup.py`` to understand it if you wish and refs.
3. Now you can do pip install -e . or `pip install -e $HOME/evals-for-autoformalization` (assuming you have your python env/conda env activated).
Now you should be able to import statements for this library in the expected way! e.g.,
# TODO# This script demonstrates the use of conda for managing Python environments and pip for installing Python packages.
# Conda is an open-source package management and environment management system.
# 1. List all the available conda environments on your system.
# The command 'conda info -e' will list all the environments available.
conda info -e
# 2. Update conda to the latest version.
# It's good practice to keep conda updated to the latest version to avoid any compatibility issues.
conda update --all
# 3. Upgrade pip to the latest version.
# Pip is the package installer for Python. Upgrading it ensures that you can install packages without issues.
pip install --upgrade pip
# 4. Create a new conda environment.
# 'conda create -n maf python=3.10' creates a new environment named 'maf' with Python version 3.10 installed.
# '-n maf' specifies the name of the environment, and 'python=3.10' specifies the Python version.
conda create -n af_evals python=3.10
# 5. Activate the newly created conda environment.
# 'conda activate maf' activates the 'maf' environment. Once activated, any Python packages installed will be specific to this environment.
conda activate af_evals
# To deactivate the current environment and return to the base environment, you can use:
# conda deactivate
# If you want to remove the 'maf' environment completely, you can use:
# conda remove --name af_evals --all
# 6. Install Python packages using pip in editable mode.
# 'pip install -e <path>' installs a package in 'editable' mode, meaning changes to the source files will immediately affect the installed package without needing a reinstall.
# Replace '<path>' with the path to the directory containing the 'setup.py' file of the package you want to install.
# pip install -e $HOME/evals-for-autoformalization
pip install -e .
# Test pytorch install with GPU
python -c "import torch; print(torch.version.cuda); print((torch.randn(2, 4).cuda() @ torch.randn(4, 1).cuda()))"
# Note: It's crucial to activate the correct conda environment before using pip install to avoid installing packages in the wrong environment.ref: https://chat.openai.com/c/375d5d26-7602-4888-9ef5-9f92359330dc
TODO
cd /afs/cs.stanford.edu/u/brando9/
git clone git@github.com:brando90/massive-autoformalization-maf.git
ln -s /afs/cs.stanford.edu/u/brando9/massive-autoformalization-maf $HOME/massive-autoformalization-maf
pip install -e ~/massive-autoformalization-maf
#pip uninstall ~/massive-autoformalization-maf
cd ~/massive-autoformalization-mafRecommend watching: