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How PSCP works

How to make checkpoints on every session using git stash create

Author: Sunyeop Lee (sunyeop97@gmail.com)

When I study, I always feel like saving the source code somewhere on each run, and then check out to it later or see the difference of the runs.

Old-fashioned method: using git commit

To achieve, I had logged every git commit hashes to tensorboard session. However, this way made me tired to write commit messages to every session. I lost the detailed history each time I skip it. What was worse, it made my commit log full of hyperparameter-tuning commits -- change learning rate to xx, change beta to yy, ...

Using git stash create for boosting up your research

I thought some method that could store the current workspace with unstaged files, which would neither require commit message nor make my git log messy. There is a command, git stash create, which creates a dangling commit with staged, unstaged files and outputs hash of the commit. This was the excellent fit for the problem.

Using git stash create inherits all strengths from git, which are very useful for study.

  • Recycle unchanged objects
  • Compression (zlib)
  • Show differences using git diff a..b
  • Checkout to, using git checkout
  • Create branch from, using git stash branch ... This restores staged files staged and unstaged files unstaged.

You also could stage untracked new files to include in git stash create using git add.

Example

Initialize git repository for example.

$ mkdir example && cd example

$ git init
Initialized empty Git repository in /home/qbx2/example/.git/

$ echo LEARNING_RATE=0.5 > config.txt

$ git add config.txt && git commit -m "Initial commit"
[master (root-commit) 96a145e] Initial commit
 1 file changed, 1 insertion(+)
 create mode 100644 config.txt

Make some changes and create stashes (per-session checkpoints).

$ echo LEARNING_RATE=0.3 > config.txt
$ git stash create
2741da39b09687a06acd71651ce26eded3458606

$ echo LEARNING_RATE=0.1 > config.txt
$ git stash create
5bbe8a5d956ad5176915e231750c3cc98511d622

git stash create does make neither git log nor git stash list messy.

$ git log | cat
commit 96a145e2f20eb08b9b838f7424cfba5afdca56bc
Author: Sunyeop Lee <sunyeop97@gmail.com>
Date:   Fri Feb 1 14:38:03 2019 +0900

    Initial commit

$ git stash list | cat

Log the outputs of git stash create in other way to reference them later. Then, we can see difference using git diff.

$ git diff 2741da..5bbe8a | cat
diff --git a/config.txt b/config.txt
index 214f551..7bc7046 100644
--- a/config.txt
+++ b/config.txt
@@ -1 +1 @@
-LEARNING_RATE=0.3
+LEARNING_RATE=0.1

We could check-out to a new branch using git stash branch. This command will restore staged files staged too.

$ git reset --hard && git stash branch test-restore 2741da39b09687a06acd71651ce26eded3458606
HEAD is now at 96a145e Initial commit
Switched to a new branch 'test-restore'
On branch test-restore
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   config.txt

no changes added to commit (use "git add" and/or "git commit -a")

Using git update-ref to avoid from being pruned

Because git stash create does not store the commit anywhere in the ref namespace, there is possibility to be pruned on git gc(or git prune) which is automatically executed by some commands.

For example,

$ git show 2741da39b09687a06acd71651ce26eded3458606 | cat
commit 2741da39b09687a06acd71651ce26eded3458606
... (omitted)

$ git gc --prune=now
Counting objects: 3, done.
Writing objects: 100% (3/3), done.
Total 3 (delta 0), reused 0 (delta 0)

$ git show 2741da39b09687a06acd71651ce26eded3458606 | cat
fatal: bad object 2741da39b09687a06acd71651ce26eded3458606

By storing the commit in refs, now it's safe.

(<checkpoint_id> is the output when executed git stash create) git update-ref "refs/checkpoints/$(date +%s)" <checkpoint_id>

You can see the created/updated reference using git show-ref command.

$ git update-ref "refs/checkpoints/$(date +%s)" 2741da39b09687a06acd71651ce26eded3458606
$ git show-ref
96a145e2f20eb08b9b838f7424cfba5afdca56bc refs/heads/master
2741da39b09687a06acd71651ce26eded3458606 refs/checkpoints/1548995645

$ git show 2741da39b09687a06acd71651ce26eded3458606 | cat
commit 2741da39b09687a06acd71651ce26eded3458606
... (omitted)

Pushing to remote repository

We've named git stash create-ed commits using git update-ref, now we can push them to the remote repository. For example, I set my github repository as remote origin.

$ git push origin 'refs/checkpoints/*'
Total 0 (delta 0), reused 0 (delta 0)
To https://github.com/qbx2/test
 * [new branch]      refs/checkpoints/1548995645 -> refs/checkpoints/1548995645

git push says new branch is created but it's not a branch because we specified destination reference in refs/checkpoints/ not refs/heads/. That's why we cannot see the checkpoint in the github repository branches. To see, visit <github repository>/tree/refs/checkpoints/1548995645. Also, git ls-remote shows that your remote references.

$ git ls-remote
From https://github.com/qbx2/test
96a145e2f20eb08b9b838f7424cfba5afdca56bc HEAD
96a145e2f20eb08b9b838f7424cfba5afdca56bc refs/heads/master
2741da39b09687a06acd71651ce26eded3458606 refs/checkpoints/1548995645

Delete local checkpoints

When we have low disk space, we might want to save space by pruning pushed checkpoints. First, delete the reference we've created to avoid pruning.

$ git update-ref refs/checkpoints/1548995645 -d
$ git show-ref
96a145e2f20eb08b9b838f7424cfba5afdca56bc refs/heads/master
96a145e2f20eb08b9b838f7424cfba5afdca56bc refs/remotes/origin/master

Still, the object is alive.

$ git show 2741da39b09687a06acd71651ce26eded3458606 | cat
commit 2741da39b09687a06acd71651ce26eded3458606
Merge: 7ed4dec ff70b7e
Author: Sunyeop Lee <sunyeop97@gmail.com>
Date:   Fri Feb 1 12:26:54 2019 +0900

    WIP on master: 7ed4dec test

    ... (omitted)

Prune it by git gc --prune=now.

$ git gc --prune=now
Counting objects: 10, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (10/10), done.
Total 10 (delta 1), reused 10 (delta 1)

$ git show 2741da39b09687a06acd71651ce26eded3458606 | cat
fatal: bad object 2741da39b09687a06acd71651ce26eded3458606

Fetching from remote repository

My local git repository does not know about f0951fe, which is pruned. However, we can fetch them whenever we want to because we've pushed it to the remote repository.

To create local reference, --refmap is given.

$ git ls-remote origin 'refs/checkpoints/*'
2741da39b09687a06acd71651ce26eded3458606    refs/checkpoints/1548995645

$ git fetch origin refs/checkpoints/1548995645 --refmap 'refs/checkpoints/*:refs/checkpoints/*'

To fetch multiple refs,

$ git fetch origin 'refs/checkpoints/*:refs/checkpoints/*'