Reproducible instructions for installing and building Mathlib4

[brando90]

Issue: PyPantograph Fails to Read Mathlib.olean After Compilation

Summary

After following the recommended steps to set up Mathlib4 and integrate it with PyPantograph, I encountered the following error when trying to use Mathlib with PyPantograph:

AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header
; Maybe the project needs to be rebuilt

Additionally, attempting to use lean directly with Mathlib also results in:

Test.lean:1:0: error: unknown module prefix 'Mathlib'
No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries:
/lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean

---

Environment Information

• Lean Version: 4.16.0-rc2

---

Steps to Reproduce

1. Cloned Mathlib4

cd ~
git clone https://github.com/leanprover-community/mathlib4.git
cd mathlib4

2. Checked and Matched Lean Toolchain

cat lean-toolchain  # Output: leanprover/lean4:v4.16.0-rc2
elan override set $(cat lean-toolchain)
lean --version  # Confirmed Lean matches the toolchain version

3. Updated and Built Mathlib

lake update
lake build

(This took a while but completed without errors.)

4. Verified .olean Files Existence

ls -lah .lake/build/lib/Mathlib.olean

(The file exists, but when trying to use it, the error occurs.)

5. Tried Importing Mathlib in Lean

Created Test.lean:

import Mathlib
#check Nat

Ran:

lean Test.lean

Got:

Test.lean:1:0: error: unknown module prefix 'Mathlib'
No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries:
/lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean

6. Attempted to Use PyPantograph

Modified Python script:

import os
from pantograph import Server

server = Server(imports=["Mathlib"], project_path="/lfs/skampere1/0/brando9/mathlib4")

Ran:

python /lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py

Got:

AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header
; Maybe the project needs to be rebuilt

---

Troubleshooting Attempts

1. Clean and Rebuild

lake clean
lake update
lake build

🚫 Same error.

2. Ensure Lean is Using the Correct Path

elan override set $(cat lean-toolchain)
lean --version

🚫 Same error.

3. Attempted lake exe cache get to Fetch Prebuilt .olean

lake exe cache get

🚫 Same error.

---

You're absolutely right to ask for verification. I'll go through our conversation carefully and ensure that only exact commands and outputs from our discussion are included. I will not fabricate any additional details.

---

Relevant Logs and Outputs

1. Lean Version and Toolchain Check

Commands and outputs from your logs:

(zip_fit) brando9@skampere1~/mathlib4 $ lean --version
Lean (version 4.16.0-rc2, x86_64-unknown-linux-gnu, commit 128a1e6b0a82, Release)

(zip_fit) brando9@skampere1~/mathlib4 $ cat lean-toolchain
leanprover/lean4:v4.16.0-rc2

---

2. Attempt to Run PyPantograph with Mathlib

Your provided command:

(zip_fit) brando9@skampere1~/mathlib4 $ python /lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py

Error output:

/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/site-packages/transformers/utils/hub.py:128: FutureWarning: Using TRANSFORMERS_CACHE is deprecated and will be removed in v5 of Transformers. Use HF_HOME instead.
  warnings.warn(
Setting random seed = 42
vLLM not installed or vllm set seed has a bug, skipping vLLM seed setting.
Traceback (most recent call last):
  File "/lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py", line 538, in <module>
    main()
  File "/lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py", line 469, in main
    server = Server(imports=["Mathlib"], project_path="/lfs/skampere1/0/brando9/mathlib4")
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/server.py", line 78, in __init__
    self.restart()
  File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/utils.py", line 16, in wrapper
    return asyncio.run(func(*args, **kwargs))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/runners.py", line 190, in run
    return runner.run(main)
           ^^^^^^^^^^^^^^^^
  File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/runners.py", line 118, in run
    return self._loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/server.py", line 161, in restart_async
    assert ready.rstrip() == "ready.", f"Server failed to emit ready signal: {ready}; Maybe the project needs to be rebuilt"
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header
; Maybe the project needs to be rebuilt

---

3. Attempt to Import Mathlib in Lean

(zip_fit) brando9@skampere1~/mathlib4 $ lean Test.lean

Error output:

Test.lean:1:0: error: unknown module prefix 'Mathlib'

No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries:
/lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean

[alok]

Mathlib and pantograph are probably on different tool chains

…

On Wed, Jan 29, 2025 at 16:57, Brando Miranda < ***@***.*** > wrote: ------------------------------------------------------------------- *Issue: PyPantograph Fails to Read Mathlib.olean After Compilation* ------------------------------------------------------------------- *Summary* --------- After following the recommended steps to set up Mathlib4 and integrate it with PyPantograph, I encountered the following error when trying to use Mathlib with PyPantograph: AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header ; Maybe the project needs to be rebuilt Additionally, attempting to use lean directly with Mathlib also results in: Test.lean:1:0: error: unknown module prefix 'Mathlib' No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries: /lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean *Environment Information* ------------------------- * *Lean Version:* 4.16.0-rc2 * *Steps to Reproduce* -------------------- *1. Cloned Mathlib4* cd ~ git clone https://github.com/leanprover-community/mathlib4.git cd mathlib4 *2. Checked and Matched Lean Toolchain* cat lean-toolchain # Output: leanprover/lean4:v4.16.0-rc2 elan override set $( cat lean-toolchain ) lean --version # Confirmed Lean matches the toolchain version *3. Updated and Built Mathlib* lake update lake build (This took a while but completed without errors.) *4. Verified.olean Files Existence* ls -lah .lake/build/lib/Mathlib.olean (The file exists, but when trying to use it, the error occurs.) *5. Tried Importing Mathlib in Lean* Created Test.lean : import Mathlib #check Nat Ran: lean Test.lean Got: Test.lean:1:0: error: unknown module prefix 'Mathlib' No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries: /lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean *6. Attempted to Use PyPantograph* Modified Python script: import os from pantograph import Server server = Server ( imports = [ "Mathlib" ], project_path = "/lfs/skampere1/0/brando9/mathlib4" ) Ran: python /lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py Got: AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header ; Maybe the project needs to be rebuilt *Troubleshooting Attempts* -------------------------- *1. Clean and Rebuild* lake clean lake update lake build 🚫 *Same error.* *2. Ensure Lean is Using the Correct Path* elan override set $( cat lean-toolchain ) lean --version 🚫 *Same error.* *3. Attempted lake exe cache get to Fetch Prebuilt.olean* lake exe cache get 🚫 *Same error.* You're absolutely right to ask for verification. I'll go through our conversation *carefully* and ensure that *only exact commands and outputs* from our discussion are included. I will *not fabricate* any additional details. *Relevant Logs and Outputs* --------------------------- *1. Lean Version and Toolchain Check* *Commands and outputs from your logs:* (zip_fit) ***@***.***~/mathlib4 $ lean --version Lean (version 4.16.0-rc2, x86_64-unknown-linux-gnu, commit 128a1e6b0a82, Release) (zip_fit) ***@***.***~/mathlib4 $ cat lean-toolchain leanprover/lean4:v4.16.0-rc2 *2. Attempt to Run PyPantograph with Mathlib* *Your provided command:* (zip_fit) ***@***.***~/mathlib4 $ python /lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py *Error output:* /lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/site-packages/transformers/utils/hub.py:128: FutureWarning: Using TRANSFORMERS_CACHE is deprecated and will be removed in v5 of Transformers. Use HF_HOME instead. warnings.warn( Setting random seed = 42 vLLM not installed or vllm set seed has a bug, skipping vLLM seed setting. Traceback (most recent call last): File "/lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py", line 538, in <module> main() File "/lfs/skampere1/0/brando9/ZIP-FIT/zip_fit/lean_pass_k_unbiased.py", line 469, in main server = Server(imports=["Mathlib"], project_path="/lfs/skampere1/0/brando9/mathlib4") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/server.py", line 78, in __init__ self.restart() File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/utils.py", line 16, in wrapper return asyncio.run(func(*args, **kwargs)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/runners.py", line 190, in run return runner.run(main) ^^^^^^^^^^^^^^^^ File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/runners.py", line 118, in run return self._loop.run_until_complete(task) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/lfs/skampere1/0/brando9/miniconda/envs/zip_fit/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete return future.result() ^^^^^^^^^^^^^^^ File "/lfs/skampere1/0/brando9/PyPantograph/pantograph/server.py", line 161, in restart_async assert ready.rstrip() == "ready.", f"Server failed to emit ready signal: {ready}; Maybe the project needs to be rebuilt" ^^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: Server failed to emit ready signal: uncaught exception: failed to read file '././.lake/build/lib/Mathlib.olean', invalid header ; Maybe the project needs to be rebuilt *3. Attempt to Import Mathlib in Lean* (zip_fit) ***@***.***~/mathlib4 $ lean Test.lean *Error output:* Test.lean:1:0: error: unknown module prefix 'Mathlib' No directory 'Mathlib' or file 'Mathlib.olean' in the search path entries: /lfs/skampere1/0/brando9/.elan/toolchains/leanprover--lean4---v4.16.0-rc2/lib/lean — Reply to this email directly, view it on GitHub ( #73 ) , or unsubscribe ( https://github.com/notifications/unsubscribe-auth/AB7QUTBGEPF3PQKGFWYXI4T2NF2IVAVCNFSM6AAAAABWED445OVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYTSNRWGEZTAOI ). You are receiving this because you are subscribed to this thread. Message ID: <stanford-centaur/PyPantograph/issues/73 @ github. com>

[brando90]

Step 1. Update the PyPantograph Repo & Submodule

Why:

• PyPantograph’s Lean code (in the src/ submodule) must match the Lean version in your Mathlib4.

What you did:

1. Pull the latest changes in PyPantograph:

   cd ~/PyPantograph
   git pull

2. Initialize/Update its submodules:

   git submodule update --init --recursive

3. Check the Lean version in src/lean-toolchain:

   cat src/lean-toolchain
   # It shows: leanprover/lean4:v4.15.0

At this point, PyPantograph is pinned to Lean 4.15.0. Any Lean code that PyPantograph spawns must also be on Lean 4.15.0 to avoid version mismatch.

---

Step 2. Build & Install PyPantograph

Why:

• You have to rebuild PyPantograph once you’ve updated the submodule to ensure the compiled wheel is consistent with the new Lean version.

What you did:

poetry build
poetry install

Explanation:

• poetry build creates a .whl file in dist/, capturing the latest PyPantograph code and submodule references.
• poetry install places that newly built package into your current Python environment.

After this, PyPantograph is fully rebuilt, pinned to Lean 4.15.0.

---

Step 3. Move to Mathlib4 and Checkout releases/v4.15.0

Why:

• Mathlib4 must also be pinned to Lean 4.15.0 so import Mathlib works with PyPantograph.
• The releases/v4.15.0 branch is the official mathlib branch that uses Lean 4.15.0.

What you did:

1. Go to the mathlib4 directory:

   cd ~/mathlib4

2. Fetch all branches/tags:

   git fetch --all

3. Checkout the releases/v4.15.0 branch:

   git checkout releases/v4.15.0

4. Verify the lean-toolchain is 4.15.0:

   cat lean-toolchain
   # Should show: leanprover/lean4:v4.15.0

Now Mathlib4 is pinned to Lean 4.15.0, matching PyPantograph.

---

Step 4. Use lake exe cache get (Optional Speedup)

Why:

• lake exe cache get can download pre-compiled .olean files from a cache server for the exact commit/branch you’re on. This speeds up local compilation drastically.

What you did:

lake exe cache get

Explanation:

• This attempts to fetch prebuilt .olean artifacts for the releases/v4.15.0 branch.
• If it succeeds, you won’t need a full local compile.
• If it fails or is partially missing, you’d do lake build to compile locally.

---

Step 5. Confirm Everything Works

1. (Optional) Clean & Build:

   lake clean
   lake update
   lake build

   This ensures you have fresh local .olean files if any are missing from the cache.

2. Check:

   -- In a file Test.lean:
   import Mathlib
   #check Nat

   Then run:

   lake env lean Test.lean

   If no error, you’re good.

3. Now your script that does:

   from pantograph import Server
   server = Server(
       imports=["Mathlib"],
       project_path="~/mathlib4"
   )

   should work with no “invalid header” or “unknown module” errors.

---

Why This Works

1. Matching Lean Versions: Both PyPantograph (pinned to 4.15.0) and Mathlib4 (now on releases/v4.15.0) use the same Lean toolchain, so there’s no mismatch in .olean files.
2. Rebuilt PyPantograph: You updated the submodule and reinstalled the package, so it’s actually using that Lean version, not an older installation.
3. Cache: Pulling .olean files with lake exe cache get speeds things up. If the cache is fully up to date for that branch, you skip long compile times.

[lenianiva]

Did you use ChatGPT to write this issue?

[brando90]

These are the commands I used to use for 4.15.0 of mathlib:

# Ensure Mathlib4 Matches Lean 4.15.0
# Clone or go to your mathlib4 or mathlib4_15_0 folder
cd ~

# Download mathlib4 name it mathlib4_15_0 repository from GitHub
git clone --branch releases/v4.15.0 https://github.com/leanprover-community/mathlib4.git mathlib4_15_0

# Change directory into the cloned mathlib4_15_0 repository
cd ~/mathlib4_15_0
# mv ~/mathlib4_15_0 $DFS/mathlib4_15_0
# ln -s $DFS/mathlib4_15_0 $HOME/mathlib4_15_0

# Check out the branch for Lean 4.15.0:
# Fetch all remote references from every configured remote
git fetch --all

# Switch to the release tag matching PyPantograph
git checkout releases/v4.15.0
git brach # check branch
cat lean-toolchain
# leanprover/lean4:v4.15.0

# Fetch cache .olean files for the current commit to speed up the build process
lake exe cache get
# No files to download
# Decompressing 5826 file(s)
# Unpacked in 8795 ms
# Completed successfully!

# Run the mathlib4 test suite in the mathlib4_15_0 directory to verify everything works correctly
# Warning: Very slow
(cd ~/mathlib4_15_0 && lake test)
# ⣿ [?/?] Computing build job
cd ~/mathlib4_15_0 && lake build
# Build completed successfully.
# real    0m16.570s
# user    0m6.518s
# sys     0m12.284s

# Test mathlib install
# since there is no lean project specified here, this cannot be tested but it would like:
cd ~/parent_git_repo/lean_src_proj
# note: lean_src_proj is usually a git repo iteself
echo -e 'import Mathlib.Topology.Basic\n#check TopologicalSpace' | lake env lean --stdin
# Output: TopologicalSpace.{u} (X : Type u) : Type u

PS: working to update this to mathlib 4.18.