Symbol not found: __ZN7leveldb2DB4OpenERKNS_7OptionsERKSsPPS0_ on Mavericks

[varikin]

Trying to get Plyvel working on Mavericks. I have LevelDB 1.15 installed via homebrew. In a Python 3.3 virtualenv, after pip install plyvel, I get the following:

Python 3.3.3 (default, Dec  4 2013, 09:48:34)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import plyvel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "./plyvel/__init__.py", line 6, in <module>
    from ._plyvel import (  # noqa
ImportError: dlopen(./plyvel/_plyvel.so, 2): Symbol not found:   __ZN7leveldb2DB4OpenERKNS_7OptionsERKSsPPS0_
  Referenced from: ./plyvel/_plyvel.so
  Expected in: flat namespace
 in ./plyvel/_plyvel.so 

The docs say to ensure the linker can find the shared library, but I am not sure how to do that with pip. When grepping for that symbol, I find something similar, but not exact. Is this a version mismatch or I am just not looking at the right things?

nm /usr/local/lib/libleveldb.1.dylib | grep __ZN7leveldb2DB4Open
0000000000009456 T __ZN7leveldb2DB4OpenERKNS_7OptionsERKNSt3__112basic_stringIcNS4_11char_traitsIcEENS4_9allocatorIcEEEEPPS0_

[wbolster]

Are you sure the leveldb libs are in the LD_LIBRARY_PATH?

[wbolster]

Do you have multiple LevelDB versions installed? Maybe this is a mismatch between compile time and runtime versions.

[varikin]

LD_LIBRARY_PATH wasn't set so I set it and it didn't make a difference. I then uninstalled LevelDB and Plylel and then reinstalled them with LD_LIBRARY_PATH set to see if it had any affect. It didn't. Here is the current setting of LD_LIBRARY_PATH.

$ ls /usr/local/lib/libleveldb.*
/usr/local/lib/libleveldb.1.15.dylib /usr/local/lib/libleveldb.1.dylib    /usr/local/lib/libleveldb.a          /usr/local/lib/libleveldb.dylib
$ echo $LD_LIBRARY_PATH
/usr/local/lib

[wbolster]

I don't have much experience debugging issues like these. Did you compile LevelDB yourself using the same compiler?

[varikin]

I switched to working in Ubuntu Saucy and everything works. Not sure why my Mac environment is messed up, but considering I will be ultimately running this app from a Ubuntu, I am fine with this.

[mchaput]

I don't think this issue should have been closed, since it's still broken on Mavericks. I still have this problem. Installed leveldb with brew, installed plyvel pip, and get the same missing symbol.

ImportError: dlopen(/Users/matt/Dropbox/workspace/env/py33whoosh/lib/python3.3/site-packages/plyvel/_plyvel.so, 2): Symbol not found: __ZN7leveldb2DB4OpenERKNS_7OptionsERKSsPPS0_
  Referenced from: /Users/matt/Dropbox/workspace/env/py33whoosh/lib/python3.3/site-packages/plyvel/_plyvel.so
  Expected in: flat namespace
 in /Users/matt/Dropbox/workspace/env/py33whoosh/lib/python3.3/site-packages/plyvel/_plyvel.so

[wbolster]

Reopening. Please help debugging this, I'm not sure what the problem is.

[mchaput]

I'll do what I can :)

[wbolster]

So, is this with multiple LevelDB installations? Is LevelDB installed and reachable by the loader (LD_LIBRARY_PATH maybe)?

[wbolster]

Not familiar with this problem, but this looks similar to some extent: http://stackoverflow.com/questions/19737207/openssl-and-m2crypto-not-working-together-on-os-x-mavericks

[wbolster]

And maybe this one as well: http://stackoverflow.com/questions/21867277/installing-pillow-with-mac-os-x-mavericks-10-9-1

[mchaput]

I removed all python.org Pythons from my system and reinstalled using Homebrew's pythons, and now this works. It may have been a conflict between Homebrew's Leveldb and python.org Python.

[wbolster]

Great, glad to hear that it works for you now. I'll close this issue, since it does not seem to caused by Plyvel after all.

[pinkplus]

I encountered the same problem. It looks to me that the problem is caused by different C++ standard libraries used by leveldb and plyvel.

When I install leveldb (in the standard way, make), it is linked to libc++, which is the default standard library on OS X.
However, when I install plyvel, it is linked to libstdc++ for some unknown reason.
The name mangling is different for two libraries.

This command worked for me:

CFLAGS='-mmacosx-version-min=10.7 -stdlib=libc++' pip install plyvel

[orsharir]

I've encountered this issue as well, and so far can't find a solution. If plyvel relies on LD_LIBRARY_PATH, then you should know that on OS X El Capitan you can no longer use that due to possible security restrictions by the OS. I've seen this in other open-source projects that relies on this flag for loading libraries (e.g. see BVLC/caffe#3227).

[wbolster]

i cannot reproduce this.

on osx el capitan with homebrew I can build/run plyvel just fine on different python versions after i brew install leveldb. the test suite passes; relevant snippets from the tox output:

  py26: commands succeeded
  py27: commands succeeded
  py33: commands succeeded
  py34: commands succeeded

[mitallast]

I have same problem on os x 10.11.3 with this commands:

brew install leveldb
pip install plyvel

plyvel package installed with wheels, so I try reinstall plyvel without wheels:

pip uninstall plyvel
CFLAGS='-mmacosx-version-min=10.7 -stdlib=libc++' pip install --no-use-wheel plyvel

Maybe something wrong with wheel package?

[wbolster]

plyvel does not provide wheel packages; those are built locally on your system by pip i think, so yeah, removing them from your local cache may help.

[flaviovdf]

Had the same issue, got it working by doing:

pip uninstall plyvel
CFLAGS='-mmacosx-version-min=10.7 -stdlib=libc++' pip install plyvel --no-cache-dir

The --no-cache-dir was needed, if it is not provided, pip will re-use the previous compilation.

[ysunf]

@flaviovdf
His answer works for me. 👍
I install leveldb with homebrew, and install plyvel with pip.
when i test "$python -c 'import plyvel'", it comes up the same 'Symbol' error.
So i uninstall plyvel and reinstall with :
CFLAGS='-mmacosx-version-min=10.7 -stdlib=libc++' pip install plyvel --no-cache-dir

[Ayppo]

Same problem on linux. I want to use commands like "CFLAGS='-mmacosx-version-min=10.7 -stdlib=libc++' pip install plyvel --no-cache-dir", but all failed

[wbolster]

@troyoung this is about a mac osx specific issue. please open a new issue and provide all relevant information if your problem persists.

[jakeywu]

i have solved my problem by install [email protected] which default is @1.23

https://cloud.tencent.com/developer/article/1815745

[kobiebotha]

@jakeywu Unfortunately 1.21 does not work Apple Sillicon

[ManuelSchneid3r]

Has anybody found an easy solution to this? Still an issue under ventura 13.2 (m1), leveldb 1.23, plyvel 1.5

[abhi-jha]

Yeah, this doesn't work on MacOS Sonoma 14.2.1.

I have installed leveldb on a custom path using : https://github.com/wbolster/plyvel/blob/main/scripts/install-leveldb.sh

I have a new path where both lib/ and include/ folders are available. I included these paths when running make which successfully generates the .so object.

Now when I install the libray itself using pip install ., it installs successfully. But when I do import it into a file it tells me the following :

Traceback (most recent call last):
  File "/path/temp/plyvel/leveldb_stuff.py", line 1, in <module>
    import plyvel
  File "/path/temp/plyvel/plyvel/__init__.py", line 6, in <module>
    from ._plyvel import (  # noqa
ImportError: dlopen(/path/temp/plyvel/plyvel/_plyvel.cpython-39-darwin.so, 0x0002): symbol not found in flat namespace '__ZTIN7leveldb10ComparatorE'

I am not sure if the lib path needs to be provided again somewhere. I mostly edited the setup.py file.

NOTE that make succeeded successfully and there is an .so file in the folder.