FS#66962 - [openvdb][jemalloc] pyopenvdb cannot be imported in python

Attached to Project: Community Packages
Opened by Martin Saraceno (tinux) - Tuesday, 09 June 2020, 22:01 GMT
Last edited by Sven-Hendrik Haase (Svenstaro) - Sunday, 14 June 2020, 22:40 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Sven-Hendrik Haase (Svenstaro)
Christian Hesse (eworm)
Architecture All
Severity Low
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

It is not possible to import pyopenvdb in python:

<code>
$ python
Python 3.8.3 (default, May 17 2020, 18:15:42)
[GCC 10.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyopenvdb
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: /usr/lib64/libjemalloc.so.2: cannot allocate memory in static TLS block
</code>

Additional info:
* openvdb-7.0.0-5
* python-3.8.3-1
This task depends upon

Closed by  Sven-Hendrik Haase (Svenstaro)
Sunday, 14 June 2020, 22:40 GMT
Reason for closing:  Fixed
Additional comments about closing:  New jemalloc currently in testing has the fix.
Comment by freswa (frederik) - Wednesday, 10 June 2020, 03:00 GMT
Upstream: https://github.com/jemalloc/jemalloc/issues/937
Comment by Christian Hesse (eworm) - Wednesday, 10 June 2020, 07:43 GMT
So we want to build jemalloc with `--disable-initial-exec-tls`?

https://github.com/jemalloc/jemalloc/commit/a62e42baebe09dc84aaff731faa6ff87fde6bc4e
Comment by Martin Saraceno (tinux) - Wednesday, 10 June 2020, 18:45 GMT
I can confirm that compiling with `--disable-initial-exec-tls` solves the import issue in python.

```
$ ipython
Python 3.8.3 (default, May 17 2020, 18:15:42)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.15.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import pyopenvdb

In [2]:
```

As long as there are not other drawbacks I'd say it's worth it.
Comment by Christian Hesse (eworm) - Wednesday, 10 June 2020, 21:10 GMT
Pushed in jemalloc 1:5.2.1-3 - let's give it some testing...
No idea whether or not there are any drawbacks.
Comment by Sven-Hendrik Haase (Svenstaro) - Sunday, 14 June 2020, 22:40 GMT
New package works fine for me. Let's close this. eworm, I tested a few apps depending on jemalloc and it works fine. I suppose that it would fail pretty quickly if something were wrong with the memory allocator. I think you can move the package to extra.

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