[Debian-med-packaging] Bug#953832: cannot allocate memory in static TLS block

[Andreas Tille]

Hi Faidon,

could you imagine to build jemalloc with --disable-initial-exec-tls
as Sergio suggests below to fix the issue in drmaa (and possibly other
packages)?

Should I open a separate bug report against jemalloc to request this?

Kind regards

      Andreas.

On Sat, Mar 14, 2020 at 05:18:49PM -0400, Sergio Durigan Junior wrote:
> > $ python3
> > Python 3.7.6 (default, Jan 19 2020, 22:34:52) 
> > [GCC 9.2.1 20200117] on linux
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import drmaa
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File "/home/andreas/debian-maintain/salsa/med-team/python-drmaa/drmaa/__init__.py", line 65, in <module>
> >     from .session import JobInfo, JobTemplate, Session
> >   File "/home/andreas/debian-maintain/salsa/med-team/python-drmaa/drmaa/session.py", line 39, in <module>
> >     from drmaa.helpers import (adapt_rusage, Attribute, attribute_names_iterator,
> >   File "/home/andreas/debian-maintain/salsa/med-team/python-drmaa/drmaa/helpers.py", line 36, in <module>
> >     from drmaa.wrappers import (drmaa_attr_names_t, drmaa_attr_values_t,
> >   File "/home/andreas/debian-maintain/salsa/med-team/python-drmaa/drmaa/wrappers.py", line 58, in <module>
> >     _lib = CDLL(libpath, mode=RTLD_GLOBAL)
> >   File "/usr/lib/python3.7/ctypes/__init__.py", line 364, in __init__
> >     self._handle = _dlopen(self._name, mode)
> > OSError: /usr/lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block
> 
> This is an issue with jemalloc's handling of the TLS model when being
> dlopened..  See:
> 
>   https://github.com/jemalloc/jemalloc/issues/1237
> 
> The recommended way to build a libjemalloc that is suitable for being
> dlopened is to use '--disable-initial-exec-tls' when building it.  Take
> a look at the INSTALL.md file, and look for this option:
> 
>   https://github.com/jemalloc/jemalloc/blob/dev/INSTALL.md
> 
> There is a way to workaround this bug by doing an LD_PRELOAD of
> libjemalloc when invoking python, but this will only mask the problem
> and we can't expect users to do/know this.
> 
> The way I see it, you can try to convince jemalloc's maintainer to
> enable that flag.
> 
> BTW, the reason 'find_library' can't find drmaa's library is because the
> .so is being installed in a non-standard directory.  I don't know why
> the package was made like this, though.
> 
> Thanks,
> 
> -- 
> Sergio
> GPG key ID: 237A 54B1 0287 28BF 00EF  31F4 D0EB 7628 65FC 5E36
> Please send encrypted e-mail if possible
> http://sergiodj.net/



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