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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