GNU bug report logs - #30229
Python modules installed by pip in virtualenv can't find shared objects.

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Package: guix; Reported by: Fis Trivial <ybbs.daans@HIDDEN>; dated Tue, 23 Jan 2018 11:51:01 UTC; Maintainer for guix is bug-guix@HIDDEN.

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From: Ricardo Wurmus <rekado@HIDDEN>
To: Fis Trivial <ybbs.daans@HIDDEN>
Subject: Re: bug#30229: Python modules installed by pip in virtualenv can't
 find shared objects.
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Hi,

> When a python module needs to load a dynamic shared object, it looks in t=
he
> path provided by *LD_LIBRARY_PATH*(1), but guix doesn't modify this envir=
onment
> variable to export the needed path for python.

We cannot set this environment variable by default lest we break other
packages that may be installed.  LD_LIBRARY_PATH is dangerous as it
tells the runtime linker to prefer libraries in the specified
directories.

For Guix packages we use different means to embed store paths in
binaries, which are looked up at runtime.  For binaries that=E2=80=99s achi=
eved
with RUNPATH; for others we patch the sources to ensure that libraries
are not looked up merely by name but by absolute path.

In your particular case (installing packages without Guix) I think the
best way is to manually set LD_LIBRARY_PATH on demand, or to set
LD_PRELOAD to the specific libraries that are required.

In general, though, I recommend using Guix for package management and
development instead of virtualenv and pip.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net






Information forwarded to bug-guix@HIDDEN:
bug#30229; Package guix. Full text available.

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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: Fis Trivial <ybbs.daans@HIDDEN>
Subject: Re: bug#30229: Python modules installed by pip in virtualenv can't
 find shared objects.
References: <MWHPR16MB0063656F9561DCD3EF12634592E30@HIDDEN>
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Hi,

Fis Trivial <ybbs.daans@HIDDEN> skribis:

> In my case, it's lightgbm (installed by pip), needs libgomp.so from gcc:l=
ib for
> openmp support. Here is the backtrace:
>
> Traceback (most recent call last):
>   File "ex1.py", line 5, in <module>
>     import lightgbm as lgb
>   File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-=
packages/lightgbm/__init__.py", line 8, in <module>
>     from .basic import Booster, Dataset
>   File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-=
packages/lightgbm/basic.py", line 32, in <module>
>     _LIB =3D _load_lib()
>   File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-=
packages/lightgbm/basic.py", line 27, in _load_lib
>     lib =3D ctypes.cdll.LoadLibrary(lib_path[0])
>   File "/gnu/store/jb3n0bsdpkhvyb8y70jyr8fcx8fqssr9-python-3.5.3/lib/pyth=
on3.5/ctypes/__init__.py", line 425, in LoadLibrary
>     return self._dlltype(name)
>   File "/gnu/store/jb3n0bsdpkhvyb8y70jyr8fcx8fqssr9-python-3.5.3/lib/pyth=
on3.5/ctypes/__init__.py", line 347, in __init__
>     self._handle =3D _dlopen(self._name, mode)
> OSError: libgomp.so.1: cannot open shared object file: No such file or di=
rectory

I=E2=80=99d suggest hard-coding the absolute file name of libgomp.so.1 in
lightgbm/basic.py.

This is what we do, for instance, for Guile packages that use the
foreign function interface (FFI) and dynamically load shared libraries
(see =E2=80=98guile-gdbm-ffi=E2=80=99 as an example.)

HTH,
Ludo=E2=80=99.




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From: Fis Trivial <ybbs.daans@HIDDEN>
To: Ricardo Wurmus <rekado@HIDDEN>
Subject: Re: bug#30229: Python modules installed by pip in virtualenv can't
 find shared objects.
Thread-Topic: bug#30229: Python modules installed by pip in virtualenv can't
 find shared objects.
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bug#30229; Package guix. Full text available.

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From: Fis Trivial <ybbs.daans@HIDDEN>
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Subject: Python modules installed by pip in virtualenv can't find shared
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Thread-Topic: Python modules installed by pip in virtualenv can't find shared
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Acknowledgement sent to Fis Trivial <ybbs.daans@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#30229; Package guix. Full text available.
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