Sage 7.5 binaries do not build #22175

vbraun · 2017-01-12T07:57:52Z

Sage doesn't build in long (~100 chars) directories:

169625[dochtml] Error building the documentation.
169626[dochtml] Traceback (most recent call last):
169627[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python/runpy.py", line 174, in _run_module_as_main
169628[dochtml]     "__main__", fname, loader, pkg_name)
169629[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python/runpy.py", line 72, in _run_code
169630[dochtml]     exec code in run_globals
169631[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>
169632[dochtml]     main()
169633[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 1667, in main
169634[dochtml]     builder()
169635[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 316, in _wrapper
169636[dochtml]     getattr(get_builder(document), 'inventory')(*args, **kwds)
169637[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 510, in _wrapper
169638[dochtml]     build_many(build_ref_doc, L)
169639[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 252, in build_many
169640[dochtml]     ret = x.get(99999)
169641[dochtml]   File "/home/buildbot/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidmas391yaj2/local/lib/python/multiprocessing/pool.py", line 567, in get
169642[dochtml]     raise self._value
169643[dochtml] NameError: Singular library 'freegb.lib' not found

Upstream: Fixed upstream, but not in a stable release.

CC: @jpflori @kiwifb

Component: build

Author: Volker Braun

Branch/Commit: u/vbraun/sage_7_5_binaries_do_not_build @ d31d416

Reviewer: Eric Gourgoulhon

Issue created by migration from https://trac.sagemath.org/ticket/22175

The text was updated successfully, but these errors were encountered:

jdemeyer · 2017-01-12T08:18:34Z

comment:1

Is this on every machine or just one?

jpflori · 2017-01-12T08:55:56Z

comment:3

Mmmm what is strange is that SAGE_FAT_BINARIES is not mentioned in Singular's spkg-install...
Can you post Singular's buid log?

vbraun · 2017-01-12T09:53:53Z

comment:4

Every machine, logs are at http://build.sagedev.org/#/builders?tags=%2Bbinary-pkg

egourgoulhon · 2017-01-13T12:14:20Z

comment:5

I don't know if this is relevant, but on my computer (Xeon E5-2623 running Ubuntu 16.04), I could build Sage 7.5 with SAGE_FAT_BINARY=yes without any error, simply a warning:

[ecm-6.4.4.p0] Warning: SAGE_FAT_BINARY is currently not really supported by this package.

Here is what I did:

export SAGE_FAT_BINARY=yes
MAKE="make -j8" make

jpflori · 2017-01-13T12:35:12Z

comment:6

Works as well for me on ppc64 except for #22179.

vbraun · 2017-01-13T17:45:05Z

comment:7

I think the hard-coded char libnamebuf[128]; overflows, urgh...

vbraun · 2017-01-14T16:51:13Z

comment:9

In fact plain singular fails when installed in a long path:

$ ./sage -singular
> LIB "freegb.lib";
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/freegb.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/bfun.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/presolve.lib (4.0.2.2,Jan_2016)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/elim.lib (4.0.0.1,Jan_2014)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/poly.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/ring.lib (4.0.3.5,Nov_2016)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/primdec.lib (4.0.2.0,Apr_2015)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/absfact.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/triang.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/random.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/matrix.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/general.lib (4.0.0.1,Jan_2014)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/inout.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/nctools.lib (4.0.3.3,Sep_2016)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/dmodapp.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/sing.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/gkdim.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/dmod.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/control.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/homolog.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/deform.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/gmssing.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/linalg.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/qhmoduli.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/rinvar.lib (4.0.1.1,Jan_2015)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/zeroset.lib (4.0.0.0,Jun_2013)
// ** loaded /Users/buildslave-sage/slave/binary_pkg/build/source/SageMath/jc4b6yulaujayb9sr94ia88eourzeqip0oidma/local/bin/../share/singular/LIB/primitiv.lib (4.0.0.0,Jun_2013)
   ? ...parse error
   ? error occurred in or before STDIN line 1: `LIB "freegb.lib";`

vbraun · 2017-01-14T16:53:46Z

Branch: u/vbraun/sage_7_5_binaries_do_not_build

vbraun · 2017-01-14T17:07:46Z

comment:11

Upstream at Singular/Singular#811

New commits:

`d31d416`	`Patch Singular library name buffer to decent length`

vbraun · 2017-01-14T17:07:46Z

Upstream: Reported upstream. No feedback yet.

vbraun · 2017-01-14T17:07:46Z

Commit: d31d416

egourgoulhon · 2017-01-15T10:00:24Z

comment:14

From a fresh git clone + git pull of the ticket branch, with a long path for Sage root (252 characters), build fails with the error

[singular-4.1.0p1] checking for main in -lpython2.7... yes
[singular-4.1.0p1] checking embedding python interface module... no
[singular-4.1.0p1] ./configure: /home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/verylongpath5/verylongpath6/verylongpath7/verylongpath8/verylongpath9/verylongpath10/verylongpath11/verylongpath12/verylongpath13/verylongpath14/verylongpath15/verylongpath16/sage/local/bin/python2.7-config: /home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/veryl: bad interpreter: No such file or directory
[singular-4.1.0p1] configure: PYTHON_LSPEC=
[singular-4.1.0p1] ./configure: /home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/verylongpath5/verylongpath6/verylongpath7/verylongpath8/verylongpath9/verylongpath10/verylongpath11/verylongpath12/verylongpath13/verylongpath14/verylongpath15/verylongpath16/sage/local/bin/python2.7-config: /home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/veryl: bad interpreter: No such file or directory
[singular-4.1.0p1] configure: error: Python Prefix is not known
[maxima-5.35.1.p2] ;;; Finished compiling /home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/verylongpath5/verylongpath6/verylongpath7/verylongpath8/verylongpath9/verylongpath10/verylongpath11/verylongpath12/verylongpath13/verylongpath14/verylongpath15/verylongpath16/sage/local/var/tmp/sage/build/maxima-5.35.1.p2/src/src/lesfac.lisp.
[maxima-5.35.1.p2] ;;;
[singular-4.1.0p1] Error configuring Singular.

As you can see from the error message above:

/home/eric/sage/verylongpath1/verylongpath2/verylongpath3/verylongpath4/veryl: bad interpreter: No such file or directory

there seems to remain some truncation issue.

egourgoulhon · 2017-01-15T10:01:37Z

Log of failed singular build with long path on Ubuntu 16.04

kiwifb · 2017-01-15T10:06:37Z

comment:15

Attachment: singular-4.1.0p1.log

Could you also post config.log? This is slightly different but also interesting. Volker's original error is at runtime once singular is installed. When you run singular it cannot find its own stuff because of the long path. You are seeing an error at configuration time. I'd like to know what is going wrong then.

egourgoulhon · 2017-01-15T10:30:18Z

config.log corresponding to the failed build of singular with long path

kiwifb · 2017-01-15T10:36:25Z

comment:16

Attachment: config.log

I should have been more specific. singular's config.log in SAGE_LOCAL/var/tmp/sage/build/singular-4.1.0p1/src/ I think.

egourgoulhon · 2017-01-15T10:44:05Z

The config.log in SAGE_ROOT/local/var/tmp/sage/build/singular-4.1.0p1/src

vbraun · 2017-01-15T10:58:57Z

comment:17

Attachment: config.2.log

That is the shebang line length exceeded and manifests itself in the "bad interpreter" error. On Linux, the shebang (line starting with #! at the beginning of a script) is limited to 127 chars. We already take that into account when building binaries. Note that the freegb.lib library path is a good bit longer than the path to the singular binary (which necessarily appears in the shebang).

vbraun · 2017-01-15T11:00:40Z

comment:18

Patch is now merged in upstream

vbraun · 2017-01-15T11:00:40Z

Changed upstream from Reported upstream. No feedback yet. to Fixed upstream, but not in a stable release.

vbraun · 2017-01-15T11:01:09Z

Author: Volker Braun

egourgoulhon · 2017-01-15T11:03:15Z

comment:21

Replying to @vbraun:

That is the shebang line length exceeded and manifests itself in the "bad interpreter" error. On Linux, the shebang (line starting with #! at the beginning of a script) is limited to 127 chars. We already take that into account when building binaries.

OK, sorry for the noise...
and thanks for your explanations. I may have wasted your time, but I've learned the shebang thing today.

egourgoulhon · 2017-01-15T12:38:34Z

comment:22

With a small path, build completed sucessfully. Since the patch has been merged upstream, I think we can set this to positive review. François, Jean-Pierre do you agree?

vbraun · 2017-01-15T12:53:11Z

Reviewer: Eric Gourgoulhon

vbraun added this to the sage-7.5 milestone Jan 12, 2017

vbraun added c: build labels Jan 12, 2017

vbraun added the s: needs review label Jan 14, 2017

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egourgoulhon added s: needs work and removed s: needs review labels Jan 15, 2017

vbraun added s: needs review and removed s: needs work labels Jan 15, 2017

egourgoulhon added s: positive review and removed s: needs review labels Jan 15, 2017

vbraun removed the s: positive review label Jan 18, 2017

vbraun closed this as completed in e116eb1 Jan 18, 2017

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Sage 7.5 binaries do not build #22175

Sage 7.5 binaries do not build #22175

vbraun commented Jan 12, 2017

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Sage 7.5 binaries do not build #22175

Sage 7.5 binaries do not build #22175

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