Opened 18 months ago

Closed 17 months ago

Last modified 16 months ago

#31624 closed defect (fixed)

fedora-34-standard: eclib, singular, ipykernel build failures with system ntl, zeromq

Reported by: Matthias Köppe Owned by:
Priority: blocker Milestone: sage-9.3
Component: porting Keywords:
Cc: Dima Pasechnik, Jerry James, François Bissey, Enrique Artal Bartolo, Michael Orlitzky, Martin Albrecht Merged in:
Authors: Matthias Koeppe Reviewers: Volker Braun
Report Upstream: N/A Work issues:
Branch: 3197044 (Commits, GitHub, GitLab) Commit:
Dependencies: Stopgaps:

Status badges

Description (last modified by Matthias Köppe)

from https://groups.google.com/g/sage-release/c/6WjKQt_e_B8/m/dpx1qILOCwAJ (for 9.3.rc2):

9.3.beta8> fedora-34-standard: 9.3.beta8> [eclib-20190909] /usr/bin/ld: /usr/lib64/libntl.so: undefined reference to `std::exception_ptr::exception_ptr::_M_release()@CXXABI_1.3.13'

fedora-34-standard eclib problem is unchanged in 9.3.rc2, and also issues with ntl show up in singular

See also: https://groups.google.com/g/sage-release/c/PAeKAGNJIJA/m/Rrncqdp7AQAJ

Change History (31)

comment:1 Changed 18 months ago by Matthias Köppe

Milestone: sage-9.3sage-9.4

comment:2 Changed 17 months ago by Matthias Köppe

Cc: François Bissey Enrique Artal Bartolo added
Dependencies: #29703
Description: modified (diff)

comment:3 Changed 17 months ago by Matthias Köppe

As noted in #29703, upgrading our gcc spkg to 10.3 does not fix this issue.

So we should probably improve our ntl/spkg-configure.m4 to make sure that it is usable. (Related: #31578, which will also modify ntl/spkg-configure.m4

comment:4 Changed 17 months ago by Matthias Köppe

Cc: Michael Orlitzky added
Milestone: sage-9.4sage-9.3
Priority: majorcritical

comment:5 Changed 17 months ago by Matthias Köppe

Priority: criticalblocker

As I wrote in https://groups.google.com/g/sage-release/c/PAeKAGNJIJA/m/guT9UeiYAgAJ, we could just have ntl's spkg-configure.m4 reject system NTL if we reject system gcc. I'm preparing a patch for this

comment:6 Changed 17 months ago by Matthias Köppe

Branch: u/mkoeppe/fedora_34_standard__eclib__singular_build_failures_with_system_ntl

comment:7 Changed 17 months ago by Matthias Köppe

Authors: Matthias Koeppe
Commit: 887e9918d25e1adb7fa3b52514c491de152dcb78
Status: newneeds_review

New commits:

887e991build/pkgs/ntl/spkg-configure.m4: Add depcheck for gcc

comment:8 Changed 17 months ago by Matthias Köppe

Also:

  [ipykernel-5.2.1] error installing, exit status 1. End of log file:
  [ipykernel-5.2.1]       File "/sage/local/lib64/python3.9/site-packages/zmq/backend/cython/__init__.py", line 6, in <module>
  [ipykernel-5.2.1]         from . import (constants, error, message, context,
  [ipykernel-5.2.1]     ImportError: /sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libzmq.so.5)
  [ipykernel-5.2.1]     Building wheel for ipykernel (PEP 517): finished with status 'error'
  [ipykernel-5.2.1]     ERROR: Failed building wheel for ipykernel
  [ipykernel-5.2.1]   Failed to build ipykernel

comment:9 Changed 17 months ago by Matthias Köppe

Summary: fedora-34-standard: eclib, singular build failures with system ntlfedora-34-standard: eclib, singular, ipykernel build failures with system ntl, zeromq

comment:10 Changed 17 months ago by git

Commit: 887e9918d25e1adb7fa3b52514c491de152dcb785594edd417e6a4bb7b1b21fb04b94512ddfe6be5

Branch pushed to git repo; I updated commit sha1. New commits:

5594eddbuild/pkgs/zeromq/spkg-configure.m4: Add depcheck for gcc

comment:11 Changed 17 months ago by Matthias Köppe

With these changes, make build succeeds. But building the documentation reveals another error:

[dochtml]   File "sage/matrix/matrix_modn_sparse.pyx", line 1, in init sage.matrix.matrix_modn_sparse (build/cythonized/sage/matrix/matrix_modn_sparse.cpp:17097)
[dochtml]   File "sage/matrix/matrix_integer_sparse.pyx", line 1, in init sage.matrix.matrix_integer_sparse (build/cythonized/sage/matrix/matrix_integer_sparse.cpp:17107)
[dochtml]   File "sage/matrix/matrix_integer_dense.pyx", line 1, in init sage.matrix.matrix_integer_dense (build/cythonized/sage/matrix/matrix_integer_dense.cpp:57743)
[dochtml] ImportError: /sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libvmaf.so.0)

comment:12 Changed 17 months ago by git

Commit: 5594edd417e6a4bb7b1b21fb04b94512ddfe6be5df4274ec4cd767a02df0f5819b20f3f6331382bb

Branch pushed to git repo; I updated commit sha1. New commits:

df4274ebuild/pkgs/{freetype,libgd}/spkg-configure.m4: Add depcheck for gcc

comment:13 in reply to:  11 Changed 17 months ago by Enrique Artal Bartolo

I found this error while building, I think that --with-system-libgd=no --with-system-brial=no (at least one of them) in ./configure did work.

Replying to mkoeppe:

With these changes, make build succeeds. But building the documentation reveals another error:

[dochtml]   File "sage/matrix/matrix_modn_sparse.pyx", line 1, in init sage.matrix.matrix_modn_sparse (build/cythonized/sage/matrix/matrix_modn_sparse.cpp:17097)
[dochtml]   File "sage/matrix/matrix_integer_sparse.pyx", line 1, in init sage.matrix.matrix_integer_sparse (build/cythonized/sage/matrix/matrix_integer_sparse.cpp:17107)
[dochtml]   File "sage/matrix/matrix_integer_dense.pyx", line 1, in init sage.matrix.matrix_integer_dense (build/cythonized/sage/matrix/matrix_integer_dense.cpp:57743)
[dochtml] ImportError: /sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libvmaf.so.0)

comment:14 Changed 17 months ago by Matthias Köppe

I already did the libgd above and just ran into the brial issue too.

comment:15 Changed 17 months ago by git

Commit: df4274ec4cd767a02df0f5819b20f3f6331382bb04ca24245faf39d51bfd468aeb18cf73f70107f2

Branch pushed to git repo; I updated commit sha1. New commits:

04ca242build/pkgs/brial/spkg-configure.m4: Add depcheck on gcc

comment:16 Changed 17 months ago by git

Commit: 04ca24245faf39d51bfd468aeb18cf73f70107f22012f7c31b3871769a0c49c277bcb579e29478cd

Branch pushed to git repo; I updated commit sha1. New commits:

2012f7cbuild/pkgs/ppl/spkg-configure.m4: Add depcheck on gcc

comment:17 Changed 17 months ago by git

Commit: 2012f7c31b3871769a0c49c277bcb579e29478cdcedbb31e02f260cb702c9ecfbeabe1659090408e

Branch pushed to git repo; I updated commit sha1. New commits:

cedbb31build/pkgs/fplll/spkg-configure.m4: Add depcheck on gcc

comment:18 Changed 17 months ago by Matthias Köppe

With this I am running into an fplll build error:

[fplll-5.4.0] libtool: link: g++ -std=c++11 -O2 -g -fPIC -I/sage/local/include/ -Wl,-rpath-link -Wl,/sage/local/lib -Wl,-rpath -Wl,/sage/local/lib -o .libs/fplll main.o  -L/sage/local/lib ./.libs/libfplll.so -lmpfr -lgmp -pthread -Wl,-rpath -Wl,/sage/local/lib
[fplll-5.4.0] libtool: link: g++ -std=c++11 -O2 -g -fPIC -I/sage/local/include/ -Wl,-rpath-link -Wl,/sage/local/lib -Wl,-rpath -Wl,/sage/local/lib -o .libs/latticegen latticegen.o  -L/sage/local/lib ./.libs/libfplll.so -lmpfr -lgmp -pthread -Wl,-rpath -Wl,/sage/local/lib
[fplll-5.4.0] /usr/bin/ld: /usr/lib64/libqd.so.0: undefined reference to `std::__istream_extract(std::istream&, char*, long)@GLIBCXX_3.4.29'
[fplll-5.4.0] collect2: error: ld returned 1 exit status
[fplll-5.4.0] make[6]: *** [Makefile:1119: latticegen] Error 1
[fplll-5.4.0] make[6]: *** Waiting for unfinished jobs....
[fplll-5.4.0] /usr/bin/ld: /usr/lib64/libqd.so.0: undefined reference to `std::__istream_extract(std::istream&, char*, long)@GLIBCXX_3.4.29'
[fplll-5.4.0] collect2: error: ld returned 1 exit status

comment:19 Changed 17 months ago by Matthias Köppe

Cc: Martin Albrecht added

comment:20 Changed 17 months ago by Matthias Köppe

We do not have an spkg for qd -- so we cannot fix this problem with spkg-configure. Opened #31792 for adding a package for it

comment:21 Changed 17 months ago by git

Commit: cedbb31e02f260cb702c9ecfbeabe1659090408e31970444601c16300153cddbac6e0a1658883368

Branch pushed to git repo; I updated commit sha1. New commits:

3197044build/pkgs/fplll/spkg-install.in: Configure --without-qd if we use gcc from spkg

comment:22 Changed 17 months ago by Matthias Köppe

This version works for me. Let's get it into Sage 9.3 please

comment:23 Changed 17 months ago by Dima Pasechnik

as #29703 is a dependency with 9.4 milestone, it does not seem to make sense to insist on 9.3 milestone here.

comment:24 Changed 17 months ago by Matthias Köppe

Dependencies: #29703

I forgot to remove the dependency.

comment:25 Changed 17 months ago by Volker Braun

Reviewers: Volker Braun
Status: needs_reviewpositive_review

comment:26 Changed 17 months ago by Matthias Köppe

Thanks!

comment:27 Changed 17 months ago by Volker Braun

Branch: u/mkoeppe/fedora_34_standard__eclib__singular_build_failures_with_system_ntl31970444601c16300153cddbac6e0a1658883368
Resolution: fixed
Status: positive_reviewclosed

comment:28 Changed 16 months ago by Enrique Artal Bartolo

Commit: 31970444601c16300153cddbac6e0a1658883368

I am not sure if it is related to this ticket, but I get a persistent error compiling libgd in 9.4.beta0 in Fedora 34:

/usr/bin/ld: /usr/lib64/libvmaf.so.0: undefined reference to `std::throw_bad_array_new_length()@GLIBCXX_3.4.29'

For 9.3 ./configure --with-system-zeromq=no --with-system-eclib=no --with-system-flint=no --with-system-flintqs=no --with-system-ntl=no --with-system-libgd=no --with-system-brial=no was ok

comment:29 in reply to:  28 ; Changed 16 months ago by Dima Pasechnik

Replying to enriqueartal:

I am not sure if it is related to this ticket, but I get a persistent error compiling libgd in 9.4.beta0 in Fedora 34:

can't you just use the system libgd?

comment:30 in reply to:  29 Changed 16 months ago by Enrique Artal Bartolo

Replying to dimpase:

Replying to enriqueartal:

I am not sure if it is related to this ticket, but I get a persistent error compiling libgd in 9.4.beta0 in Fedora 34:

can't you just use the system libgd?

Even after ./configure --with-system-libgd=yes it tries to compile libgd-2.3.2

comment:31 Changed 16 months ago by Matthias Köppe

libgd is rejected because of g++11. Unfortunately building libgd ourselves appears to create similar issues with other libraries that are (optional) dependencies (not shipped with Sage). The best way to fix this is to fix the remaining issues that block our use of system gcc 11 (#31786). We could also try to fix up our libgd install scripts (see #27901)

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