#31624 closed defect (fixed)
fedora34standard: eclib, singular, ipykernel build failures with system ntl, zeromq
Reported by:  mkoeppe  Owned by:  

Priority:  blocker  Milestone:  sage9.3 
Component:  porting  Keywords:  
Cc:  dimpase, ghjamesjer, fbissey, enriqueartal, mjo, malb  Merged in:  
Authors:  Matthias Koeppe  Reviewers:  Volker Braun 
Report Upstream:  N/A  Work issues:  
Branch:  3197044 (Commits, GitHub, GitLab)  Commit:  
Dependencies:  Stopgaps: 
Description (last modified by )
from https://groups.google.com/g/sagerelease/c/6WjKQt_e_B8/m/dpx1qILOCwAJ (for 9.3.rc2):
9.3.beta8> fedora34standard: 9.3.beta8> [eclib20190909] /usr/bin/ld: /usr/lib64/libntl.so: undefined reference to `std::exception_ptr::exception_ptr::_M_release()@CXXABI_1.3.13'
fedora34standard eclib problem is unchanged in 9.3.rc2, and also issues with ntl show up in singular
See also: https://groups.google.com/g/sagerelease/c/PAeKAGNJIJA/m/Rrncqdp7AQAJ
Change History (31)
comment:1 Changed 16 months ago by
 Milestone changed from sage9.3 to sage9.4
comment:2 Changed 16 months ago by
 Cc fbissey enriqueartal added
 Dependencies set to #29703
 Description modified (diff)
comment:3 Changed 16 months ago by
comment:4 Changed 16 months ago by
 Cc mjo added
 Milestone changed from sage9.4 to sage9.3
 Priority changed from major to critical
comment:5 Changed 16 months ago by
 Priority changed from critical to blocker
As I wrote in https://groups.google.com/g/sagerelease/c/PAeKAGNJIJA/m/guT9UeiYAgAJ, we could just have ntl's spkgconfigure.m4
reject system NTL if we reject system gcc.
I'm preparing a patch for this
comment:6 Changed 16 months ago by
 Branch set to u/mkoeppe/fedora_34_standard__eclib__singular_build_failures_with_system_ntl
comment:7 Changed 16 months ago by
 Commit set to 887e9918d25e1adb7fa3b52514c491de152dcb78
 Status changed from new to needs_review
New commits:
887e991  build/pkgs/ntl/spkgconfigure.m4: Add depcheck for gcc

comment:8 Changed 16 months ago by
Also:
[ipykernel5.2.1] error installing, exit status 1. End of log file: [ipykernel5.2.1] File "/sage/local/lib64/python3.9/sitepackages/zmq/backend/cython/__init__.py", line 6, in <module> [ipykernel5.2.1] from . import (constants, error, message, context, [ipykernel5.2.1] ImportError: /sage/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /lib64/libzmq.so.5) [ipykernel5.2.1] Building wheel for ipykernel (PEP 517): finished with status 'error' [ipykernel5.2.1] ERROR: Failed building wheel for ipykernel [ipykernel5.2.1] Failed to build ipykernel
comment:9 Changed 16 months ago by
 Summary changed from fedora34standard: eclib, singular build failures with system ntl to fedora34standard: eclib, singular, ipykernel build failures with system ntl, zeromq
comment:10 Changed 16 months ago by
 Commit changed from 887e9918d25e1adb7fa3b52514c491de152dcb78 to 5594edd417e6a4bb7b1b21fb04b94512ddfe6be5
Branch pushed to git repo; I updated commit sha1. New commits:
5594edd  build/pkgs/zeromq/spkgconfigure.m4: Add depcheck for gcc

comment:11 followup: ↓ 13 Changed 16 months ago by
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 16 months ago by
 Commit changed from 5594edd417e6a4bb7b1b21fb04b94512ddfe6be5 to df4274ec4cd767a02df0f5819b20f3f6331382bb
Branch pushed to git repo; I updated commit sha1. New commits:
df4274e  build/pkgs/{freetype,libgd}/spkgconfigure.m4: Add depcheck for gcc

comment:13 in reply to: ↑ 11 Changed 16 months ago by
I found this error while building, I think that withsystemlibgd=no withsystembrial=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 16 months ago by
I already did the libgd
above and just ran into the brial
issue too.
comment:15 Changed 16 months ago by
 Commit changed from df4274ec4cd767a02df0f5819b20f3f6331382bb to 04ca24245faf39d51bfd468aeb18cf73f70107f2
Branch pushed to git repo; I updated commit sha1. New commits:
04ca242  build/pkgs/brial/spkgconfigure.m4: Add depcheck on gcc

comment:16 Changed 16 months ago by
 Commit changed from 04ca24245faf39d51bfd468aeb18cf73f70107f2 to 2012f7c31b3871769a0c49c277bcb579e29478cd
Branch pushed to git repo; I updated commit sha1. New commits:
2012f7c  build/pkgs/ppl/spkgconfigure.m4: Add depcheck on gcc

comment:17 Changed 16 months ago by
 Commit changed from 2012f7c31b3871769a0c49c277bcb579e29478cd to cedbb31e02f260cb702c9ecfbeabe1659090408e
Branch pushed to git repo; I updated commit sha1. New commits:
cedbb31  build/pkgs/fplll/spkgconfigure.m4: Add depcheck on gcc

comment:18 Changed 16 months ago by
With this I am running into an fplll build error:
[fplll5.4.0] libtool: link: g++ std=c++11 O2 g fPIC I/sage/local/include/ Wl,rpathlink 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 [fplll5.4.0] libtool: link: g++ std=c++11 O2 g fPIC I/sage/local/include/ Wl,rpathlink 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 [fplll5.4.0] /usr/bin/ld: /usr/lib64/libqd.so.0: undefined reference to `std::__istream_extract(std::istream&, char*, long)@GLIBCXX_3.4.29' [fplll5.4.0] collect2: error: ld returned 1 exit status [fplll5.4.0] make[6]: *** [Makefile:1119: latticegen] Error 1 [fplll5.4.0] make[6]: *** Waiting for unfinished jobs.... [fplll5.4.0] /usr/bin/ld: /usr/lib64/libqd.so.0: undefined reference to `std::__istream_extract(std::istream&, char*, long)@GLIBCXX_3.4.29' [fplll5.4.0] collect2: error: ld returned 1 exit status
comment:19 Changed 16 months ago by
 Cc malb added
comment:20 Changed 16 months ago by
We do not have an spkg for qd  so we cannot fix this problem with spkgconfigure. Opened #31792 for adding a package for it
comment:21 Changed 16 months ago by
 Commit changed from cedbb31e02f260cb702c9ecfbeabe1659090408e to 31970444601c16300153cddbac6e0a1658883368
Branch pushed to git repo; I updated commit sha1. New commits:
3197044  build/pkgs/fplll/spkginstall.in: Configure withoutqd if we use gcc from spkg

comment:22 Changed 16 months ago by
This version works for me. Let's get it into Sage 9.3 please
comment:23 Changed 16 months ago by
as #29703 is a dependency with 9.4 milestone, it does not seem to make sense to insist on 9.3 milestone here.
comment:25 Changed 16 months ago by
 Reviewers set to Volker Braun
 Status changed from needs_review to positive_review
comment:26 Changed 15 months ago by
Thanks!
comment:27 Changed 15 months ago by
 Branch changed from u/mkoeppe/fedora_34_standard__eclib__singular_build_failures_with_system_ntl to 31970444601c16300153cddbac6e0a1658883368
 Resolution set to fixed
 Status changed from positive_review to closed
comment:28 followup: ↓ 29 Changed 15 months ago by
 Commit 31970444601c16300153cddbac6e0a1658883368 deleted
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 withsystemzeromq=no withsystemeclib=no withsystemflint=no withsystemflintqs=no withsystemntl=no withsystemlibgd=no withsystembrial=no was ok
comment:29 in reply to: ↑ 28 ; followup: ↓ 30 Changed 15 months ago by
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 15 months ago by
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 withsystemlibgd=yes it tries to compile libgd2.3.2
comment:31 Changed 15 months ago by
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)
As noted in #29703, upgrading our gcc spkg to 10.3 does not fix this issue.
So we should probably improve our
ntl/spkgconfigure.m4
to make sure that it is usable. (Related: #31578, which will also modifyntl/spkgconfigure.m4