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

[mkoeppe]

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

[mkoeppe]

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

[mkoeppe]

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

[mkoeppe]

New commits:

​887e991

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

[mkoeppe]

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

[git]

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

​5594edd

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

[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)

[git]

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

​df4274e

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

[enriqueartal]

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)

[mkoeppe]

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

[git]

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

​04ca242

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

[git]

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

​2012f7c

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

[git]

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

​cedbb31

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

[mkoeppe]

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

[mkoeppe]

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

[git]

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

​3197044

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

[mkoeppe]

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

[dimpase]

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

[mkoeppe]

I forgot to remove the dependency.

[mkoeppe]

Thanks!

[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:

/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

[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?

[enriqueartal]

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

[mkoeppe]

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)