Linux install fails

[Sz Tengely]

Hi,

I tried to install SageMath 8.9 from source and there was an error message at the end related to sagenb-1.1.2 (attached the log file). Google search directed me to the post https://groups.google.com/forum/#!topic/sage-devel/icbegwpf_3I where Dima Pasechnik wrote that one should try to run ./sage, so I did so and the appropriate crash report is attached as well.

Operating system: 64 bit Linux, Manjaro 18.1.2

Sage was installed: source, version 8.9, with export MAKE="make -j4"

Reproduce the crash: I followed the README.md file, extracted the tarball, export MAKE="make -j4" and make.

Thank you for your help in advance.

With kind regards,

 Szabolcs

[Dima Pasechnik]

ImportError: /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0: undefined symbol: GOMP_loop_ull_maybe_nonmonotonic_runtime_next

something went wrong with installing linbox.

please post the relevant log.

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[Sz Tengely]

The log file is attached.

On Thursday, November 7, 2019 at 10:08:51 PM UTC+1, Dima Pasechnik wrote:

ImportError: /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0: undefined symbol: GOMP_loop_ull_maybe_nonmonotonic_runtime_next

something went wrong with installing linbox.

please post the relevant log.

On Thu, 7 Nov 2019, 21:01 Sz Tengely, <szte...@gmail.com> wrote:

Hi,

I tried to install SageMath 8.9 from source and there was an error message at the end related to sagenb-1.1.2 (attached the log file). Google search directed me to the post https://groups.google.com/forum/#!topic/sage-devel/icbegwpf_3I where Dima Pasechnik wrote that one should try to run ./sage, so I did so and the appropriate crash report is attached as well.

Operating system: 64 bit Linux, Manjaro 18.1.2

Sage was installed: source, version 8.9, with export MAKE="make -j4"

Reproduce the crash: I followed the README.md file, extracted the tarball, export MAKE="make -j4" and make.

Thank you for your help in advance.

With kind regards,

 Szabolcs

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[Dima Pasechnik]

this seems to be related to OpenMP.

are you doing anything special related to this?

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[Sz Tengely]

install.log contains the following:

[sagenb-1.1.2] Exception occurred:
[sagenb-1.1.2]   File "sage/misc/lazy_import.pyx", line 218, in sage.misc.lazy_i
mport.LazyImport._get_object (build/cythonized/sage/misc/lazy_import.c:2502)
[sagenb-1.1.2]     raise RuntimeError(f"resolving lazy import {self._name} durin
g startup")
[sagenb-1.1.2] RuntimeError: resolving lazy import dumps during startup
[sagenb-1.1.2] The full traceback has been saved in /tmp/sphinx-err-F4trNY.log,
if you want to report the issue to the developers.
[sagenb-1.1.2] Please also report this if it was a user error, so that a better
error message can be provided next time.
[sagenb-1.1.2] A bug report can be filed in the tracker at <https://github.com/s
phinx-doc/sphinx/issues>. Thanks!
[sagenb-1.1.2] make[4]: *** [Makefile:20: html] Error 2
[sagenb-1.1.2] make[4]: Leaving directory '/home/tengely/software/sage-8.9/local
/var/tmp/sage/build/sagenb-1.1.2/src/doc'
[sagenb-1.1.2] *****************************************************************
***************
[sagenb-1.1.2] Error building the documentation

[Dima Pasechnik]

sagenb build error is a red herring here.

the problem is that Sage, needed to build sagenb, does not start.

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[Isuru Fernando]

What does

ldd /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0

give you? Looks like libgomp used at runtime is older than what is at build time.

Isuru

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[Sz Tengely]

I have a working binary version of SageMath, however I would like to install a few optional packages via sage -i. That is the reason I go for this method. Now I found an old post https://sage-release.narkive.com/Cad5BdS6/sage-8-5-beta3-released in which a similar issue is mentioned (problem with lazy_import.pyx).

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[Sz Tengely]

ldd /home/tengely/software/sage-8.9/local/lib/liblinbox.so.0
        linux-vdso.so.1 (0x00007ffc6d5a9000)
    libntl.so.42 => /usr/lib/libntl.so.42 (0x00007f3971b4a000)
    libflint.so.13 => /usr/lib/libflint.so.13 (0x00007f39717db000)
    libfflas.so.1 => /home/tengely/software/sage-8.9/local/lib/libfflas.so.1 (0x00007f39716ef000)
    libffpack.so.1 => /home/tengely/software/sage-8.9/local/lib/libffpack.so.1 (0x00007f39715b1000)
    libopenblas.so.0 => /home/tengely/software/sage-8.9/local/lib/libopenblas.so.0 (0x00007f3970883000)
    libgivaro.so.9 => /usr/lib/libgivaro.so.9 (0x00007f397082a000)
    libgmp.so.10 => /usr/lib/libgmp.so.10 (0x00007f3970794000)
    libgmpxx.so.4 => /usr/lib/libgmpxx.so.4 (0x00007f397078b000)
    libmpfr.so.6 => /usr/lib/libmpfr.so.6 (0x00007f397070c000)
    libiml.so.0 => /home/tengely/software/sage-8.9/local/lib/libiml.so.0 (0x00007f39706e6000)
    libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f39704fc000)
    libm.so.6 => /usr/lib/libm.so.6 (0x00007f39703b6000)
    libc.so.6 => /usr/lib/libc.so.6 (0x00007f39701ed000)
    libgcc_s.so.1 => /home/tengely/software/sage-8.9/local/lib/libgcc_s.so.1 (0x00007f39701d4000)
    libgomp.so.1 => /home/tengely/software/sage-8.9/local/lib/libgomp.so.1 (0x00007f39701a4000)
    libgf2x.so.1 => /usr/lib/libgf2x.so.1 (0x00007f3970187000)
    libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f3970165000)
    /usr/lib64/ld-linux-x86-64.so.2 (0x00007f3971eb9000)
    libgfortran.so.4 => /home/tengely/software/sage-8.9/local/lib/libgfortran.so.4 (0x00007f396ff8d000)
    libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f396ff88000)
    libquadmath.so.0 => /home/tengely/software/sage-8.9/local/lib/../lib/libquadmath.so.0 (0x00007f396ff46000)

[Sz Tengely]

As a test I also tried to install SageMath 8.8 and that went fine.

[Dima Pasechnik]

> libgcc_s.so.1 => /home/tengely/software/sage-8.9/local/lib/libgcc_s.so.1 (0x00007f39701d4000)
> libgomp.so.1 => /home/tengely/software/sage-8.9/local/lib/libgomp.so.1 (0x00007f39701a4000)

This looks strange. Are you building Sage's gcc for some reason?
(Most probably you're building gfortran, which does build parts of gcc)

What if you install system gfortran and tried to rebuild Sage 8.9
from scratch?

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[Sz Tengely]

Thank you for the help, installing gcc-fortran in fact solved the problem, Sage 8.9 is working now.

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[E. Madison Bray]

By the way, I've been having problems with OpenMP ever since
https://trac.sagemath.org/ticket/27444, if anyone wants to take a look
at that...

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