Upgrade OpenBLAS 0.3.13 #29913

slel · 2020-06-20T10:42:08Z

This is to upgrade to OpenBLAS 0.3.13, released Dec 13, 2020.
https://github.com/xianyi/OpenBLAS/releases

Update OpenBLAS to 0.3.9 - fixes build error of iml on fedora-32-standard #29378 Update OpenBLAS to 0.3.9

CC: @slel @dimpase @kiwifb @antonio-rojas @kliem

Component: packages: standard

Keywords: upgrade, openblas

Author: Matthias Koeppe

Branch/Commit: 1971508

Reviewer: Jonathan Kliem

Issue created by migration from https://trac.sagemath.org/ticket/29913

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

slel · 2020-06-20T10:42:19Z

comment:1

This would solve #28768.

mkoeppe · 2020-11-17T03:09:02Z

comment:5

Numpy is having trouble with OpenBLAS 0.3.12 - https://numpy.org/devdocs/release/1.19.4-notes.html

So we should probably wait before we make updates to OpenBLAS

NathanDunfield · 2020-12-05T01:59:58Z

comment:6

Just commenting to note that upgrading to the (as yet unreleased) 0.3.13 would close #31007.

mkoeppe · 2020-12-20T00:38:17Z

comment:7

Our current OpenBLAS 0.3.9 also does not build on cygwin-minimal (https://github.com/mkoeppe/sage/runs/1582256022):

  [openblas-0.3.9]   gcc -O2 -g -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -DNO_AVX512 -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=2 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DVERSION=\"0.3.9\" -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I. -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -DNO_AVX512 -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=2 -DMAX_PARALLEL_NUMBER=1 -DUSE_TLS -DVERSION=\"0.3.9\" -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -L/opt/sage-cf31b79036db96b5fd9e0b22f44c3692bc22356b/lib -Wl,-rpath,/opt/sage-cf31b79036db96b5fd9e0b22f44c3692bc22356b/lib  cygopenblas.def dllinit.o \
  [openblas-0.3.9]   -shared -o ../cygopenblas.dll -Wl,--out-implib,../libopenblas.dll.a \
  [openblas-0.3.9]   -Wl,--whole-archive ../cygopenblas_atomp-r0.3.9.a -Wl,--no-whole-archive -L/c/mingw810/x86_64-810-posix-seh-rt_v6-rev0/mingw64/opt/lib -L/c/mingw810/prerequisites/x86_64-zlib-static/lib -L/c/mingw810/prerequisites/x86_64-w64-mingw32-static/lib -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0 -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/../../../../x86_64-w64-mingw32/lib/../lib -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/../../../../lib -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/../../../../x86_64-w64-mingw32/lib -LC:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/../../..  -lgfortran -lmingw32 -lmoldname -lmingwex -lmsvcrt -lquadmath -lm -lmingw32 -lmoldname -lmingwex -lmsvcrt -lpthread -liconv -lmingw32 -lmoldname -lmingwex -lmsvcrt   -lgfortran -lgfortran
  [openblas-0.3.9]   C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/libgfortran.a(read.o):(.text$_gfortrani_convert_real+0x6e): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `strtoflt128'
  [openblas-0.3.9]   C:/ProgramData/Chocolatey/lib/mingw/tools/install/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.1.0/libgfortran.a(read.o):(.text$_gfortrani_convert_infnan+0x46): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `strtoflt128'
  [openblas-0.3.9]   collect2: error: ld returned 1 exit status
  [openblas-0.3.9]   make[4]: *** [Makefile:98: ../cygopenblas.dll] Error 1

It should be checked whether the proposed upgrades fix this error.

mkoeppe · 2020-12-20T01:00:55Z

Branch: u/mkoeppe/upgrade_openblas_0_3_13

mkoeppe · 2020-12-20T01:07:54Z

Author: Matthias Koeppe

mkoeppe · 2020-12-20T01:07:54Z

Reviewer: https://github.com/mkoeppe/sage/actions/runs/433187403

mkoeppe · 2020-12-20T01:07:54Z

New commits:

`1971508`	`build/pkgs/openblas: Update to 0.3.13, drop patch`

mkoeppe · 2020-12-20T01:07:54Z

Commit: 1971508

mkoeppe · 2020-12-20T19:16:58Z

comment:11

Replying to @mkoeppe:

Our current OpenBLAS 0.3.9 also does not build on cygwin-minimal [...]
It should be checked whether the proposed upgrades fix this error.

Same error with 0.3.13

mkoeppe · 2020-12-20T19:20:19Z

comment:12

Otherwise this update looks unproblematic.

mkoeppe · 2020-12-21T18:07:40Z

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/433187403 to https://github.com/mkoeppe/sage/actions/runs/433187403, ...

mkoeppe · 2020-12-21T18:59:51Z

comment:14

Replying to @mkoeppe:

Replying to @mkoeppe:

Our current OpenBLAS 0.3.9 also does not build on cygwin-minimal [...]
It should be checked whether the proposed upgrades fix this error.

Same error with 0.3.13

This really had nothing to do with openblas; see #31091.

kliem · 2021-01-06T09:31:42Z

comment:16

The testsuite on ubuntu bionic was not run

https://github.com/mkoeppe/sage/runs/1583194874?check_suite_focus=true

 ./sage -t -p --all --logfile=logs/ptest.log
no stored timings available
Running doctests with ID 2020-12-20-03-25-13-c92ee485.
Using --optional=debian,dochtml,memlimit,pip,sage,sage_spkg
Doctesting entire Sage library.
Traceback (most recent call last):
  File "/sage/src/bin/sage-runtests", line 182, in <module>
    err = DC.run()
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 1233, in run
    self.expand_files_into_sources()
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 816, in expand_files_into_sources
    self.sources = [FileDocTestSource(path, self.options) for path in expand()]
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 816, in <listcomp>
    self.sources = [FileDocTestSource(path, self.options) for path in expand()]
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 811, in expand
    if not skipfile(os.path.join(root,file)):
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 228, in skipfile
    for line in F:
  File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 5109: ordinal not in range(128)
Makefile:189: recipe for target 'ptest' failed
make: *** [ptest] Error 1
(error ignored)

Is this related to this ticket?

kliem · 2021-01-06T09:51:04Z

comment:17

Never mind. openblas isn't installed in this case, so it can't be the cause.

dimpase · 2021-01-06T09:56:43Z

comment:18

seems like an unrelated update broke python 3.6. Maybe we should stop foolong around with 3.6 already in 9.3?

If that 1% of Sage users without a better Python want to build Sage, they can first install a better Python.

kliem · 2021-01-06T10:05:41Z

comment:19

This ticket looks good to me.

There are a few occasions where https://github.com/mkoeppe/sage/actions/runs/433187403

fails, but it looks like github related failures (running out of disk space etc). I can't discover any new failures and I checked that the doctests still look good.

kliem · 2021-01-06T10:05:41Z

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/433187403, ... to Jonathan Kliem

mkoeppe · 2021-01-06T18:53:29Z

comment:20

Thanks!

mkoeppe · 2021-01-06T18:58:43Z

comment:21

Replying to @kliem:

The testsuite on ubuntu bionic was not run

https://github.com/mkoeppe/sage/runs/1583194874?check_suite_focus=true

 ./sage -t -p --all --logfile=logs/ptest.log
no stored timings available
Running doctests with ID 2020-12-20-03-25-13-c92ee485.
Using --optional=debian,dochtml,memlimit,pip,sage,sage_spkg
Doctesting entire Sage library.
Traceback (most recent call last):
  File "/sage/src/bin/sage-runtests", line 182, in <module>
    err = DC.run()
  File "/sage/local/lib/python3.6/site-packages/sage/doctest/control.py", line 1233, in run
....
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 5109: ordinal not in range(128)
Makefile:189: recipe for target 'ptest' failed
make: *** [ptest] Error 1
(error ignored)

Thanks for catching this - I did not see it because unfortunately it does not show up in a log file. I have created #31191 for it.

vbraun · 2021-01-17T13:46:06Z

Changed branch from u/mkoeppe/upgrade_openblas_0_3_13 to 1971508

slel added this to the sage-9.2 milestone Jun 20, 2020

slel added c: packages: standard labels Jun 20, 2020

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mkoeppe modified the milestones: sage-9.2, sage-9.3 Oct 24, 2020

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mkoeppe changed the title ~~Upgrade OpenBLAS 0.3.10~~ Upgrade OpenBLAS 0.3.13 Dec 20, 2020

mkoeppe added the s: needs review label Dec 20, 2020

kliem removed the s: needs review label Jan 6, 2021

kliem added the s: positive review label Jan 6, 2021

vbraun removed the s: positive review label Jan 17, 2021

vbraun closed this as completed in 60e3d32 Jan 17, 2021

zimmermann6 mentioned this issue Jun 22, 2020

OpenBLAS build failure with MAKEFLAGS='-j4 -l4' #28768

Closed

This was referenced Dec 21, 2020

configure: Add better tests for a working gfortran #31091

Closed

ubuntu-bionic-standard (python 3.6): make ptest fails with UnicodeDecodeError #31191

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Upgrade OpenBLAS 0.3.13 #29913

Upgrade OpenBLAS 0.3.13 #29913

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