#30351 closed defect (fixed)

Fix building html documentation on macOS

Reported by: slelievre Owned by:
Priority: blocker Milestone: sage-9.2
Component: build Keywords:
Cc: jhpalmieri, slelievre, embray, fbissey, klee, tscrim, chapoton, vbraun Merged in:
Authors: Dima Pasechnik Reviewers: John Palmieri
Report Upstream: N/A Work issues:
Branch: 4b11a70 (Commits, GitHub, GitLab) Commit: 4b11a706e1267b385099d8691b4468efd974f94d
Dependencies: #29552 Stopgaps:

Status badges

Description

Building html documentation fails on macOS for Sage 9.2.beta8.

Initial report:

Attachments (1)

t.py (3.4 KB) - added by dimpase 21 months ago.
demo of hangs with OMP_NUM_THREADS>1

Download all attachments as: .zip

Change History (80)

comment:1 Changed 22 months ago by slelievre

I'll try to bisect using the list of commits from 9.2.beta7 to 9.2.beta8:

At commit ed79ba3a3f, make dochtml hangs. Now trying commit 9911c15488.

comment:2 Changed 22 months ago by mkoeppe

  • Priority changed from major to blocker

comment:3 Changed 22 months ago by jhpalmieri

I think this is caused by #29766. I don't know why, but please try 9.2.beta7 first, then try 9.2.beta7 + #29766 and see if the problem arises.

comment:4 follow-up: Changed 21 months ago by dimpase

  • Cc embray added

Erik (in cc) was the last who changed parallel docbuild.

If noone understands the parallel docbuild system, it might be tempting to dump it, and replace by a straight sphinx build.

The current system looks like something inviting trouble, with explicit checks for OS flags, etc etc.

comment:5 Changed 21 months ago by slelievre

Not related to parallel docbuild a priori: I was always building with make -j1.

Homebrew-related. See below two trials on a MacBook Air (early 2014) with macOS 10.14.6 Mojave.

The error occurs when using Homebrew packages:

$ ORIGIN=https://github.com/sagemath/sage.git
$ git clone --single-branch --branch develop --tags $ORIGIN
$ cd sage
$ MAKE='make -j1'

$ source .homebrew-build-env

$ git checkout 9.2.beta7
$ git log --oneline -1
83caa4befa (HEAD, tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap
$ CC=clang CXX=clang++ OBJCC=clang OBJCXX=clang++ ./configure -q
$ make
--> OK

$ git checkout 3925b0f008
$ git log --oneline -2
3925b0f008 (HEAD) Trac #30230: Fix docstrings in sage/coding/linear_rank_metric.py
83caa4befa (HEAD, tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap && ./configure -q && make doc-clean && make
--> OK

$ git checkout 34e01d1ef4
$ git log --oneline -3
34e01d1ef4 (HEAD) Trac #29766: NumPy 1.19.1, SciPy 1.5.2, networkx 2.4, pybind11
3925b0f008 Trac #30230: Fix docstrings in sage/coding/linear_rank_metric.py
83caa4befa (tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap && ./configure -q && make doc-clean && make
--> hangs on "constructions"

It does not occur when using the least system things possible:

$ ORIGIN=https://github.com/sagemath/sage.git
$ git clone --single-branch --branch develop --tags $ORIGIN
$ cd sage
$ MAKE='make -j1'

$ git checkout 9.2.beta7
$ git log --oneline -1
83caa4befa (HEAD, tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap
$ CC=clang CXX=clang++ OBJCC=clang OBJCXX=clang++ \
  ./configure \
  --enable-openssl=yes \
  --with-python=3 \
  --with-system-arb=no \
  --with-system-gcc=no \
  --with-system-flint=no \
  --with-system-mpfr=no \
  --with-system-mpir=no \
  --with-mp=mpir \
  --with-system-ntl=no \
  --with-system-openblas=no \
  --with-blas=openblas \
  --with-system-boost_cropped=no \
  --with-system-brial=no \
  --with-system-m4ri=no \
  --with-system-libpng=no \
  --with-system-zlib=no \
  --with-system-bzip2=no \
  --with-system-cddlib=no \
  --with-system-cliquer=no \
  --with-system-curl=no \
  --with-system-eclib=no \
  --with-system-pari=no \
  --with-system-readline=no \
  --with-system-ncurses=no \
  --with-system-ecm=no \
  --with-system-fflas_ffpack=no \
  --with-system-givaro=no \
  --with-system-flintqs=no \
  --with-system-fplll=no \
  --with-system-freetype=no \
  --with-system-gf2x=no \
  --with-system-gfan=no \
  --with-system-glpk=no \
  --with-system-gsl=no \
  --with-system-iconv=no \
  --with-system-iml=no \
  --with-system-lcalc=no \
  --with-system-libatomic_ops=no \
  --with-system-libbraiding=no \
  --with-system-libffi=no \
  --with-system-libgd=no \
  --with-system-lrcalc=no \
  --with-system-m4rie=no \
  --with-system-mpc=no \
  --with-system-mpfi=no \
  --with-system-nauty=no \
  --with-system-palp=no \
  --with-system-pari_galdata=no \
  --with-system-pari_nftables=no \
  --with-system-pari_seadata_small=no \
  --with-system-patch=no \
  --with-system-pcre=no \
  --with-system-pkgconf=no \
  --with-system-planarity=no \
  --with-system-ppl=no \
  --with-system-python3=no \
  --with-system-sqlite=no \
  --with-system-xz=no \
  --with-system-r=no \
  --with-system-rw=no \
  --with-system-suitesparse=no \
  --with-system-symmetrica=no \
  --with-system-sympow=no \
  --with-system-tachyon=no \
  --with-system-yasm=no \
  --with-system-zeromq=no \
  -q
$ make openssl && make
--> OK

$ git checkout 3925b0f008
$ git log --oneline -2
3925b0f008 (HEAD) Trac #30230: Fix docstrings in sage/coding/linear_rank_metric.py
83caa4befa (HEAD, tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap && ./configure -q && make doc-clean && make
--> OK

$ git checkout 34e01d1ef4
$ git log --oneline -3
34e01d1ef4 (HEAD) Trac #29766: NumPy 1.19.1, SciPy 1.5.2, networkx 2.4, pybind11
3925b0f008 Trac #30230: Fix docstrings in sage/coding/linear_rank_metric.py
83caa4befa (tag: 9.2.beta7) Updated SageMath version to 9.2.beta7

$ ./bootstrap && ./configure -q && make doc-clean && make
--> OK

Next piece of fun could be: isolate which Homebrew package causes trouble.

comment:6 follow-ups: Changed 21 months ago by jhpalmieri

The problem goes away if I do

./configure --with-system-gsl=no --with-system-openblas=no

(I have Homebrew packages for these installed.)

Note that

./configure --with-system-openblas=no

triggers building both openblas and gsl. Note also that gsl fails to build with

./configure --with-system-gsl=no

The log file complains

configure: error: in `/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/sage-9.2.beta8/local/var/tmp/sage/build/gsl-2.5/src':
configure: error: C compiler cannot create executables

So I don't know if it's Homebrew's openblas or gsl that's causing the problem.


Actually, I really don't understand the gsl issue. I started with make distclean and ./configure --with-system-gsl=no. Then if I do make, it builds about half a dozen packages (cliquer, m4ri, pari_galdata, pari_seadata_small, libatomic_ops) before starting the gsl build, which fails with the error above. The gsl config.log file says

configure:3482: checking whether the C compiler works
configure:3504: gcc -g -O2   -L/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/sage-9.2.beta8/local/lib -Wl,-rpath,/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/sage-9.2.beta8/local/lib  conftest.c -lopenblas -lm >&5
ld: library not found for -lopenblas
clang: error: linker command failed with exit code 1 (use -v to see invocation)

The confusing part: if I instead do make distclean, ./configure --with-system-gsl=no, and then make gsl, it succeeds. If I build the half dozen packages by hand (make cliquer etc.), then make gsl succeeds. So I don't know how to debug this side issue. Does plain make do something extra that make PKG doesn't do?

comment:7 Changed 21 months ago by jhpalmieri

Given my problems with gsl, take this with a grain of salt, but with ./configure --with-system-gsl=no, if I then do make gsl followed by make, the process hangs while building the documentation. So the Homebrew package openblas seems to be the problem, since the documentation builds with ./configure --with-system-gsl=no --with-system-openblas=no.

Can anyone else verify?

Last edited 21 months ago by jhpalmieri (previous) (diff)

comment:8 Changed 21 months ago by mkoeppe

At which point during the docbuild does it hang?

Does make doc-html-no-plot also hang?

comment:9 Changed 21 months ago by mkoeppe

I think I have reproduced the bug on my system. Using

./sage -python -m pdb -m sage_setup.docbuild --verbose 3 --no-pdf-links all html

and then interrupting when it has stalled shows that it's in wait_for_one, waiting for a child to exit.

comment:10 follow-up: Changed 21 months ago by mkoeppe

  • Cc fbissey klee tscrim chapoton arojas vbraun added

I'm hoping that people who know about sage_setup.docbuild can help here.

It hangs in sage_setup.docbuild.utils.build_many.

It needs to be investigated whether one of the worker processes hangs and therefore os.wait waits forever, or whether something else is the problem.

comment:11 in reply to: ↑ 10 ; follow-up: Changed 21 months ago by mkoeppe

Replying to mkoeppe:

It needs to be investigated whether one of the worker processes hangs and therefore os.wait waits forever

This seems to be the case. Easier to test by setting SAGE_NUM_THREADS=1. Killing the worker process (unique child) with kill -INT had no effect. Killing it with kill -TERM leads to:

  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 285, in build_many
    raise worker_exc
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 257, in build_many
    if reap_workers(waited_pid, waited_exitcode):
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 215, in reap_workers
    w = bring_out_yer_dead(w, task, exitcode)
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 153, in bring_out_yer_dead
    "{}".format(task[1], w.exitcode))
sage_setup.docbuild.utils.WorkerDiedException: worker for ('en/constructions', 'html', {}) died with non-zero exit code -15
Uncaught exception. Entering post mortem debugging

comment:12 Changed 21 months ago by jhpalmieri

I don't have time over the next few days, but two potential parallel lines of investigation: why do Homebrew's openblas combined with #29766 cause this? And are there problems in the rst source for constructions and thematic_tutorials that, if fixed, could avoid this issue?

comment:13 Changed 21 months ago by mkoeppe

Some superficial debugging revealed the following: The worker process is stuck with all threads waiting in __psynch_cvwait (invoked from the depths of a BLAS call). Why this happens is unclear.

Some directions to explore:

  • the ad-hoc multiprocessing code in sage_setup.docbuild might interfere with the pthreads implementation
  • gsl confused about gslblas vs openblas

comment:14 Changed 21 months ago by mkoeppe

This is not good:

local/lib/libgiac.dylib:
        /Users/mkoeppe/s/sage/sage-rebasing/worktree-homebrew-py38/local/lib/libgiac.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/local/opt/ntl/lib/libntl.43.dylib (compatibility version 44.0.0, current version 44.1.0)
        /Users/mkoeppe/s/sage/sage-rebasing/worktree-homebrew-py38/local/lib/libpari-gmp.dylib (compatibility version 2.11.0, current version 2.11.4)
        /usr/local/opt/gsl/lib/libgsl.25.dylib (compatibility version 26.0.0, current version 26.0.0)
        /usr/local/opt/gsl/lib/libgslcblas.0.dylib (compatibility version 1.0.0, current version 1.0.0)

comment:15 Changed 21 months ago by fbissey

Yes, giac link to gslcblas if it can find it by default when gsl is enabled. Even if you provide a blas/lapack. A long time ago I rewrote that part of the configure.in in sage-on-gentoo to avoid any double linking of cblas. https://github.com/cschwan/sage-on-gentoo/blob/master/sci-mathematics/giac/files/giac-1.5.0.87-gsl_lapack.patch

comment:16 Changed 21 months ago by slelievre

  • Cc frederichan added
  • Keywords macos openblas glsblas giac added

comment:17 Changed 21 months ago by fbissey

  • Cc frederichan removed
  • Keywords macos openblas glsblas giac removed

The patch didn't include anything about cblas because I don't think cblas is used in giac's code, it is only pulled by libgsl which need a cblas. If you link libgsl against a cblas it should all work whatever it is without providing it for linking to libgiac.

comment:18 follow-up: Changed 21 months ago by mkoeppe

homebrew's libgsl is underlinked and can be linked against openblas. But its gsl.pc uses gslcblas...:

prefix=/usr/local/Cellar/gsl/2.6
exec_prefix=/usr/local/Cellar/gsl/2.6
libdir=/usr/local/Cellar/gsl/2.6/lib
includedir=/usr/local/Cellar/gsl/2.6/include
GSL_CBLAS_LIB=-lgslcblas

Name: GSL
Description: GNU Scientific Library
Version: 2.6
Libs: -L/usr/local/Cellar/gsl/2.6/lib -lgsl ${GSL_CBLAS_LIB}  -lm 
Cflags: -I/usr/local/Cellar/gsl/2.6/include

comment:19 Changed 21 months ago by mkoeppe

Probably best to take care of this on the giac upgrade ticket #29552

Last edited 21 months ago by mkoeppe (previous) (diff)

comment:20 Changed 21 months ago by fbissey

I never tried it, is it possible to override .pc defined variable by environment variables? I would guess not but that would be interesting.

comment:21 Changed 21 months ago by mkoeppe

We already take care of the gsl.pc file by installing a patched version in $SAGE_LOCAL/lib/pkgconfig.

So only libraries that do not use pkgconfig can still fall into the gslblas trap

comment:22 Changed 21 months ago by fbissey

Just for the record

$ pkg-config --libs gsl
-lgsl -lcblas -lm
$ pkg-config --define-variable=GSL_CBLAS_LIB=-lfoo --libs gsl
-lgsl -lfoo -lm

comment:23 follow-up: Changed 21 months ago by mkoeppe

Sure, but the problem is of course that the pkg-config invocation is usually in a package's configure script, so one cannot add the --define-variable without patching.

comment:24 in reply to: ↑ 23 Changed 21 months ago by fbissey

Replying to mkoeppe:

Sure, but the problem is of course that the pkg-config invocation is usually in a package's configure script, so one cannot add the --define-variable without patching.

Unfortunately you are right. It is even less useful than I thought it could be.

comment:25 in reply to: ↑ 6 Changed 21 months ago by mkoeppe

The gsl.pc business, by the way, also may explain the issues that jhpalmieri was reporting:

Replying to jhpalmieri:

Actually, I really don't understand the gsl issue. I started with make distclean and ./configure --with-system-gsl=no. [...] The confusing part: if I instead do make distclean, ./configure --with-system-gsl=no, and then make gsl, it succeeds. If I build the half dozen packages by hand (make cliquer etc.), then make gsl succeeds. So I don't know how to debug this side issue. Does plain make do something extra that make PKG doesn't do?

We currently install this .pc file but we do not have a clean uninstall mechanism. I have a plan for this in #29387, but I think this is Sage 9.3 territory.

comment:26 Changed 21 months ago by fbissey

Could be. There is actually a way to use --define-variable from configure scripts. Any configure script using pkg-config should include PKG_PROG_PKG_CONFIG which by default will look for the variable PKG_CONFIG for a user provided command, so that variable could be used to override the stuff we want by providing an expanded pkg-config command.

That's stretching things a bit. I am just putting it out there so we know the possibility exists. That doesn't help with the default giac configure script.

comment:27 Changed 21 months ago by mkoeppe

Thanks, that's good to know.

comment:28 Changed 21 months ago by mkoeppe

Let's continue with the discussion of changes to giac installation in #29552

comment:29 Changed 21 months ago by mkoeppe

  • Dependencies set to #29552

Please try with #29552. It seems to fix the problem for me -- but I have only tested this on top of #29456 (gcc/gfortran 10) and #27754 (python 3.8).

comment:30 in reply to: ↑ 18 ; follow-up: Changed 21 months ago by dimpase

Replying to mkoeppe:

homebrew's libgsl is underlinked and can be linked against openblas. But its gsl.pc uses gslcblas...:

can you report it on https://github.com/Homebrew/homebrew-core/blob/master/Formula/gsl.rb ?

prefix=/usr/local/Cellar/gsl/2.6
exec_prefix=/usr/local/Cellar/gsl/2.6
libdir=/usr/local/Cellar/gsl/2.6/lib
includedir=/usr/local/Cellar/gsl/2.6/include
GSL_CBLAS_LIB=-lgslcblas

Name: GSL
Description: GNU Scientific Library
Version: 2.6
Libs: -L/usr/local/Cellar/gsl/2.6/lib -lgsl ${GSL_CBLAS_LIB}  -lm 
Cflags: -I/usr/local/Cellar/gsl/2.6/include

comment:31 in reply to: ↑ 30 Changed 21 months ago by mkoeppe

Replying to dimpase:

Replying to mkoeppe:

homebrew's libgsl is underlinked and can be linked against openblas. But its gsl.pc uses gslcblas...:

can you report it on https://github.com/Homebrew/homebrew-core/blob/master/Formula/gsl.rb ?

There's no bug, it's working as intended

comment:32 Changed 21 months ago by jhpalmieri

Just #29552 doesn't fix it for me. I'll try with #29456 and/or #27754.

comment:33 Changed 21 months ago by mkoeppe

Could you check with otool -L whether there is still some gslcblas linked in local/lib, local/lib/python*/site-packages...?

comment:34 Changed 21 months ago by jhpalmieri

What command do you want me to run? otool -L alone gives me an error.

comment:35 Changed 21 months ago by mkoeppe

find local/lib -name "*.dylib" -o -name "*.so" | xargs otool -L

comment:36 Changed 21 months ago by jhpalmieri

If I do that followed by | grep gslcblas, it comes up empty.

comment:37 Changed 21 months ago by mkoeppe

In my test with the python 3.8 upgrade ticket, I used ./configure PYTHON3=/usr/local/opt/python@3.8/bin/python3.8 to make sure I get a homebrew-built python. Then one does not have to fight against Apple's system integrity protection when trying to attach a debugger to the process

comment:38 in reply to: ↑ 4 Changed 21 months ago by embray

Replying to dimpase:

Erik (in cc) was the last who changed parallel docbuild.

If noone understands the parallel docbuild system, it might be tempting to dump it, and replace by a straight sphinx build.

The current system looks like something inviting trouble, with explicit checks for OS flags, etc etc.

Problems that occur in parallel doc building are rarely related to the doc build system itself, but the fact of how it forks processes, and some libraries that have their own parallelism code (esp. things like PARI and OpenBlas?) sometimes do not play nicely in this environment. So usually it points to an issue with a specific library on a specific platform, rather than something to do with the docbuild itself.

comment:39 in reply to: ↑ 6 Changed 21 months ago by embray

Replying to jhpalmieri:

The problem goes away if I do

./configure --with-system-gsl=no --with-system-openblas=no

What version of OpenBLAS was it using from the system? Since I don't use MacOS I'm not familiar with OpenBLAS multiprocessing bugs on MacOS but it would not surprise me if it has one (as I have fixed problems with it on other platforms in the past, and it is not an area of expertise for most of the current maintainers).

comment:40 in reply to: ↑ 11 ; follow-up: Changed 21 months ago by embray

Replying to mkoeppe:

Replying to mkoeppe:

It needs to be investigated whether one of the worker processes hangs and therefore os.wait waits forever

This seems to be the case. Easier to test by setting SAGE_NUM_THREADS=1. Killing the worker process (unique child) with kill -INT had no effect. Killing it with kill -TERM leads to:

  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 285, in build_many
    raise worker_exc
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 257, in build_many
    if reap_workers(waited_pid, waited_exitcode):
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 215, in reap_workers
    w = bring_out_yer_dead(w, task, exitcode)
  File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", line 153, in bring_out_yer_dead
    "{}".format(task[1], w.exitcode))
sage_setup.docbuild.utils.WorkerDiedException: worker for ('en/constructions', 'html', {}) died with non-zero exit code -15
Uncaught exception. Entering post mortem debugging

That's a good intuition, as os.wait() is more likely than not the only place where this code can hang. But if some worker goes off into the weeds and never exits then os.wait() can hang on it forever (after all, it makes no assumption as to how long a worker should take).

I wonder what state the working process was in before you killed it. Was it running? Sleeping? Zombie? Was it using the CPU at all or not? Perhaps it would be useful if this code implemented a timeout for inactive workers.

Nevertheless it would need to be checked what code exactly is run when building that documentation section that is causing it to hang. I would not be surprised if it it's an np.dot() call buried in some plotting code (by way of matplotlib) as this is where this kind of issue has shown up during docbuilds in the past.

Last edited 21 months ago by embray (previous) (diff)

comment:41 in reply to: ↑ 40 ; follow-up: Changed 21 months ago by mkoeppe

Replying to embray:

That's a good intuition, as os.wait() is more likely than not the only place where this code can hang. But if some worker goes off into the weeds and never exits then os.wait() can hang on it forever (after all, it makes no assumption as to how long a worker should take).

I wonder what state the working process was in before you killed it. Was it running? Sleeping? Zombie? Was it using the CPU at all or not? Perhaps it would be useful if this code implemented a timeout for inactive workers.

See comment 13

comment:42 follow-up: Changed 21 months ago by mkoeppe

But that was before I fixed the gslcblas problem in #29552. Currently it works fine on my machine.

comment:43 Changed 21 months ago by jhpalmieri

Still doesn't work for me, with #29552 + #27754 + #29456. I just used ./configure, but config.log says result: python3-3.8.5, which is Homebrew's Python.

Other comments: I have both gcc and gcc@9 installed. brew info openblas says openblas: stable 0.3.10 (bottled), HEAD [keg-only].

comment:44 in reply to: ↑ 41 Changed 21 months ago by dimpase

Replying to mkoeppe:

Replying to embray:

That's a good intuition, as os.wait() is more likely than not the only place where this code can hang. But if some worker goes off into the weeds and never exits then os.wait() can hang on it forever (after all, it makes no assumption as to how long a worker should take).

I wonder what state the working process was in before you killed it. Was it running? Sleeping? Zombie? Was it using the CPU at all or not? Perhaps it would be useful if this code implemented a timeout for inactive workers.

See comment 13

another piece of info: ./sage -t --long src/sage/parallel all pass, but one gets a nasty pop-up saying that Python has quit unexpectedly, details as follows:

Process:               Python [72515]
Path:                  /usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.7.8 (3.7.8)
Code Type:             X86-64 (Native)
Parent Process:        Python [72394]
Responsible:           Terminal [1420]
User ID:               505

Date/Time:             2020-08-20 10:38:35.633 +0100
OS Version:            Mac OS X 10.15.6 (19G2021)
Report Version:        12
Bridge OS Version:     4.6 (17P6610)
Anonymous UUID:        06B914DC-3FFE-1EAC-F2D3-AF6B6B71DB13

Sleep/Wake UUID:       A42244D5-09C5-485D-8879-AF02012B886F

Time Awake Since Boot: 49000 seconds
Time Since Wake:       460 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0:
--> 
    __TEXT                 0000000103b21000-0000000103b23000 [    8K] r-x/r-x SM=COW  /usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python

Application Specific Information:
crashed on child side of fork pre-exec

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff6e07633a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6e132e60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff6df8d93e raise + 26
3   signals.cpython-37m-darwin.so 	0x0000000105561293 sigdie + 83
4   signals.cpython-37m-darwin.so 	0x0000000105561213 sigdie_for_sig + 307
5   libsystem_platform.dylib      	0x00007fff6e1275fd _sigtramp + 29
6   ???                           	000000000000000000 0 + 0
7   org.python.python             	0x0000000103b385d6 PyBytes_FromString + 19
8   _Users_dima__sage_temp_oucl13243_lan_72394_tmp_62k79rjh_pyx_0.cpython-37m-darwin.so	0x0000000154a983a5 __pyx_pw_61_Users_dima__sage_temp_oucl13243_lan_72394_tmp_62k79rjh_pyx_0_1f + 21 (_Users_dima__sage_temp_oucl13243_lan_72394_tmp_62k79rjh_pyx_0.c:1129)
9   org.python.python             	0x0000000103b40c8c _PyMethodDef_RawFastCallKeywords + 580
10  org.python.python             	0x0000000103b401b7 _PyCFunction_FastCallKeywords + 41
11  org.python.python             	0x0000000103bd5974 call_function + 628
12  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
13  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
14  org.python.python             	0x0000000103bd31da _PyEval_EvalFrameDefault + 26248
15  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
16  org.python.python             	0x0000000103b3fdec _PyFunction_FastCallDict + 444
17  org.python.python             	0x0000000103b40efb _PyObject_Call_Prepend + 131
18  org.python.python             	0x0000000103b402c4 PyObject_Call + 136
19  org.python.python             	0x0000000103bd31da _PyEval_EvalFrameDefault + 26248
20  org.python.python             	0x0000000103b4bc00 gen_send_ex + 244
21  org.python.python             	0x0000000103b5424d list_extend + 169
22  org.python.python             	0x0000000103b5544d list___init__ + 131
23  org.python.python             	0x0000000103b7b073 type_call + 172
24  org.python.python             	0x0000000103b40022 _PyObject_FastCallKeywords + 358
25  org.python.python             	0x0000000103bd59da call_function + 730
26  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
27  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
28  org.python.python             	0x0000000103b4017f _PyFunction_FastCallKeywords + 223
29  org.python.python             	0x0000000103bd59e1 call_function + 737
30  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
31  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
32  org.python.python             	0x0000000103bccaaf PyEval_EvalCode + 51
33  org.python.python             	0x0000000103bca54b builtin_exec + 563
34  org.python.python             	0x0000000103b40c2d _PyMethodDef_RawFastCallKeywords + 485
35  org.python.python             	0x0000000103b401b7 _PyCFunction_FastCallKeywords + 41
36  org.python.python             	0x0000000103bd5974 call_function + 628
37  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
38  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
39  org.python.python             	0x0000000103bd59e1 call_function + 737
40  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
41  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
42  org.python.python             	0x0000000103b4017f _PyFunction_FastCallKeywords + 223
43  org.python.python             	0x0000000103bd59e1 call_function + 737
44  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
45  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
46  org.python.python             	0x0000000103b4017f _PyFunction_FastCallKeywords + 223
47  org.python.python             	0x0000000103bd59e1 call_function + 737
48  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
49  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
50  org.python.python             	0x0000000103bd59e1 call_function + 737
51  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
52  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
53  org.python.python             	0x0000000103b3fdec _PyFunction_FastCallDict + 444
54  org.python.python             	0x0000000103b40efb _PyObject_Call_Prepend + 131
55  org.python.python             	0x0000000103b7d955 slot_tp_call + 71
56  org.python.python             	0x0000000103b40022 _PyObject_FastCallKeywords + 358
57  org.python.python             	0x0000000103bd59da call_function + 730
58  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
59  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
60  org.python.python             	0x0000000103bd59e1 call_function + 737
61  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
62  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
63  org.python.python             	0x0000000103bd59e1 call_function + 737
64  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
65  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
66  org.python.python             	0x0000000103bd59e1 call_function + 737
67  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
68  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
69  org.python.python             	0x0000000103b40efb _PyObject_Call_Prepend + 131
70  org.python.python             	0x0000000103b7e349 slot_tp_init + 80
71  org.python.python             	0x0000000103b7b073 type_call + 172
72  org.python.python             	0x0000000103b40022 _PyObject_FastCallKeywords + 358
73  org.python.python             	0x0000000103bd59da call_function + 730
74  org.python.python             	0x0000000103bd2f4e _PyEval_EvalFrameDefault + 25596
75  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
76  org.python.python             	0x0000000103bd59e1 call_function + 737
77  org.python.python             	0x0000000103bd2ea8 _PyEval_EvalFrameDefault + 25430
78  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
79  org.python.python             	0x0000000103bd59e1 call_function + 737
80  org.python.python             	0x0000000103bd2ea8 _PyEval_EvalFrameDefault + 25430
81  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
82  org.python.python             	0x0000000103bd59e1 call_function + 737
83  org.python.python             	0x0000000103bd2ea8 _PyEval_EvalFrameDefault + 25430
84  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
85  org.python.python             	0x0000000103b4017f _PyFunction_FastCallKeywords + 223
86  org.python.python             	0x0000000103bd59e1 call_function + 737
87  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
88  org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
89  org.python.python             	0x0000000103b4017f _PyFunction_FastCallKeywords + 223
90  org.python.python             	0x0000000103bd59e1 call_function + 737
91  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
92  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
93  org.python.python             	0x0000000103bd59e1 call_function + 737
94  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
95  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
96  org.python.python             	0x0000000103bd59e1 call_function + 737
97  org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
98  org.python.python             	0x0000000103b4058b function_code_fastcall + 106
99  org.python.python             	0x0000000103bd59e1 call_function + 737
100 org.python.python             	0x0000000103bd2e8c _PyEval_EvalFrameDefault + 25402
101 org.python.python             	0x0000000103bd61c5 _PyEval_EvalCodeWithName + 1682
102 org.python.python             	0x0000000103bccaaf PyEval_EvalCode + 51
103 org.python.python             	0x0000000103bfb264 run_mod + 54
104 org.python.python             	0x0000000103bfa28f PyRun_FileExFlags + 160
105 org.python.python             	0x0000000103bf9946 PyRun_SimpleFileExFlags + 270
106 org.python.python             	0x0000000103c11f9a pymain_main + 5034
107 org.python.python             	0x0000000103c12794 _Py_UnixMain + 56
108 libdyld.dylib                 	0x00007fff6df2ecc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000000010e324dc0  rcx: 0x00007ffeec0d9418  rdx: 0x0000000000000000
  rdi: 0x0000000000000303  rsi: 0x000000000000000b  rbp: 0x00007ffeec0d9440  rsp: 0x00007ffeec0d9418
   r8: 0x00000000000130a8   r9: 0x0000000000000000  r10: 0x000000010e324dc0  r11: 0x0000000000000246
  r12: 0x0000000000000303  r13: 0x0000000154a9a238  r14: 0x000000000000000b  r15: 0x0000000000000016
  rip: 0x00007fff6e07633a  rfl: 0x0000000000000246  cr2: 0x000000010e2f74c0
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


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so this is on Homebrew's Python 3.7.

comment:45 in reply to: ↑ 42 ; follow-up: Changed 21 months ago by dimpase

Replying to mkoeppe:

But that was before I fixed the gslcblas problem in #29552. Currently it works fine on my machine.

is #29552 the correct ticket here? I don't see what it did with gslblas.

comment:46 Changed 21 months ago by dimpase

#29552 does not help, the docbuild still hangs in the same way.

Last edited 21 months ago by slelievre (previous) (diff)

comment:47 Changed 21 months ago by dimpase

the following in sage_setup/docbuild/utils.py

  from multiprocessing import Process, Queue, cpu_count
  from six.moves.queue import Empty
 ...
  result_queue = Queue()
 ...
       # Get result from the queue; depending on ordering this may not be
       # *the* result for this worker, but for each completed worker there
       # should be *a* result so let's get it
       try:
           result = result_queue.get_nowait()
       except Empty:
           # Generally shouldn't happen but could in case of a race condition;
           # don't worry we'll collect any remaining results at the end.
           pass

looks dodgy to me. Why would Queue from multiprocessing throw Empty from some obsolete class ?

(that six must go in any case)

comment:48 Changed 21 months ago by dimpase

this code should be corrected to be

from queue import Empty

(this isEmpty used in Queue in question)

comment:49 in reply to: ↑ 45 Changed 21 months ago by mkoeppe

Replying to dimpase:

Replying to mkoeppe:

But that was before I fixed the gslcblas problem in #29552. Currently it works fine on my machine.

is #29552 the correct ticket here? I don't see what it did with gslblas.

Yes, it patches configure (via spkg-src) so that it links gsl against openblas.

comment:50 Changed 21 months ago by dimpase

  • Work issues set to ensure OMP_NUM_THREADS=1

I think I found the root of the problem, it is OpenMP used in Homebrew's openblas. Namely, the build completes if I do

$ OMP_NUM_THREADS=1 make

so this is probably a bug in OpenMP on macOS 10.15, or something like this.

comment:51 Changed 21 months ago by dimpase

running test without OMP_NUM_THREADS=1 leads to quite a few errors of the kind

age: show(plot(sin(x) + sin(1.6*x), 0, 40)) ## line 69 ##
------------------------------------------------------------------------
0   signals.cpython-37m-darwin.so       0x0000000103afa4e2 print_backtrace + 66
1   signals.cpython-37m-darwin.so       0x0000000103afe267 sigdie + 39
2   signals.cpython-37m-darwin.so       0x0000000103afe1a0 sigdie_for_sig + 192
3   libsystem_platform.dylib            0x00007fff6e1275fd _sigtramp + 29
4   ???                                 0x0000000154b3c850 0x0 + 5716035664
5   libgomp.1.dylib                     0x0000000105fce2cb gomp_sem_wait + 43
------------------------------------------------------------------------

(and libgomp.1.dylib always last features in such a stackdump)

Can we do anything about it, or we just hardcode OMP_NUM_THREADS=1 for Darwin?

comment:52 Changed 21 months ago by mkoeppe

In src/bin/sage-env we already set OPENBLAS_NUM_THREADS=1 with comment that sounds like it is/was a workaround for something similar...

comment:53 Changed 21 months ago by mkoeppe

Also which libgomp is this? Perhaps this is another library version mismatch between gcc 9 and 10?

comment:54 Changed 21 months ago by dimpase

this libopenmp comes with gcc/gfortran (used in Homebrew's openblas)

% otool -L /usr/local/Cellar/openblas/0.3.10_1/lib/libopenblas.dylib
/usr/local/Cellar/openblas/0.3.10_1/lib/libopenblas.dylib:
	/usr/local/opt/openblas/lib/libopenblas.0.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/usr/local/opt/gcc/lib/gcc/10/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.100.1)
	/usr/local/opt/gcc/lib/gcc/10/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/local/lib/gcc/10/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

comment:55 Changed 21 months ago by dimpase

there is also

   # Limit the number of threads to 2 to save system resources.
    # See Trac #23713 and #23892
    os.environ["OMP_NUM_THREADS"] = "2"

in src/bin/sage-runtests

So we should look at #23713 and #23892

Last edited 21 months ago by dimpase (previous) (diff)

comment:56 Changed 21 months ago by mkoeppe

Question is whether other libraries might be linked to another version of libgomp...

comment:57 Changed 21 months ago by dimpase

I don't think there is another version of libgomp on the box. Homebrew provides libomp (no g in the name) - but it is not installed.

comment:59 Changed 21 months ago by dimpase

make ptest passes for me with

  • src/bin/sage-runtests

    diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
    index 32d3fddc77..2bb55ea41f 100755
    a b if __name__ == "__main__": 
    171171
    172172    # Limit the number of threads to 2 to save system resources.
    173173    # See Trac #23713 and #23892
    174     os.environ["OMP_NUM_THREADS"] = "2"
     174    os.environ["OMP_NUM_THREADS"] = "1"
    175175    os.environ["SAGE_NUM_THREADS"] = "2"
    176176
    177177    from sage.doctest.control import DocTestController

comment:60 follow-up: Changed 21 months ago by jhpalmieri

So we need OMP_NUM_THREADS=1 both to build the docs and in sage-runtests, right? Does it have to be set when actually building Sage?

comment:61 in reply to: ↑ 60 Changed 21 months ago by dimpase

Replying to jhpalmieri:

So we need OMP_NUM_THREADS=1 both to build the docs and in sage-runtests, right? Does it have to be set when actually building Sage?

OpenMP is either not used for building, or it does, but it is invoked correctly. Also, there are different flavours of OpenMP available on macOS

And OpenMP can be statically linked, too...

Changed 21 months ago by dimpase

demo of hangs with OMP_NUM_THREADS>1

comment:62 Changed 21 months ago by arojas

  • Cc arojas removed

comment:63 Changed 21 months ago by dimpase

I attached a fixed for Python 3 code from https://stackoverflow.com/questions/15414027/multiprocessing-pool-makes-numpy-matrix-multiplication-slower/15415690#15415690

which demonstrates hangs on macOS 10.15. It works with OMP_NUM_THREADS=1 ./sage --python t.py but hangs with OMP_NUM_THREADS=2 ./sage --python t.py. It uses multiprocessing.Process and numpy (which in turn uses OpenMP-enabled openblas).

OMP_NUM_THREADS=2 ./sage --python t.py
Creating input matrices in parent process.
Crunching input with 1 child(ren).

I presume it can be cut down to a smaller quicker test (I which it did crash rather than hang though :-))

Last edited 21 months ago by dimpase (previous) (diff)

comment:64 Changed 21 months ago by dimpase

In contrast, on Linux with OpenMP-enabled openblas, Crunching input with 1 child(ren). always succeeds if OMP_NUM_THREADS=2. [With more than 1 child it's hit and miss, probably due to some bug in the Python code.]

comment:65 Changed 21 months ago by jhpalmieri

With these changes, everything works for me:

  • build/bin/sage-site

    diff --git a/build/bin/sage-site b/build/bin/sage-site
    index 44d8e3acff..33437d30ba 100755
    a b if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then 
    157157    # cause the build to hang. If stdin is /dev/null, TeX just aborts.
    158158    shift
    159159    export LANG=C # to ensure it is possible to scrape out non-EN locale warnings
     160    # See #30351: bugs in OS X implementations of openblas can cause
     161    # doctesting to hang if multiple threads are allowed.
     162    if [ `uname` = 'Darwin' ]; then
     163        export OMP_NUM_THREADS=1
     164    fi
    160165    exec sage-python -m sage_setup.docbuild "$@" </dev/null
    161166fi
    162167
  • src/bin/sage-runtests

    diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
    index 32d3fddc77..4abf396a0b 100755
    a b if __name__ == "__main__": 
    170170                    options.memlimit = -1
    171171
    172172    # Limit the number of threads to 2 to save system resources.
    173     # See Trac #23713 and #23892
    174     os.environ["OMP_NUM_THREADS"] = "2"
     173    # See Trac #23713, #23892, #30351
     174    if sys.platform == 'darwin':
     175        os.environ["OMP_NUM_THREADS"] = "1"
     176    else:
     177        os.environ["OMP_NUM_THREADS"] = "2"
    175178    os.environ["SAGE_NUM_THREADS"] = "2"
    176179
    177180    from sage.doctest.control import DocTestController

comment:66 Changed 21 months ago by dimpase

The question is whether allowing OMP_NUM_THREADS>1 after the build leaves Sage broken - I think tests in src/sage/parallel/ need to be improved to involve numpy calls (with OMP_NUM_THREADS>1) to test for the situation we have here.

comment:67 Changed 21 months ago by jhpalmieri

I think adding doctests would be good. For me, though, running doctests on the file src/doc/en/a_tour_of_sage/index.rst leads to a hang (as you say in comment:54), but running those tests one by one in the Sage console does not lead to a hang. Does this mean that Sage itself is not broken, only something in the doctesting framework?

comment:68 Changed 21 months ago by dimpase

The problem is that Sage (and Python - cf. attachment :-)) contains multiprocessing/parallel stuff which uses fork(), and thus does not play well with extension modules, e.g. numpy, which may use OpenMP (in particular an implementation of OpenMP that is not fork-safe, such as libgopenmp).

So in principle this means that Sage was already broken years ago :-)

I think that in addition to the patch at comment:65, some docs should be updated to reflect the issue.

comment:69 Changed 21 months ago by dimpase

I tried

  • src/bin/sage-runtests

    a b def _get_optional_defaults(): 
    2727
    2828
    2929if __name__ == "__main__":
     30    import multiprocessing
     31    multiprocessing.set_start_method('spawn')
     32
    3033    parser = optparse.OptionParser()
    3134
    3235    def optional_argument(option, opt_str, value, parser, typ, default_arg):

instead of os.environ["OMP_NUM_THREADS"] = "1", but this immediately errors out with

$ make test
...
Traceback (most recent call last):
  File "/Users/dima/software/sagetrac-mirror/src/bin/sage-runtests", line 182, in <module>
    err = DC.run()
  File "/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage/doctest/control.py", line 1230, in run
    self.run_doctests()
  File "/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage/doctest/control.py", line 931, in run_doctests
    self.dispatcher.dispatch()
  File "/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2046, in dispatch
    self.parallel_dispatch()
  File "/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1941, in parallel_dispatch
    w.start()  # This might take some time
  File "/Users/dima/software/sagetrac-mirror/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 2213, in start
    super(DocTestWorker, self).start()
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/process.py", line 112, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/context.py", line 223, in _Popen
    return _default_context.get_context().Process._Popen(process_obj)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/context.py", line 284, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/popen_fork.py", line 20, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/popen_spawn_posix.py", line 47, in _launch
    reduction.dump(process_obj, fp)
  File "/usr/local/Cellar/python@3.7/3.7.8_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/multiprocessing/reduction.py", line 60, in dump
    ForkingPickler(file, protocol).dump(obj)
AttributeError: Can't pickle local object 'DocTestDispatcher.parallel_dispatch.<locals>.sel_exit'

This is due to spawn using a different way to copy local data into another thread - probably it can be fixed, but not so easy.


similar problem pops up trying spawn with the docbuilding.

Last edited 21 months ago by dimpase (previous) (diff)

comment:70 Changed 21 months ago by dimpase

  • Authors set to Dima Pasechnik
  • Branch set to public/ticket/30351public/ticket/30351
  • Reviewers set to John Palmieri
  • Status changed from new to needs_review
  • Work issues ensure OMP_NUM_THREADS=1 deleted

comment:71 Changed 21 months ago by dimpase

  • Branch changed from public/ticket/30351public/ticket/30351 to public/ticket/30351
  • Commit set to f8dcff3edb530322723ee2773f46cecc090ba29c

New commits:

f8dcff3on macOS set OMP_NUM_THREADS to 1 for docbuild and tests

comment:72 Changed 21 months ago by dimpase

  • Dependencies changed from #29552 to #29552, #29456

to try this on home-brew, one needs to install a fresh openblas, which in turn needs #29456 (that's why I put the latter In deps, it's not yet in beta)

comment:73 Changed 21 months ago by dimpase

I've tested this on the macOS 10.15.6, with updated Homebrew with all the packages we can use in Sage, used (with #29552, #29456) - all tests pass.

comment:74 Changed 21 months ago by git

  • Commit changed from f8dcff3edb530322723ee2773f46cecc090ba29c to 488bba4768c034c741fa7e929168d354a5a86306

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

488bba4on macOS set OMP_NUM_THREADS to 1 for docbuild and tests

comment:75 Changed 21 months ago by dimpase

  • Dependencies changed from #29552, #29456 to #29552

rebased over beta10

comment:76 Changed 21 months ago by git

  • Commit changed from 488bba4768c034c741fa7e929168d354a5a86306 to 4b11a706e1267b385099d8691b4468efd974f94d

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

4b11a70use the correct import location, not six.*

comment:77 Changed 21 months ago by jhpalmieri

  • Status changed from needs_review to positive_review

This works for me (although I didn't use #29552).

comment:78 Changed 21 months ago by dcoudert

while running make ptest, I got the following time outs

sage -t --random-seed=0 src/sage/dynamics/arithmetic_dynamics/projective_ds.py  # Timed out
sage -t --random-seed=0 src/sage/manifolds/differentiable/tensorfield.py  # Timed out
sage -t --random-seed=0 src/sage/plot/plot.py  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/base.pyx  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/implicit_plot3d.py  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/parametric_plot3d.py  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/plot3d.py  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/shapes.pyx  # Timed out
sage -t --random-seed=0 src/sage/plot/plot3d/shapes2.py  # Timed out
sage -t --random-seed=0 src/sage/schemes/elliptic_curves/ell_number_field.py  # Timed out

but the tests pass independently, e.g.,

sapristi:sage dcoudert$ ./sage -tp src/sage/dynamics/arithmetic_dynamics/projective_ds.py
Running doctests with ID 2020-08-25-19-17-07-e834b51b.
Git branch: HEAD
Using --optional=benzene,bliss,build,dochtml,igraph,plantri,python_igraph,sage,tdlib
Doctesting 1 file using 8 threads.
sage -t --warn-long 138.0 --random-seed=0 src/sage/dynamics/arithmetic_dynamics/projective_ds.py
    [1238 tests, 71.66 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 71.9 seconds
    cpu time: 59.7 seconds
    cumulative wall time: 71.7 seconds

So for me it's ok too. Thank you all !

comment:79 Changed 21 months ago by vbraun

  • Branch changed from public/ticket/30351 to 4b11a706e1267b385099d8691b4468efd974f94d
  • Resolution set to fixed
  • Status changed from positive_review to closed
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