Fix building html documentation on macOS
slel opened this issue · 90 comments
slel commented
Building html documentation fails on macOS for Sage 9.2.beta8.
Initial report:
Depends on #29552
CC: @jhpalmieri @slel @embray @kiwifb @kwankyu @tscrim @fchapoton @vbraun
Component: build
Author: Dima Pasechnik
Branch/Commit: 4b11a70
Reviewer: John Palmieri
Issue created by migration from https://trac.sagemath.org/ticket/30351
slel commented
jhpalmieri commented
dimpase commented
comment:4
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.
slel commented
comment:5
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.
jhpalmieri commented
comment:6
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?
jhpalmieri commented
comment:7
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?
mkoeppe commented
comment:8
At which point during the docbuild does it hang?
Does make doc-html-no-plot also hang?
mkoeppe commented
comment:9
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.
mkoeppe commented
comment:10
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.
mkoeppe commented
comment:11
Replying to @mkoeppe:
It needs to be investigated whether one of the worker processes hangs and therefore
os.waitwaits 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
jhpalmieri commented
comment:12
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?
mkoeppe commented
comment:13
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.docbuildmight interfere with the pthreads implementation - gsl confused about gslblas vs openblas
mkoeppe commented
comment:14
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)
kiwifb commented
comment:15
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
slel commented
Changed keywords from none to macos, openblas, glsblas, giac
kiwifb commented
Changed keywords from macos, openblas, glsblas, giac to none
kiwifb commented
comment:17
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.
mkoeppe commented
comment:18
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
kiwifb commented
comment:20
I never tried it, is it possible to override .pc defined variable by environment variables? I would guess not but that would be interesting.
mkoeppe commented
comment:21
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
kiwifb commented
comment:22
Just for the record
$ pkg-config --libs gsl
-lgsl -lcblas -lm
$ pkg-config --define-variable=GSL_CBLAS_LIB=-lfoo --libs gsl
-lgsl -lfoo -lm
mkoeppe commented
comment:23
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.
kiwifb commented
comment:24
Replying to @mkoeppe:
Sure, but the problem is of course that the pkg-config invocation is usually in a package's
configurescript, so one cannot add the--define-variablewithout patching.
Unfortunately you are right. It is even less useful than I thought it could be.
mkoeppe commented
comment:25
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
gslissue. I started withmake distcleanand./configure --with-system-gsl=no. [...]
The confusing part: if I instead domake distclean,./configure --with-system-gsl=no, and thenmake gsl, it succeeds. If I build the half dozen packages by hand (make cliqueretc.), thenmake gslsucceeds. So I don't know how to debug this side issue. Does plainmakedo something extra thatmake PKGdoesn'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.
kiwifb commented
comment:26
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.
mkoeppe commented
comment:27
Thanks, that's good to know.
mkoeppe commented
comment:28
Let's continue with the discussion of changes to giac installation in #29552
mkoeppe commented
dimpase commented
comment:30
Replying to @mkoeppe:
homebrew's libgsl is underlinked and can be linked against openblas.
But itsgsl.pcuses 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
mkoeppe commented
comment:31
Replying to @dimpase:
Replying to @mkoeppe:
homebrew's libgsl is underlinked and can be linked against openblas.
But itsgsl.pcuses 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
jhpalmieri commented
mkoeppe commented
comment:33
Could you check with otool -L whether there is still some gslcblas linked in local/lib, local/lib/python*/site-packages...?
jhpalmieri commented
comment:34
What command do you want me to run? otool -L alone gives me an error.
mkoeppe commented
comment:35
find local/lib -name "*.dylib" -o -name "*.so" | xargs otool -L
jhpalmieri commented
comment:36
If I do that followed by | grep gslcblas, it comes up empty.
mkoeppe commented
comment:37
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
embray commented
comment:38
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.
embray commented
comment:39
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).
embray commented
comment:40
Replying to @mkoeppe:
Replying to @mkoeppe:
It needs to be investigated whether one of the worker processes hangs and therefore
os.waitwaits foreverThis seems to be the case. Easier to test by setting
SAGE_NUM_THREADS=1. Killing the worker process (unique child) withkill -INThad no effect. Killing it withkill -TERMleads 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.
mkoeppe commented
comment:41
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 thenos.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
mkoeppe commented
comment:42
But that was before I fixed the gslcblas problem in #29552. Currently it works fine on my machine.
jhpalmieri commented
dimpase commented
comment:44
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 thenos.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
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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
Binary Images:
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0x7fff6df14000 - 0x7fff6df4afff libdyld.dylib (750.6) <789A18C2-8AC7-3C88-813D-CD674376585D> /usr/lib/system/libdyld.dylib
0x7fff6df4b000 - 0x7fff6df4bffb libkeymgr.dylib (30) <DB3337BE-01CA-3425-BD0C-87774FC0CDC0> /usr/lib/system/libkeymgr.dylib
0x7fff6df4c000 - 0x7fff6df58ff3 libkxld.dylib (6153.141.1) <756B1F0D-2E37-31A7-A6F0-2E5C22E62C3D> /usr/lib/system/libkxld.dylib
0x7fff6df59000 - 0x7fff6df59ff7 liblaunch.dylib (1738.140.1) <AFBCBDD3-0B55-3ECD-8E04-A73A3A57356B> /usr/lib/system/liblaunch.dylib
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0x7fff6df63000 - 0x7fff6df64ff7 libremovefile.dylib (48) <7C7EFC79-BD24-33EF-B073-06AED234593E> /usr/lib/system/libremovefile.dylib
0x7fff6df65000 - 0x7fff6df7cff3 libsystem_asl.dylib (377.60.2) <1563EE02-0657-3B78-99BE-A947C24122EF> /usr/lib/system/libsystem_asl.dylib
0x7fff6df7d000 - 0x7fff6df7dff7 libsystem_blocks.dylib (74) <0D53847E-AF5F-3ACF-B51F-A15DEA4DEC58> /usr/lib/system/libsystem_blocks.dylib
0x7fff6df7e000 - 0x7fff6e005fff libsystem_c.dylib (1353.100.2) <BBDED5E6-A646-3EED-B33A-91E4331EA063> /usr/lib/system/libsystem_c.dylib
0x7fff6e006000 - 0x7fff6e009ffb libsystem_configuration.dylib (1061.141.1) <0EE84C33-64FD-372B-974A-AF7A136F2068> /usr/lib/system/libsystem_configuration.dylib
0x7fff6e00a000 - 0x7fff6e00dfff libsystem_coreservices.dylib (114) <A199156E-058D-3ABB-BCE9-4B9F20DCED0F> /usr/lib/system/libsystem_coreservices.dylib
0x7fff6e00e000 - 0x7fff6e016fff libsystem_darwin.dylib (1353.100.2) <5B12B5DB-3F30-37C1-8ECC-49A66B1F2864> /usr/lib/system/libsystem_darwin.dylib
0x7fff6e017000 - 0x7fff6e01efff libsystem_dnssd.dylib (1096.100.3) <EBB4C2C2-E031-3094-B40A-E67BF261D295> /usr/lib/system/libsystem_dnssd.dylib
0x7fff6e01f000 - 0x7fff6e020ffb libsystem_featureflags.dylib (17) <29FD922A-EC2C-3F25-BCCC-B58D716E60EC> /usr/lib/system/libsystem_featureflags.dylib
0x7fff6e021000 - 0x7fff6e06eff7 libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib
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0x7fff6e09c000 - 0x7fff6e0e3fff libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib
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0x7fff6e10c000 - 0x7fff6e119ffb libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib
0x7fff6e11a000 - 0x7fff6e123ff7 libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib
0x7fff6e124000 - 0x7fff6e12cfef libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib
0x7fff6e12d000 - 0x7fff6e137fff libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib
0x7fff6e138000 - 0x7fff6e13cff3 libsystem_sandbox.dylib (1217.141.1) <6DE13684-5A67-3009-A53A-C9086CF241C3> /usr/lib/system/libsystem_sandbox.dylib
0x7fff6e13d000 - 0x7fff6e13ffff libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib
0x7fff6e140000 - 0x7fff6e147ffb libsystem_symptoms.dylib (1238.120.1) <5820A2AF-CE72-3AB3-ABCC-273A3419FB55> /usr/lib/system/libsystem_symptoms.dylib
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 102328
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=681.2M resident=0K(0%) swapped_out_or_unallocated=681.2M(100%)
Writable regions: Total=375.6M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=375.6M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Kernel Alloc Once 8K 1
MALLOC 126.2M 107
MALLOC guard page 16K 4
MALLOC_LARGE (reserved) 768K 3 reserved VM address space (unallocated)
SBRK (reserved) 4096K 1 reserved VM address space (unallocated)
STACK GUARD 4K 1
Stack 18.0M 3
Stack Guard 4K 1
VM_ALLOCATE 1.0G 488
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 28.7M 846
__DATA_CONST 3536K 491
__LINKEDIT 438.4M 496
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 242.9M 615
__UNICODE 564K 1
mapped file 4K 1
shared memory 12K 3
=========== ======= =======
TOTAL 1.9G 3066
TOTAL, minus reserved VM space 1.9G 3066
Model: MacBookPro15,2, BootROM 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0), 4 processors, Quad-Core Intel Core i5, 2.4 GHz, 16 GB, SMC
Graphics: kHW_IntelIrisGraphics655Item, Intel Iris Plus Graphics 655, spdisplays_builtin
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, LPDDR3, 2133 MHz, Samsung, K4EBE304EC-EGCG
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, LPDDR3, 2133 MHz, Samsung, K4EBE304EC-EGCG
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Feb 28 2020 15:24:56 version 9.30.357.35.32.5.47 FWID 01-9ce4adf3
Bluetooth: Version 7.0.6f7, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB 3.1 Bus
USB Device: Apple T2 Bus
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4
so this is on Homebrew's Python 3.7.
dimpase commented
dimpase commented
comment:47
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)
dimpase commented
comment:48
this code should be corrected to be
from queue import Empty
(this isEmpty used in Queue in question)
mkoeppe commented
comment:49
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.
dimpase commented
comment:50
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.
dimpase commented
Work Issues: ensure OMP_NUM_THREADS=1
dimpase commented
comment:51
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?
mkoeppe commented
comment:52
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...
mkoeppe commented
comment:53
Also which libgomp is this? Perhaps this is another library version mismatch between gcc 9 and 10?
dimpase commented
comment:54
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)
dimpase commented
mkoeppe commented
comment:56
Question is whether other libraries might be linked to another version of libgomp...
dimpase commented
comment:57
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.
dimpase commented
comment:58
The problem is perhaps due to libgomp not being fork-safe, see https://joblib.readthedocs.io/en/latest/parallel.html#bad-interaction-of-multiprocessing-and-third-party-libraries
dimpase commented
comment:59
make ptest passes for me with
diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
index 32d3fddc77..2bb55ea41f 100755
--- a/src/bin/sage-runtests
+++ b/src/bin/sage-runtests
@@ -171,7 +171,7 @@ if __name__ == "__main__":
# Limit the number of threads to 2 to save system resources.
# See Trac #23713 and #23892
- os.environ["OMP_NUM_THREADS"] = "2"
+ os.environ["OMP_NUM_THREADS"] = "1"
os.environ["SAGE_NUM_THREADS"] = "2"
from sage.doctest.control import DocTestControllerjhpalmieri commented
comment:60
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?
dimpase commented
comment:61
Replying to @jhpalmieri:
So we need
OMP_NUM_THREADS=1both to build the docs and insage-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
- libgomp (from gcc), not fork-safe
- libiomp5 (from MKL - Intel's blas/lapack) -
- libomp (from LLVM/Clang, https://formulae.brew.sh/formula/libomp) fork-safe
And OpenMP can be statically linked, too...
dimpase commented
comment:63
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 :-))
dimpase commented
comment:64
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.]
jhpalmieri commented
comment:65
With these changes, everything works for me:
diff --git a/build/bin/sage-site b/build/bin/sage-site
index 44d8e3acff..33437d30ba 100755
--- a/build/bin/sage-site
+++ b/build/bin/sage-site
@@ -157,6 +157,11 @@ if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
# cause the build to hang. If stdin is /dev/null, TeX just aborts.
shift
export LANG=C # to ensure it is possible to scrape out non-EN locale warnings
+ # See #30351: bugs in OS X implementations of openblas can cause
+ # doctesting to hang if multiple threads are allowed.
+ if [ `uname` = 'Darwin' ]; then
+ export OMP_NUM_THREADS=1
+ fi
exec sage-python -m sage_setup.docbuild "$@" </dev/null
fi
diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
index 32d3fddc77..4abf396a0b 100755
--- a/src/bin/sage-runtests
+++ b/src/bin/sage-runtests
@@ -170,8 +170,11 @@ if __name__ == "__main__":
options.memlimit = -1
# Limit the number of threads to 2 to save system resources.
- # See Trac #23713 and #23892
- os.environ["OMP_NUM_THREADS"] = "2"
+ # See Trac #23713, #23892, #30351
+ if sys.platform == 'darwin':
+ os.environ["OMP_NUM_THREADS"] = "1"
+ else:
+ os.environ["OMP_NUM_THREADS"] = "2"
os.environ["SAGE_NUM_THREADS"] = "2"
from sage.doctest.control import DocTestControllerdimpase commented
comment:66
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.
jhpalmieri commented
comment:67
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?
dimpase commented
comment:68
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.
dimpase commented
comment:69
I tried
--- a/src/bin/sage-runtests
+++ b/src/bin/sage-runtests
@@ -27,6 +27,9 @@ def _get_optional_defaults():
if __name__ == "__main__":
+ import multiprocessing
+ multiprocessing.set_start_method('spawn')
+
parser = optparse.OptionParser()
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.
dimpase commented
Changed work issues from ensure OMP_NUM_THREADS=1 to none
dimpase commented
Reviewer: John Palmieri
dimpase commented
Author: Dima Pasechnik
dimpase commented
dimpase commented
Changed branch from public/ticket/30351public/ticket/30351 to public/ticket/30351
dimpase commented
comment:72
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)
dimpase commented
sagetrac-git commented
sagetrac-git commented
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
488bba4 | on macOS set OMP_NUM_THREADS to 1 for docbuild and tests |
dimpase commented
comment:75
rebased over beta10
sagetrac-git commented
Branch pushed to git repo; I updated commit sha1. New commits:
4b11a70 | use the correct import location, not six.* |
sagetrac-git commented
jhpalmieri commented
comment:77
This works for me (although I didn't use #29552).
dcoudert commented
comment:78
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 !
vbraun commented
Changed branch from public/ticket/30351 to 4b11a70