Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Dima Pasechnik]

this is most probably https://trac.sagemath.org/ticket/32424

On Wed, 1 Sep 2021, 22:30 Max Alekseyev,  wrote:

> I'm also seeing illegal instruction in Sage 9.3 and 9.4 (and not in 9.2)
> while doing some linear algebra, although I'm not sure if it's the same bug
> or not.
> In either case, my bugreport is submitted to
> https://trac.sagemath.org/ticket/32447
>
> Regards,
> Max
>
> On Thursday, August 26, 2021 at 2:38:10 PM UTC-4 Nathan Dunfield wrote:
>
>> I suspect the cause is OpenBLAS.  While this library is built with
>> DYNAMIC_ARCH=1, there is still the non-performance critical code which will
>> use whatever instructions are available on the machine at compile time
>> unless you also set TARGET.  See
>>
>> https://github.com/xianyi/OpenBLAS/issues/3056
>>
>> For the macOS app, Marc Culler had to set TARGET=CORE2 so that it would
>> run on a 2013 cylindrical Mac Pro (this version is not yet posted).
>>
>> Best,
>>
>> Nathan
>>
>> On Wednesday, August 25, 2021 at 10:15:02 PM William Stein wrote:
>>
>>> Hi,
>>>
>>> I release cocalc-docker ([1], [2]) a few days ago with sage-9.4, and had
>>> people reporting back "illegal instruction" issues.  Sage is built there
>>> with SAGE_FAT_BINARY="yes", using this script [3].  One person who reported
>>> a problem had a "Dell PowerEdge R710." and I built on an intel Dell
>>> PowerEdge R630, for what it is worth.  They got the error "An illegal
>>> instructor occurred" when computing "5+2" in Sage.
>>>
>>> My solution for now is to keep cocalc-docker at sage-9.3 for the time
>>> being, and suggest that people build sage from source on their own machine
>>> if necessary.   I'll let you know if I have any further information, but I
>>> just wanted to add this data point.
>>>
>>> [1] https://github.com/sagemathinc/cocalc-docker
>>> [2] https://hub.docker.com/r/sagemathinc/cocalc
>>> [3]
>>> https://github.com/sagemathinc/cocalc-docker/blob/master/scripts/install_sage.sh
>>>
>>> On Wednesday, August 25, 2021 at 8:57:44 AM UTC-7 Marco Streng wrote:
>>>
 In the end I build 9.4 from source and that worked perfectly. And it
 turned out that the Ubuntu 18.04 binaries of 9.2 also work on this
 particular machine (though we went for 9.4 in the end). Thanks again for
 the help.

 Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:

> 2021-08-24 05:48 UTC, Dima Pasechnik:
> >
> > These "illegal instruction" errors are an indication
> > that the binary was built for a more advanced CPU
> > than yours - which does not support certain CPU
> > commands. It's a bug in "fat binary" build process
> > we see for some time.
> >
> > Build Sage yourself, or use Conda.
>
> I opened a ticket at binary-pkg for that:
> https://github.com/sagemath/binary-pkg/issues/31
>
 --
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> 
> .
>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Max Alekseyev]

I'm also seeing illegal instruction in Sage 9.3 and 9.4 (and not in 9.2) 
while doing some linear algebra, although I'm not sure if it's the same bug 
or not.
In either case, my bugreport is submitted 
to https://trac.sagemath.org/ticket/32447

Regards,
Max

On Thursday, August 26, 2021 at 2:38:10 PM UTC-4 Nathan Dunfield wrote:

> I suspect the cause is OpenBLAS.  While this library is built with 
> DYNAMIC_ARCH=1, there is still the non-performance critical code which will 
> use whatever instructions are available on the machine at compile time 
> unless you also set TARGET.  See
>
> https://github.com/xianyi/OpenBLAS/issues/3056
>
> For the macOS app, Marc Culler had to set TARGET=CORE2 so that it would 
> run on a 2013 cylindrical Mac Pro (this version is not yet posted).
>
> Best,
>
> Nathan
>
> On Wednesday, August 25, 2021 at 10:15:02 PM William Stein wrote:
>
>> Hi,
>>
>> I release cocalc-docker ([1], [2]) a few days ago with sage-9.4, and had 
>> people reporting back "illegal instruction" issues.  Sage is built there 
>> with SAGE_FAT_BINARY="yes", using this script [3].  One person who reported 
>> a problem had a "Dell PowerEdge R710." and I built on an intel Dell 
>> PowerEdge R630, for what it is worth.  They got the error "An illegal 
>> instructor occurred" when computing "5+2" in Sage. 
>>
>> My solution for now is to keep cocalc-docker at sage-9.3 for the time 
>> being, and suggest that people build sage from source on their own machine 
>> if necessary.   I'll let you know if I have any further information, but I 
>> just wanted to add this data point.
>>
>> [1] https://github.com/sagemathinc/cocalc-docker
>> [2] https://hub.docker.com/r/sagemathinc/cocalc
>> [3] 
>> https://github.com/sagemathinc/cocalc-docker/blob/master/scripts/install_sage.sh
>>
>> On Wednesday, August 25, 2021 at 8:57:44 AM UTC-7 Marco Streng wrote:
>>
>>> In the end I build 9.4 from source and that worked perfectly. And it 
>>> turned out that the Ubuntu 18.04 binaries of 9.2 also work on this 
>>> particular machine (though we went for 9.4 in the end). Thanks again for 
>>> the help.
>>>
>>> Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:
>>>
 2021-08-24 05:48 UTC, Dima Pasechnik: 
 > 
 > These "illegal instruction" errors are an indication 
 > that the binary was built for a more advanced CPU 
 > than yours - which does not support certain CPU 
 > commands. It's a bug in "fat binary" build process 
 > we see for some time. 
 > 
 > Build Sage yourself, or use Conda. 

 I opened a ticket at binary-pkg for that: 
 https://github.com/sagemath/binary-pkg/issues/31 

>>>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Nathan Dunfield]

I suspect the cause is OpenBLAS.  While this library is built with 
DYNAMIC_ARCH=1, there is still the non-performance critical code which will 
use whatever instructions are available on the machine at compile time 
unless you also set TARGET.  See

https://github.com/xianyi/OpenBLAS/issues/3056

For the macOS app, Marc Culler had to set TARGET=CORE2 so that it would run 
on a 2013 cylindrical Mac Pro (this version is not yet posted).

Best,

Nathan

On Wednesday, August 25, 2021 at 10:15:02 PM William Stein wrote:

> Hi,
>
> I release cocalc-docker ([1], [2]) a few days ago with sage-9.4, and had 
> people reporting back "illegal instruction" issues.  Sage is built there 
> with SAGE_FAT_BINARY="yes", using this script [3].  One person who reported 
> a problem had a "Dell PowerEdge R710." and I built on an intel Dell 
> PowerEdge R630, for what it is worth.  They got the error "An illegal 
> instructor occurred" when computing "5+2" in Sage. 
>
> My solution for now is to keep cocalc-docker at sage-9.3 for the time 
> being, and suggest that people build sage from source on their own machine 
> if necessary.   I'll let you know if I have any further information, but I 
> just wanted to add this data point.
>
> [1] https://github.com/sagemathinc/cocalc-docker
> [2] https://hub.docker.com/r/sagemathinc/cocalc
> [3] 
> https://github.com/sagemathinc/cocalc-docker/blob/master/scripts/install_sage.sh
>
> On Wednesday, August 25, 2021 at 8:57:44 AM UTC-7 Marco Streng wrote:
>
>> In the end I build 9.4 from source and that worked perfectly. And it 
>> turned out that the Ubuntu 18.04 binaries of 9.2 also work on this 
>> particular machine (though we went for 9.4 in the end). Thanks again for 
>> the help.
>>
>> Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:
>>
>>> 2021-08-24 05:48 UTC, Dima Pasechnik: 
>>> > 
>>> > These "illegal instruction" errors are an indication 
>>> > that the binary was built for a more advanced CPU 
>>> > than yours - which does not support certain CPU 
>>> > commands. It's a bug in "fat binary" build process 
>>> > we see for some time. 
>>> > 
>>> > Build Sage yourself, or use Conda. 
>>>
>>> I opened a ticket at binary-pkg for that: 
>>> https://github.com/sagemath/binary-pkg/issues/31 
>>>
>>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Samuel Lelièvre]

Would it help to set `CFLAGS` to `-mno-avx -mno-avx2 -mno-bmi2`
as is done for building the Sage macOS app? --Samuel

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Matthias Koeppe]

I've opened https://trac.sagemath.org/ticket/32424 for this issue with Sage 
9.4.


On Wednesday, August 25, 2021 at 8:15:02 PM UTC-7 wst...@gmail.com wrote:

> Hi,
>
> I release cocalc-docker ([1], [2]) a few days ago with sage-9.4, and had 
> people reporting back "illegal instruction" issues.  Sage is built there 
> with SAGE_FAT_BINARY="yes", using this script [3].  One person who reported 
> a problem had a "Dell PowerEdge R710." and I built on an intel Dell 
> PowerEdge R630, for what it is worth.  They got the error "An illegal 
> instructor occurred" when computing "5+2" in Sage. 
>
> My solution for now is to keep cocalc-docker at sage-9.3 for the time 
> being, and suggest that people build sage from source on their own machine 
> if necessary.   I'll let you know if I have any further information, but I 
> just wanted to add this data point.
>
> [1] https://github.com/sagemathinc/cocalc-docker
> [2] https://hub.docker.com/r/sagemathinc/cocalc
> [3] 
> https://github.com/sagemathinc/cocalc-docker/blob/master/scripts/install_sage.sh
>
> On Wednesday, August 25, 2021 at 8:57:44 AM UTC-7 Marco Streng wrote:
>
>> In the end I build 9.4 from source and that worked perfectly. And it 
>> turned out that the Ubuntu 18.04 binaries of 9.2 also work on this 
>> particular machine (though we went for 9.4 in the end). Thanks again for 
>> the help.
>>
>> Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:
>>
>>> 2021-08-24 05:48 UTC, Dima Pasechnik: 
>>> > 
>>> > These "illegal instruction" errors are an indication 
>>> > that the binary was built for a more advanced CPU 
>>> > than yours - which does not support certain CPU 
>>> > commands. It's a bug in "fat binary" build process 
>>> > we see for some time. 
>>> > 
>>> > Build Sage yourself, or use Conda. 
>>>
>>> I opened a ticket at binary-pkg for that: 
>>> https://github.com/sagemath/binary-pkg/issues/31 
>>>
>>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[William Stein]

Hi,

I release cocalc-docker ([1], [2]) a few days ago with sage-9.4, and had 
people reporting back "illegal instruction" issues.  Sage is built there 
with SAGE_FAT_BINARY="yes", using this script [3].  One person who reported 
a problem had a "Dell PowerEdge R710." and I built on an intel Dell 
PowerEdge R630, for what it is worth.  They got the error "An illegal 
instructor occurred" when computing "5+2" in Sage. 

My solution for now is to keep cocalc-docker at sage-9.3 for the time 
being, and suggest that people build sage from source on their own machine 
if necessary.   I'll let you know if I have any further information, but I 
just wanted to add this data point.

[1] https://github.com/sagemathinc/cocalc-docker
[2] https://hub.docker.com/r/sagemathinc/cocalc
[3] 
https://github.com/sagemathinc/cocalc-docker/blob/master/scripts/install_sage.sh

On Wednesday, August 25, 2021 at 8:57:44 AM UTC-7 Marco Streng wrote:

> In the end I build 9.4 from source and that worked perfectly. And it 
> turned out that the Ubuntu 18.04 binaries of 9.2 also work on this 
> particular machine (though we went for 9.4 in the end). Thanks again for 
> the help.
>
> Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:
>
>> 2021-08-24 05:48 UTC, Dima Pasechnik:
>> >
>> > These "illegal instruction" errors are an indication
>> > that the binary was built for a more advanced CPU
>> > than yours - which does not support certain CPU
>> > commands. It's a bug in "fat binary" build process
>> > we see for some time.
>> >
>> > Build Sage yourself, or use Conda.
>>
>> I opened a ticket at binary-pkg for that:
>> https://github.com/sagemath/binary-pkg/issues/31
>>
>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Marco Streng]

In the end I build 9.4 from source and that worked perfectly. And it turned 
out that the Ubuntu 18.04 binaries of 9.2 also work on this particular 
machine (though we went for 9.4 in the end). Thanks again for the help.

Op dinsdag 24 augustus 2021 om 18:03:01 UTC+2 schreef slelievre:

> 2021-08-24 05:48 UTC, Dima Pasechnik:
> >
> > These "illegal instruction" errors are an indication
> > that the binary was built for a more advanced CPU
> > than yours - which does not support certain CPU
> > commands. It's a bug in "fat binary" build process
> > we see for some time.
> >
> > Build Sage yourself, or use Conda.
>
> I opened a ticket at binary-pkg for that:
> https://github.com/sagemath/binary-pkg/issues/31
>

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Samuel Lelièvre]

2021-08-24 05:48 UTC, Dima Pasechnik:
>
> These "illegal instruction" errors are an indication
> that the binary was built for a more advanced CPU
> than yours - which does not support certain CPU
> commands. It's a bug in "fat binary" build process
> we see for some time.
>
> Build Sage yourself, or use Conda.

I opened a ticket at binary-pkg for that:
https://github.com/sagemath/binary-pkg/issues/31

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Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Marco Streng]

Thanks, I'll do that.

Op dinsdag 24 augustus 2021 om 07:48:00 UTC+2 schreef dim...@gmail.com:

> These "illegal instruction" errors are an indication that the binary was 
> built for a more advanced CPU than yours - which does not support certain 
> CPU commands. It's a bug in "fat binary" build process we see for some time.
>
> Build Sage yourself, or use Conda.
>
>
> On Mon, 23 Aug 2021, 23:33 share the sage,  wrote:
>
>> Hi Marco, How are you?
>>
>> In my case, upgrading to Ubuntu 20.04 base, didn't solve the issue. 
>> Building did.
>>
>> I had the same SignalError on Linux Mint 20.1 (based on Ubuntu 20.04) 
>> with the corresponding Sage prebuild binaries as in Linux Mint 18.3 (based 
>> on Ubuntu 16.04).
>>
>> So, I took courage and face the build process myself.
>>
>> In your case, if I understand correctly, your system administrator might 
>> be doing the Sage build, right?
>>
>> Buenaventura,
>>
>> Share_The_Sage! 
>>
>> On 2021/08/23 10:43, Marco Streng wrote:
>>
>> Hi everyone, 
>>
>> I'm having the same problem, on Ubuntu 18.04:
>>
>> I unpack the binaries sage-9.3-Ubuntu_18.04-x86_64.tar.bz2 and run ./sage
>> Then I see a few lines that look like
>>
>> /home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/traitlets/config/loader.py:795:
>>  
>> SyntaxWarning: "is" with a literal. Did you mean "=="?
>>   if len(key) is 1:
>>
>> or
>>
>> /home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/psutil/_pslinux.py:551:
>>  
>> DeprecationWarning: invalid escape sequence \d
>> (with various python files and sometimes with \s instead of \d).
>>
>> And then (in SageMath in the terminal) some things work without problem, 
>> but there are also various inputs that give the "Illegal instruction" error 
>> on a "sig_on()" line of a pyx file. For example, the same input of 
>> share-the-sage, but also the following example from the documentation, give 
>> the error:
>> K. = NumberField(x^10 - 2)
>> L. = K.relativize(a^4 + a^2 + 2); L
>> (full in- and output below)
>>
>> Do you have any suggestions for fixing this without asking my system 
>> administrator to upgrade to Ubuntu 20.04 and/or rebuilding? How likely is 
>> it that upgrading to Ubuntu 20.04 will fix the problem for me too?
>>
>> Thanks!
>> Marco
>>
>>
>> ./sage
>>
>> ┌┐
>>
>> │ SageMath version 9.3, Release Date: 2021-05-09 │
>>
>> │ Using Python 3.9.2. Type "help()" for help.│
>>
>> └┘
>>
>> sage: print(version()) 
>>
>> : m=matrix(QQ,[*0*, *0*, *2*, *1*]) 
>>
>> : print(m) 
>>
>> : m_rs=m.row_space() 
>>
>> : print(m_rs) 
>>
>> : facet_z_plus_basis=m.right_kernel().basis() 
>>
>> :
>> 
>> 
>>
>>
>> SageMath version 9.3, Release Date: 2021-05-09
>>
>> [0 0 2 1]
>>
>> Vector space of degree 4 and dimension 1 over Rational Field
>>
>> Basis matrix:
>>
>> [  0   0   1 1/2]
>>
>>
>> ---
>>
>> SignalError   Traceback (most recent call 
>> last)
>>
>>  in 
>>
>> *  4* m_rs=m.row_space()
>>
>> *  5* print(m_rs)
>>
>> > 6 facet_z_plus_basis=m.right_kernel().basis()
>>
>>
>> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx
>>  
>> in sage.matrix.matrix2.Matrix.right_kernel 
>> (build/cythonized/sage/matrix/matrix2.c:31059)()
>>
>> *   4717* 
>>
>> *   4718* # Go get the kernel matrix, this is where it all 
>> happens
>>
>> -> 4719 M = self.right_kernel_matrix(*args, **kwds)
>>
>> *   4720* 
>>
>> *   4721* ambient = R**self.ncols()
>>
>>
>> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx
>>  
>> in sage.matrix.matrix2.Matrix.right_kernel_matrix 
>> (build/cythonized/sage/matrix/matrix2.c:29696)()
>>
>> *   4318* if M is None:
>>
>> *   4319* try:
>>
>> -> 4320 format, M = 
>> self._right_kernel_matrix(algorithm=algorithm, proof=proof)
>>
>> *   4321* except AttributeError:
>>
>> *   4322* pass
>>
>>
>> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_rational_dense.pyx
>>  
>> in 
>> sage.matrix.matrix_rational_dense.Matrix_rational_dense._right_kernel_matrix 
>> (build/cythonized/sage/matrix/matrix_rational_dense.cpp:14103)()
>>
>> *   1424* else:
>>
>> *   1425* A, _ = self._clear_denom()
>>
>> -> 1426 K = 
>> A._rational_kernel_iml().transpose().change_ring(QQ)
>>
>> *   1427* verbose("done computing right kernel matrix over the 
>> rationals for %sx%s matrix" % 

Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Dima Pasechnik]

These "illegal instruction" errors are an indication that the binary was
built for a more advanced CPU than yours - which does not support certain
CPU commands. It's a bug in "fat binary" build process we see for some time.

Build Sage yourself, or use Conda.


On Mon, 23 Aug 2021, 23:33 share the sage,  wrote:

> Hi Marco, How are you?
>
> In my case, upgrading to Ubuntu 20.04 base, didn't solve the issue.
> Building did.
>
> I had the same SignalError on Linux Mint 20.1 (based on Ubuntu 20.04) with
> the corresponding Sage prebuild binaries as in Linux Mint 18.3 (based on
> Ubuntu 16.04).
>
> So, I took courage and face the build process myself.
>
> In your case, if I understand correctly, your system administrator might
> be doing the Sage build, right?
>
> Buenaventura,
>
> Share_The_Sage!
>
> On 2021/08/23 10:43, Marco Streng wrote:
>
> Hi everyone,
>
> I'm having the same problem, on Ubuntu 18.04:
>
> I unpack the binaries sage-9.3-Ubuntu_18.04-x86_64.tar.bz2 and run ./sage
> Then I see a few lines that look like
>
> /home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/traitlets/config/loader.py:795:
> SyntaxWarning: "is" with a literal. Did you mean "=="?
>   if len(key) is 1:
>
> or
>
> /home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/psutil/_pslinux.py:551:
> DeprecationWarning: invalid escape sequence \d
> (with various python files and sometimes with \s instead of \d).
>
> And then (in SageMath in the terminal) some things work without problem,
> but there are also various inputs that give the "Illegal instruction" error
> on a "sig_on()" line of a pyx file. For example, the same input of
> share-the-sage, but also the following example from the documentation, give
> the error:
> K. = NumberField(x^10 - 2)
> L. = K.relativize(a^4 + a^2 + 2); L
> (full in- and output below)
>
> Do you have any suggestions for fixing this without asking my system
> administrator to upgrade to Ubuntu 20.04 and/or rebuilding? How likely is
> it that upgrading to Ubuntu 20.04 will fix the problem for me too?
>
> Thanks!
> Marco
>
>
> ./sage
>
> ┌┐
>
> │ SageMath version 9.3, Release Date: 2021-05-09 │
>
> │ Using Python 3.9.2. Type "help()" for help.│
>
> └┘
>
> sage: print(version())
>
> : m=matrix(QQ,[*0*, *0*, *2*, *1*])
>
> : print(m)
>
> : m_rs=m.row_space()
>
> : print(m_rs)
>
> : facet_z_plus_basis=m.right_kernel().basis()
>
> :
>
>
>
>
> SageMath version 9.3, Release Date: 2021-05-09
>
> [0 0 2 1]
>
> Vector space of degree 4 and dimension 1 over Rational Field
>
> Basis matrix:
>
> [  0   0   1 1/2]
>
> ---
>
> SignalError   Traceback (most recent call last)
>
>  in 
>
> *  4* m_rs=m.row_space()
>
> *  5* print(m_rs)
>
> > 6 facet_z_plus_basis=m.right_kernel().basis()
>
>
> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx
> in sage.matrix.matrix2.Matrix.right_kernel
> (build/cythonized/sage/matrix/matrix2.c:31059)()
>
> *   4717*
>
> *   4718* # Go get the kernel matrix, this is where it all happens
>
> -> 4719 M = self.right_kernel_matrix(*args, **kwds)
>
> *   4720*
>
> *   4721* ambient = R**self.ncols()
>
>
> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx
> in sage.matrix.matrix2.Matrix.right_kernel_matrix
> (build/cythonized/sage/matrix/matrix2.c:29696)()
>
> *   4318* if M is None:
>
> *   4319* try:
>
> -> 4320 format, M =
> self._right_kernel_matrix(algorithm=algorithm, proof=proof)
>
> *   4321* except AttributeError:
>
> *   4322* pass
>
>
> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_rational_dense.pyx
> in
> sage.matrix.matrix_rational_dense.Matrix_rational_dense._right_kernel_matrix
> (build/cythonized/sage/matrix/matrix_rational_dense.cpp:14103)()
>
> *   1424* else:
>
> *   1425* A, _ = self._clear_denom()
>
> -> 1426 K =
> A._rational_kernel_iml().transpose().change_ring(QQ)
>
> *   1427* verbose("done computing right kernel matrix over the
> rationals for %sx%s matrix" % (self.nrows(), self.ncols()),level=1, t=tm)
>
> *   1428* return 'computed-iml-rational', K
>
>
> ~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.pyx
> in
> sage.matrix.matrix_integer_dense.Matrix_integer_dense._rational_kernel_iml
> (build/cythonized/sage/matrix/matrix_integer_dense.cpp:32352)()
>
> *   3880* time = verbose('computing null space of %s x %s matrix
> using IML'%(self._nrows, self._ncols))
>
> *   3881* cdef mpz_t * m = fmpz_mat_to_mpz_array(self._matrix)
>
> -> 3882 sig_on()
>
> *   

Re: [sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[share the sage]

Hi Marco, How are you?

In my case, upgrading to Ubuntu 20.04 base, didn't solve the issue. 
Building did.


I had the same SignalError on Linux Mint 20.1 (based on Ubuntu 20.04) 
with the corresponding Sage prebuild binaries as in Linux Mint 18.3 
(based on Ubuntu 16.04).


So, I took courage and face the build process myself.

In your case, if I understand correctly, your system administrator might 
be doing the Sage build, right?


Buenaventura,

Share_The_Sage!

On 2021/08/23 10:43, Marco Streng wrote:

Hi everyone,

I'm having the same problem, on Ubuntu 18.04:

I unpack the binaries sage-9.3-Ubuntu_18.04-x86_64.tar.bz2 and run ./sage
Then I see a few lines that look like

/home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/traitlets/config/loader.py:795: 
SyntaxWarning: "is" with a literal. Did you mean "=="?

  if len(key) is 1:

or

/home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/psutil/_pslinux.py:551: 
DeprecationWarning: invalid escape sequence \d


(with various python files and sometimes with \s instead of \d).

And then (in SageMath in the terminal) some things work without 
problem, but there are also various inputs that give the "Illegal 
instruction" error on a "sig_on()" line of a pyx file. For example, 
the same input of share-the-sage, but also the following example from 
the documentation, give the error:

K. = NumberField(x^10 - 2)
L. = K.relativize(a^4 + a^2 + 2); L
(full in- and output below)

Do you have any suggestions for fixing this without asking my system 
administrator to upgrade to Ubuntu 20.04 and/or rebuilding? How likely 
is it that upgrading to Ubuntu 20.04 will fix the problem for me too?


Thanks!
Marco


./sage

┌┐

│ SageMath version 9.3, Release Date: 2021-05-09         │

│ Using Python 3.9.2. Type "help()" for help.         │

└┘

sage: print(version())

: m=matrix(QQ,[*0*, *0*, *2*, *1*])

: print(m)

: m_rs=m.row_space()

: print(m_rs)

: facet_z_plus_basis=m.right_kernel().basis()

:

SageMath version 9.3, Release Date: 2021-05-09

[0 0 2 1]

Vector space of degree 4 and dimension 1 over Rational Field

Basis matrix:

[  0   0   1 1/2]

---

SignalError                               Traceback (most recent call 
last)


 in 

*      4* m_rs=m.row_space()

*      5* print(m_rs)

> 6 facet_z_plus_basis=m.right_kernel().basis()


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx 
in sage.matrix.matrix2.Matrix.right_kernel 
(build/cythonized/sage/matrix/matrix2.c:31059)()


*   4717*

*   4718*         # Go get the kernel matrix, this is where it all happens

-> 4719         M = self.right_kernel_matrix(*args, **kwds)

*   4720*

*   4721*         ambient = R**self.ncols()


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx 
in sage.matrix.matrix2.Matrix.right_kernel_matrix 
(build/cythonized/sage/matrix/matrix2.c:29696)()


*   4318*         if M is None:

*   4319*             try:

-> 4320                 format, M = 
self._right_kernel_matrix(algorithm=algorithm, proof=proof)


*   4321*             except AttributeError:

*   4322*                 pass


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_rational_dense.pyx 
in 
sage.matrix.matrix_rational_dense.Matrix_rational_dense._right_kernel_matrix 
(build/cythonized/sage/matrix/matrix_rational_dense.cpp:14103)()


*   1424*         else:

*   1425*             A, _ = self._clear_denom()

-> 1426             K = 
A._rational_kernel_iml().transpose().change_ring(QQ)


*   1427*         verbose("done computing right kernel matrix over the 
rationals for %sx%s matrix" % (self.nrows(), self.ncols()),level=1, t=tm)


*   1428*         return 'computed-iml-rational', K


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.pyx 
in 
sage.matrix.matrix_integer_dense.Matrix_integer_dense._rational_kernel_iml 
(build/cythonized/sage/matrix/matrix_integer_dense.cpp:32352)()


*   3880*         time = verbose('computing null space of %s x %s 
matrix using IML'%(self._nrows, self._ncols))


*   3881*         cdef mpz_t * m = fmpz_mat_to_mpz_array(self._matrix)

-> 3882         sig_on()

*   3883*         dim = nullspaceMP(self._nrows, self._ncols, m, _N)

*   3884*         sig_off()


SignalError: Illegal instruction

sage: *1*+*1*

2

sage: K. = NumberField(x^*10* - *2*)

:

sage: L. = K.relativize(a^*4* + a^*2* + *2*); L

:

---

SignalError                               Traceback (most recent call 
last)


 in 

> 1 L = K.relativize(a**Integer(4) + a**Integer(2) + Integer(2), 
names=('c', 'd',)); (c, d,) = L._first_ngens(2); L

[sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[Marco Streng]

Hi everyone,

I'm having the same problem, on Ubuntu 18.04:

I unpack the binaries sage-9.3-Ubuntu_18.04-x86_64.tar.bz2 and run ./sage
Then I see a few lines that look like

/home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/traitlets/config/loader.py:795:
 
SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(key) is 1:

or

/home/strengtc/software/sage-9.3/local/lib/python3.9/site-packages/psutil/_pslinux.py:551:
 
DeprecationWarning: invalid escape sequence \d
(with various python files and sometimes with \s instead of \d).

And then (in SageMath in the terminal) some things work without problem, 
but there are also various inputs that give the "Illegal instruction" error 
on a "sig_on()" line of a pyx file. For example, the same input of 
share-the-sage, but also the following example from the documentation, give 
the error:
K. = NumberField(x^10 - 2)
L. = K.relativize(a^4 + a^2 + 2); L
(full in- and output below)

Do you have any suggestions for fixing this without asking my system 
administrator to upgrade to Ubuntu 20.04 and/or rebuilding? How likely is 
it that upgrading to Ubuntu 20.04 will fix the problem for me too?

Thanks!
Marco


./sage

┌┐

│ SageMath version 9.3, Release Date: 2021-05-09 │

│ Using Python 3.9.2. Type "help()" for help.│

└┘

sage: print(version()) 

: m=matrix(QQ,[*0*, *0*, *2*, *1*]) 

: print(m) 

: m_rs=m.row_space() 

: print(m_rs) 

: facet_z_plus_basis=m.right_kernel().basis() 

:  


 

SageMath version 9.3, Release Date: 2021-05-09

[0 0 2 1]

Vector space of degree 4 and dimension 1 over Rational Field

Basis matrix:

[  0   0   1 1/2]

---

SignalError   Traceback (most recent call last)

 in 

*  4* m_rs=m.row_space()

*  5* print(m_rs)

> 6 facet_z_plus_basis=m.right_kernel().basis()


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx 
in sage.matrix.matrix2.Matrix.right_kernel 
(build/cythonized/sage/matrix/matrix2.c:31059)()

*   4717* 

*   4718* # Go get the kernel matrix, this is where it all happens

-> 4719 M = self.right_kernel_matrix(*args, **kwds)

*   4720* 

*   4721* ambient = R**self.ncols()


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix2.pyx 
in sage.matrix.matrix2.Matrix.right_kernel_matrix 
(build/cythonized/sage/matrix/matrix2.c:29696)()

*   4318* if M is None:

*   4319* try:

-> 4320 format, M = 
self._right_kernel_matrix(algorithm=algorithm, proof=proof)

*   4321* except AttributeError:

*   4322* pass


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_rational_dense.pyx
 
in 
sage.matrix.matrix_rational_dense.Matrix_rational_dense._right_kernel_matrix 
(build/cythonized/sage/matrix/matrix_rational_dense.cpp:14103)()

*   1424* else:

*   1425* A, _ = self._clear_denom()

-> 1426 K = A._rational_kernel_iml().transpose().change_ring(QQ)

*   1427* verbose("done computing right kernel matrix over the 
rationals for %sx%s matrix" % (self.nrows(), self.ncols()),level=1, t=tm)

*   1428* return 'computed-iml-rational', K


~/software/sage-9.3/local/lib/python3.9/site-packages/sage/matrix/matrix_integer_dense.pyx
 
in 
sage.matrix.matrix_integer_dense.Matrix_integer_dense._rational_kernel_iml 
(build/cythonized/sage/matrix/matrix_integer_dense.cpp:32352)()

*   3880* time = verbose('computing null space of %s x %s matrix 
using IML'%(self._nrows, self._ncols))

*   3881* cdef mpz_t * m = fmpz_mat_to_mpz_array(self._matrix)

-> 3882 sig_on()

*   3883* dim = nullspaceMP(self._nrows, self._ncols, m, _N)

*   3884* sig_off()


SignalError: Illegal instruction

sage: *1*+*1*  


 

2

sage: K. = NumberField(x^*10* - *2*) 

:  


 

sage: L. = K.relativize(a^*4* + a^*2* + *2*); L 

:  

[sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[slelievre]

2021-07-02 03:49:48 UTC+2, share the sage:
>
> Hi there!
>
> I've upgraded to Linux Mint 20.1 Ulyssa (kernel 5.4.0-77-generic),
> and then I've build Sage 9.3 from source.
>
> Now the issue is solved. Thanks for this amazing software!

Thanks for the news and your detailed report.

> I downloaded sources tarball for sage 9.3 via torrent. Then, before
> proceeding, I studied README.md and source.rst from the tarball
> (sage-9.3/README.md and sage-9.3/src/doc/en/installation/source.rst)
>
> I installed all the required and recommended packages for Linux Mint
> (Debian, Ubuntu) pointed at source.rst (link to debian.txt was broken
> at README.md) I took the advice to set export MAKE='make -j2'
> as I have two cores.

The broken link is fixed in Sage Trac ticket 31909
https://trac.sagemath.org/ticket/31909
which was merged in Sage 9.4.beta4.

> [dochtml] Done building the documentation!
> make --no-print-directory 'SAGE_ROOT/local/etc/sage-started.txt'
> "SAGE_ROOT/build/bin/sage-starts"
>
> Testing that Sage starts...
> [2021-06-30 21:50:55] SageMath version 9.3, Release Date: 2021-05-09
> Yes, Sage starts.
> make[2]: Leaving directory 'SAGE_ROOT/build/make'
>
> real223m53,530s  == 3 hours 40 minutes!!
> user459m24,031s
> sys17m32,635s
> Sage build/upgrade complete!
>
> And then I ran parallel testing:
>
> sage -t --long --random-seed=0 src/sage/tests/parigp.py
> [13 tests, 1166.50 s]
> --
> All tests passed!
> --
> Total time for all tests: 12934.5 seconds  == 3 hours 35 minutes!!
> cpu time: 39406.1 seconds
> cumulative wall time: 47546.7 seconds
>
> So, happy! ^_^
>
> Thank you again!
> Share_The_Sage!

Wonderful. happy Sage usage!   --Samuel

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[sage-support] Re: after upgrade to 9.3, SignalError: Illegal instruction

[share the sage]

Hi there!

I've upgraded to Linux Mint 20.1 Ulyssa (kernel 5.4.0-77-generic), and 
then I've build Sage 9.3 from source.


Now the issue is solved. Thanks for this amazing software!

I downloaded sources tarball for sage 9.3 via torrent. Then, before 
proceeding, I studied README.md and source.rst from the tarball ( 
sage-9.3/README.md and sage-9.3/src/doc/en/installation/source.rst)


I installed all the required and recommended packages for Linux Mint 
(Debian, Ubuntu) pointed at source.rst (link to debian.txt was broken at 
README.md) I took the advice to set export MAKE='make -j2' as I have two 
cores.


   [dochtml] Done building the documentation!
   make --no-print-directory 'SAGE_ROOT/local/etc/sage-started.txt'
   "SAGE_ROOT/build/bin/sage-starts"

   Testing that Sage starts...
   [2021-06-30 21:50:55] SageMath version 9.3, Release Date: 2021-05-09
   Yes, Sage starts.
   make[2]: Leaving directory 'SAGE_ROOT/build/make'

   real    223m53,530s  == 3 hours 40 minutes!!
   user    459m24,031s
   sys    17m32,635s
   Sage build/upgrade complete!

And then I ran parallel testing:

   sage -t --long --random-seed=0 src/sage/tests/parigp.py
    [13 tests, 1166.50 s]
   --
   All tests passed!
   --
   Total time for all tests: 12934.5 seconds  == 3 hours 35 minutes!!
    cpu time: 39406.1 seconds
    cumulative wall time: 47546.7 seconds

So, happy! ^_^

Thank you again!

Share_The_Sage!


On 2021/06/17 22:31, share the sage wrote:

Hi there!

First, I want to share my appreciation and joy for this software Sage, 
that I really love. Thank you all the developers that continue growing 
SageMath everyday. Thank you.


Today, I've upgraded to 9.3. I've been using 9.0 until yesterday.

I've downloaded the binaries for my Linux Mint 18.3, that is, for 
Ubuntu 16.04.


Both versions of Sage, were downloaded via torrent, 
sage-9.0-Ubuntu_16.04-x86_64.tar.bz2 and 
sage-9.3-Ubuntu_16.04-x86_64.tar.bz2


But this operation that worked on the notebook yesterday with Sage 9.0 
gives me this error today with Sage 9.3:


In[1]:
print(version())
m=matrix(QQ,[0, 0, 2, 1])
print(m)
m_rs=m.row_space()
print(m_rs)
facet_z_plus_basis=m.right_kernel().basis()
facet_z_plus_basis

Out[1]:
SageMath version 9.3, Release Date: 2021-05-09
[0 0 2 1]
Vector space of degree 4 and dimension 1 over Rational Field
Basis matrix:
[ 0 0 1 1/2]

SignalError
...
*-> 3882sig_on() *
3883 dim = nullspaceMP(self._nrows, self._ncols, m, _N)
3884 sig_off()

SignalError: Illegal instruction

I've attached a notebook and html export with the full traceback.

This code works fine on SageCell (permalink here 
)


So, I would like to know how to fix this issue and make it work again, 
without rolling back to  previous version of Sage.


Looking forward for your answers.
Thanks in advance,

Share_The_Sage!

PS: Some specs from my system (parsed from inxi -z and hostnamectl):

    SageMath: version 9.3, Release Date: 2021-05-09
Operating System: Linux Mint 18.3
  Kernel: Linux 4.4.0-190-generic
    Architecture: x86-64
 CPU: Dual core Intel Core i3-3217U (-HT-MCP-)
   Max speed: 1800 MHz
      Memory: 7875.4MB


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