[sage-devel] ulimit issues and IPython 5.0

[Enrique Artal]

I start a new thread in this list as a continuation of "How to limit heavy 
computations" in sage-support. I try to summarize the problem. In my 
University, we have two servers to run math labs; it is done in several 
instances of sagenb using server_pool to enhance (at least a little bit) 
security. The sagenb instances are launched with ulimit options but it 
seems they have no effect.
In the first term of this academic year, we had several issues affecting 
the use of this server. Some students started long loops or heavy 
computations that stop the server (basically their computations blocked one 
instance and the error messages of the nginx processes grew so much that 
filled the hard disk). After restarting the machines, the problems came 
back again; at this point, when we detected such a process it was 
immediately stopped, but for some reason its instance of sagenb became 
unusable, causing problems to other students, since it needed restarting 
(and someone to do it). It was possible (not easy, thanks to Jori 
Mäntysalo) to identify the actual owner of the process, since stopping the 
computation by himself caused less harm.

Using ulimit in the OS, namely with the restrictions hard  "as   600" 
and "hard   cpu   10", it worked. If a computation was too heavy, the 
process stopped with some error message, but the instance was usable by any 
other user of the sagenb instance (including the person with the long 
computation). This was true for Sage 7.3, but no more in Sage 7.4 (and 7.5) 
where the process was stopped by the instance became unusable in few 
minutes.

Dima Pasechnik proposed to git-bisect and with the help of Miguel Marco, I 
think I found the patch causing this behavior. I started checking with 7.4 
beta and rc and I saw that beta0 had the issue. Looking at the history of 
changes, it worked after 
2b3eb14 Trac #20621: Simpler code and better error messages in Sequence()
and it didn't work after
9831d4b Trac #21006: Upgrade to IPython 5.0

Is there any chance to look into this change in order to localize and solve 
the problem?

Regards, Enrique.

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Re: [sage-devel] Sage runs in Window's 10's new Unix subsystem

[GK]

I recently updated Sage to version 7.5.1 (from the ppa) and although the 
behavior is still the same, a new warning message might give us some 
insight:

/usr/lib/sagemath/local/lib/python2.7/site-packages/psutil/_pslinux.py:364: 
RuntimeWarning: 'sin' and 'sout' swap memory stats couldn't be determined 
and were set to 0 ([Errno 2] No such file or directory: '/proc/vmstat')

Also, I found this , 
so maybe the problem is with that WSL does not properly support virtual 
memory?

On Thursday, January 19, 2017 at 2:26:21 PM UTC+3, GK wrote:
>
>
> On Thursday, January 12, 2017 at 2:00:37 PM UTC+3, David Joyner wrote:
>>
>> On Thu, Jan 12, 2017 at 3:43 AM, GK  wrote: 
>> > 
>> >> 
>> >> I am not having any problem starting the notebook. You might genuinely 
>> be 
>> >> out of memory, or hard drive space. 
>> >> 
>> > 
>> > I am not having trouble starting the notebook either, but I can not do 
>> > anything with it, also, no, I am not running out of memory nor hard 
>> disk 
>> > space. 
>> > 
>>
>> I've tested the notebook out at work where there's a windows machine. 
>> (a) It doesn't seem to work in IE. 
>> (b) In chrome and FF, the initial command is very slow. Maybe 15 
>> seconds or more. After that, it speeds up but is never snappy like the 
>> CLI. 
>> (c) I only tried the CLI once in windows and it seems to work fine. I 
>> don't remember it being slow. 
>>
>> GK: Does your experience match this? 
>>
>
> Dear David,
>
> (a) I haven't tried IE or Chrome, I tried FF and Edge and did not notice 
> any difference between the browsers.
> (b) Even when it was working, the notebook indeed needed a lot of time to 
> load, just as you describe. After that, the speed was OK.
> (c) Although I haven't done any complex work on the CLI, it does indeed 
> seem to work normally and snappy.
>  
>
>>
>> > I have increased the amount of virtual memory usable by windows to a 
>> > ridiculous amount and I am running everything and monitoring my system 
>> at 
>> > the same time and memory/hard disk space do not run out. Perhaps the 
>> amount 
>> > of memory or hard disk space allocated by windows to the linux 
>> subsystem 
>> > does actually run out, but I do not know how to check that. I related 
>> the 
>> > problem with the windows update, as exactly before the update 
>> everything ran 
>> > smoothly and right after the update sage never ran again. I do not 
>> think 
>> > this is a coincidence... 
>> > 
>> > -- 
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Re: [sage-devel] Too many Maximas!

[Ralf Stephan]

On Tuesday, February 7, 2017 at 5:47:40 PM UTC+1, William wrote:
>
> Basic question: is there any reason whatsoever for us to even have a 
> pexpect interface to maxima anymore?


Please see 
https://trac.sagemath.org/wiki/symbolics/maxima
and the metaticket
https://trac.sagemath.org/ticket/17753
for progress with this.

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[sage-devel] Re: GSoC 2017 kickoff

[Ralf Stephan]

On Tuesday, February 7, 2017 at 11:13:40 PM UTC+1, mmarco wrote:
>
> I don't plan to have much time available to mentor, but I think the 
> project of porting rubi to sage would be doable. Someone wants to step in 
> as a co-mentor?
>

No GSoC commitment from me but a support statement.

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Re: [sage-devel] Too many Maximas!

[Nils Bruin]

On Tuesday, February 7, 2017 at 2:12:30 PM UTC-8, William wrote:
>
> On Tue, Feb 7, 2017 at 5:08 PM, Nils Bruin > 
> wrote: 
> > On Tuesday, February 7, 2017 at 8:47:40 AM UTC-8, William wrote: 
> >> 
> >> 
> >> Basic question: is there any reason whatsoever for us to even have a 
> >> pexpect interface to maxima anymore?  Nils Bruin (and others) put a 
> >> massive amount of effort into a C library version (using ecl) over the 
> >> years... 
> >> 
> > Not for the use of calculus in sage. 
>
> Wow.  Calculus in Sage is nearly the only critical reason we have 
> Maxima in Sage; I didn't realize all that C library interface work 
> wasn't useful for that.  Oh well.   Thanks for the clarification.  Is 
> the issue that Maxima tries to ask questions? 
>
> I think you misunderstood my answer. Having a pexpect interface to maxima 
is not useful for calculus, because calculus uses the maxima_lib interface. 
In some places it is still communicating with maxima_lib through 
constructing and parsing strings, pretending that maxima_lib offers a 
pexpect interface. Apparently this is not a bottle neck, so people haven't 
bothered converting to the more efficient APIs that maxima_lib offers.

The "ask questions" problem doesn't arise: maxima_lib gets monkey-patched 
to raise an error instead of expecting the question to be answered.

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Re: [sage-devel] Too many Maximas!

[William Stein]

On Tue, Feb 7, 2017 at 5:08 PM, Nils Bruin  wrote:
> On Tuesday, February 7, 2017 at 8:47:40 AM UTC-8, William wrote:
>>
>>
>> Basic question: is there any reason whatsoever for us to even have a
>> pexpect interface to maxima anymore?  Nils Bruin (and others) put a
>> massive amount of effort into a C library version (using ecl) over the
>> years...
>>
> Not for the use of calculus in sage.

Wow.  Calculus in Sage is nearly the only critical reason we have
Maxima in Sage; I didn't realize all that C library interface work
wasn't useful for that.  Oh well.   Thanks for the clarification.  Is
the issue that Maxima tries to ask questions?





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Re: [sage-devel] Too many Maximas!

[Nils Bruin]

On Tuesday, February 7, 2017 at 8:47:40 AM UTC-8, William wrote:
>
>
> Basic question: is there any reason whatsoever for us to even have a 
> pexpect interface to maxima anymore?  Nils Bruin (and others) put a 
> massive amount of effort into a C library version (using ecl) over the 
> years... 
>
> Not for the use of calculus in sage. However, sage's pexpect interfaces in 
general are pretty useful and it can be worthwhile to be able to compute 
with separate maxima executables (so that the lisp is *inside* the sage 
process, and can be a different (higher performance?) lisp. So yes, I think 
there is some benefit to maintaining the maxima pexpect interface, and for 
ease of transition, maintain a side to maxima_lib that is compatible with 
pexpect interfaces. Whether the benefit is worth the cost is another matter 
...

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Re: [sage-devel] Too many Maximas!

[Jean-Pierre Flori]

Our pexpect interface happily leaves zombies around on linux because it 
never waits on the processes it forks.
At least for each instantiation of the pexpect class it tries to launch 
sage-cleaner to have at least one instance running and only the first does 
actual work, the other ones becoming zombies.
Not sure about the real process, i.e. maxima, magma, ..., anymore.

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[sage-devel] Re: a 7(!) year old (Singular) overflow issue still holds

[kcrisman]

Probably closely related:
https://ask.sagemath.org/question/36480/restricted-usability-of-singular-after-upgrade/

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[sage-devel] Re: GSoC 2017 kickoff

[Dima Pasechnik]

I've added a project on modular decomposition of graphs and digraphs.

How many more we would like to have?

On Thursday, January 19, 2017 at 6:05:19 PM UTC, Harald Schilly wrote:
>
> Hello, this year's Google Summer of Code 2017 just started. 
>
> I assume we will try again to be part of it, and therefore I've 
> started the registration process. 
>
> The most important aspect is to have mentors and project proposals. 
> For that, I've started this year's wiki page as a copy of last year: 
>
> https://wiki.sagemath.org/GSoC/2017 (compare with 2016) 
>
> The deadline for the application is Feb. 9th and I'm again working on 
> this like in the past 5 years. 
>
> -- Harald 
>

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Re: [sage-devel] Too many Maximas!

[Jeroen Demeyer]

On 2017-02-07 17:30, Erik Bray wrote:

A problem I've been having lately when running Sage's test suite on
Cygwin (i.e. sage -t -a).

Several of the tests that use Maxima are spinning up Maxima processes
(I guess interacted with via pexpect?) and not killing them.


This is probably Cygwin-specific. It would help if you could give some 
more details. For example: is the problem reproducible or does it only 
happen sometimes? Do you know which files cause the problem? Do the 
doctests actually pass? Does Cygwin have something like strace which 
might help to debug this?


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Re: [sage-devel] Too many Maximas!

[Jeroen Demeyer]

On 2017-02-07 17:46, William Stein wrote:

Basic question: is there any reason whatsoever for us to even have a
pexpect interface to maxima anymore?  Nils Bruin (and others) put a
massive amount of effort into a C library version (using ecl) over the
years...


Basic answer: there are tons of things in Sage which don't have any 
reason to exist whatsoever except for historical reasons. Most of these 
can and should be fixed, but that takes time...


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Re: [sage-devel] Too many Maximas!

[William Stein]

> On this I have no idea. It might be that the pexpect interface is
> retained for backwards compat, and that the tests for it are causing
> problems.  But I don't know--this is why I'm asking.

That is my understanding/guess, and we could probably deprecate it or
consider it unsupported/experimental.  But I could be wrong...


-- 
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Re: [sage-devel] Too many Maximas!

[Erik Bray]

On Tue, Feb 7, 2017 at 5:46 PM, William Stein  wrote:
> On Tue, Feb 7, 2017 at 11:30 AM, Erik Bray  wrote:
>> A problem I've been having lately when running Sage's test suite on
>> Cygwin (i.e. sage -t -a).
>>
>> Several of the tests that use Maxima are spinning up Maxima processes
>> (I guess interacted with via pexpect?) and not killing them.  And
>> what's worse, is that each one seems to sit in a busy wait.  So even
>> once the test suite has long since moved on to other tests I'm left
>> with dozens of maxima processes chewing up my CPU for nothing.  I can
>> kill them manually and it doesn't seem to break any tests.
>>
>> But in the meantime, can anyone point me in the right direction to
>> look for what might be causing this?  It seems to only be maxima
>> that's the problem.  Other pexpect interfaces don't leave processes
>> running (much less eating up CPU).
>
> Basic question: is there any reason whatsoever for us to even have a
> pexpect interface to maxima anymore?  Nils Bruin (and others) put a
> massive amount of effort into a C library version (using ecl) over the
> years...

On this I have no idea. It might be that the pexpect interface is
retained for backwards compat, and that the tests for it are causing
problems.  But I don't know--this is why I'm asking.

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Re: [sage-devel] Too many Maximas!

[William Stein]

On Tue, Feb 7, 2017 at 11:30 AM, Erik Bray  wrote:
> A problem I've been having lately when running Sage's test suite on
> Cygwin (i.e. sage -t -a).
>
> Several of the tests that use Maxima are spinning up Maxima processes
> (I guess interacted with via pexpect?) and not killing them.  And
> what's worse, is that each one seems to sit in a busy wait.  So even
> once the test suite has long since moved on to other tests I'm left
> with dozens of maxima processes chewing up my CPU for nothing.  I can
> kill them manually and it doesn't seem to break any tests.
>
> But in the meantime, can anyone point me in the right direction to
> look for what might be causing this?  It seems to only be maxima
> that's the problem.  Other pexpect interfaces don't leave processes
> running (much less eating up CPU).

Basic question: is there any reason whatsoever for us to even have a
pexpect interface to maxima anymore?  Nils Bruin (and others) put a
massive amount of effort into a C library version (using ecl) over the
years...

>
> Thanks,
> Erik
>
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[sage-devel] Too many Maximas!

[Erik Bray]

A problem I've been having lately when running Sage's test suite on
Cygwin (i.e. sage -t -a).

Several of the tests that use Maxima are spinning up Maxima processes
(I guess interacted with via pexpect?) and not killing them.  And
what's worse, is that each one seems to sit in a busy wait.  So even
once the test suite has long since moved on to other tests I'm left
with dozens of maxima processes chewing up my CPU for nothing.  I can
kill them manually and it doesn't seem to break any tests.

But in the meantime, can anyone point me in the right direction to
look for what might be causing this?  It seems to only be maxima
that's the problem.  Other pexpect interfaces don't leave processes
running (much less eating up CPU).

Thanks,
Erik

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[sage-devel] Re: GSoC 2017 kickoff

[Travis Scrimshaw]

On Tuesday, February 7, 2017 at 9:33:22 AM UTC-6, Travis Scrimshaw wrote:
>
> I added two projects with the somewhat broad subject areas:
>
> - Improve the representation theory in Sage
> - Improve the root system code in Sage
>
> I added another one for quantum cluster algebras (based on a suggestion 
from Gregg Musiker).

Best,
Travis

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[sage-devel] Re: GSoC 2017 kickoff

[Travis Scrimshaw]

I added two projects with the somewhat broad subject areas:

- Improve the representation theory in Sage
- Improve the root system code in Sage

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[sage-devel] Re: cc1 killed in iMac

[Travis Scrimshaw]

>
> Btw, what is the oldest and slowest computer where SageMath currently can 
> be compiled (without docs, as docbuilding should preferably be done in a 
> supercomputer near you...)? 
>
>
Slowest is almost certainly a Raspberry Pi with compile times in the 
multiple days (to a week)?

Best,
Travis

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[sage-devel] Python3 regressions

[Jeroen Demeyer]

On 2017-01-19 08:47, Frédéric Chapoton wrote:

We need to have the doctest framework itself check that there is no bad
print and a few other solved issues. I have required help to do that,
but nobody stepped in.


I think that this is just not easy to do. Are the issues that you have 
in mind covered by 2to3? It might be possible to use 2to3 to check that 
certain fixes are not needed.


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[sage-devel] Re: cc1 killed in iMac

[Dima Pasechnik]

On Tuesday, February 7, 2017 at 6:58:22 AM UTC, Jori Mäntysalo wrote:
>
> Just for fun I tried to compile SageMath on an old iMac with 1 GB RAM and 
> 2 x T7400 Intel Core 2. 
>
> It stops when compiling m4rie, see 
> http://www.sis.uta.fi/~jm58660/m4rie-20150908.txt for a full log. Error 
> message is 
>
> gcc: internal compiler error: Killed (program cc1) 
>
> I report this, as it might be a real bug. The hardware should be OK, I 
> just wiped HD and installed 32-bit Ubuntu 16.04.1 LTS. 
>
>   * * * 
>
> Btw, what is the oldest and slowest computer where SageMath currently can 
> be compiled (without docs, as docbuilding should preferably be done in a 
> supercomputer near you...)? 
>
> not sure at what point we stopped supporting 32-bit PPC, probably a G4 PPC 
Powerbook would work...
(I still have one in my cupboard :))

 

> -- 
> Jori Mäntysalo 
>

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Re: [sage-devel] cc1 killed in iMac

[Jori Mäntysalo]

On Tue, 7 Feb 2017, Jeroen Demeyer wrote:


It stops when compiling m4rie, see
http://www.sis.uta.fi/~jm58660/m4rie-20150908.txt for a full log. Error
message is

gcc: internal compiler error: Killed (program cc1)


Most likely, this is because your system ran out of memory (check dmesg to be 
sure).


Yes, that was it.

Ubuntu installer had made 1 GB swap, so I had total of 2 GB. I made a 5 GB 
swapfile, and now it seems to compile. Very very slowly, but compiling 
anyways.


--
Jori Mäntysalo

Re: [sage-devel] cc1 killed in iMac

[Jeroen Demeyer]

On 2017-02-07 07:58, Jori Mäntysalo wrote:

Just for fun I tried to compile SageMath on an old iMac with 1 GB RAM
and 2 x T7400 Intel Core 2.

It stops when compiling m4rie, see
http://www.sis.uta.fi/~jm58660/m4rie-20150908.txt for a full log. Error
message is

gcc: internal compiler error: Killed (program cc1)

I report this, as it might be a real bug.


Most likely, this is because your system ran out of memory (check dmesg 
to be sure).


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