Re: [sage-support] Computation just stops, no output or error message

[Robin van der veer]

Thank you!
this oom-killer did indeed kill my processes.
This solve my problem:)
thanks again

Op woensdag 7 juni 2017 17:49:13 UTC+2 schreef Jan Groenewald:
>
> Hi
>
> On 7 June 2017 at 17:33, Robin van der veer  > wrote:
>
>> Hi,
>>
>> I'm running a windows 10 host, and I have sage running in virtualbox; I 
>> just downloaded the .ova file from the website.
>> I have virutalbox set up so it uses 6/8 of my cores, and 5GB of mem. 
>> It could be the case the 6 processes combined exceed this 5GB. Would this 
>> explain Sage quitting in the way I described?
>>
>
> Try 
> https://serverfault.com/questions/548736/how-to-read-oom-killer-syslog-messages
>
> Regards,
> Jan\
>
>
> -- 
>   .~. 
>   /V\ Jan Groenewald
>  /( )\www.aims.ac.za
>  ^^-^^ 
>

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Re: [sage-support] Computation just stops, no output or error message

[Jan Groenewald]

Hi

On 7 June 2017 at 17:33, Robin van der veer  wrote:

> Hi,
>
> I'm running a windows 10 host, and I have sage running in virtualbox; I
> just downloaded the .ova file from the website.
> I have virutalbox set up so it uses 6/8 of my cores, and 5GB of mem.
> It could be the case the 6 processes combined exceed this 5GB. Would this
> explain Sage quitting in the way I described?
>

Try
https://serverfault.com/questions/548736/how-to-read-oom-killer-syslog-messages

Regards,
Jan\


-- 
  .~.
  /V\ Jan Groenewald
 /( )\www.aims.ac.za
 ^^-^^

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Re: [sage-support] Computation just stops, no output or error message

[Robin van der veer]

Dear John,

I am already flushing after every file.write(), so this cannot be the 
problem. (this was the first thing I tried when I noticed the problem, and 
after another 2 hour wait I concluded that it did not solve my problem)

Robin

Op woensdag 7 juni 2017 17:37:32 UTC+2 schreef John Cremona:
>
> My guess is that the output is buffered, i.e. it does not get actually 
> written out unti lthe buffer reaches some size.  You can get python to 
> flush the output after every output statement and then see what is 
> happening a bit better. 
>
> John 
>
> On 7 June 2017 at 16:33, Robin van der veer  > wrote: 
> > Hi, 
> > 
> > I'm running a windows 10 host, and I have sage running in virtualbox; I 
> just 
> > downloaded the .ova file from the website. 
> > I have virutalbox set up so it uses 6/8 of my cores, and 5GB of mem. 
> > It could be the case the 6 processes combined exceed this 5GB. Would 
> this 
> > explain Sage quitting in the way I described? 
> > 
> > Op woensdag 7 juni 2017 17:30:37 UTC+2 schreef Jan Groenewald: 
> >> 
> >> Hi 
> >> 
> >> 
> >> On 7 June 2017 at 17:24, Robin van der veer  
> wrote: 
> >>> 
> >>> I'm running Sage on my local machine (so not the sage math cloud), and 
> >>> some of my computations just stop with no output or error message. 
> >>> My code looks essentially like this: 
> >>> 
> >>> @parallel 
> >>> def compute(revLex): 
> >>> long computations 
> >>> print some stuff 
> >>> write some stuff to files 
> >>> return 
> >>> 
> >>> r = compute(L) 
> >>> for x in r: 
> >>> x 
> >>> 
> >>> When I work with small cases, everything is fine. However for bigger 
> >>> cases the computations tend to take upwards of 2 hours, and then just 
> stop. 
> >>> The only reason why I know one of the computations even stopped is 
> >>> because I'm staring at TOP in a console window and see the uptime jump 
> from 
> >>> 110 orso minutes to 0 minutes, meaning that one job was finished, and 
> it 
> >>> started working on the next. 
> >>> When this happens no output is printen, and the file to which some 
> stuff 
> >>> should have been written is empty. 
> >>> 
> >>> What could cause this (besides a programming error on my part)? Is 
> there 
> >>> some timeout even when running on your local machine? Or some resource 
> >>> limitations that just quit Sage if its using too much memory orso? 
> >>> 
> >>> I really hope that someone has an idea here, because each of these 
> >>> computations takes around 2 hours, so its very impracticle to just 
> keep 
> >>> trying to see what works. 
> >> 
> >> 
> >> What is your OS and where can you check for out of memory messages? 
> >> 
> >> Regards, 
> >> Jan 
> >> 
> >> 
> >> -- 
> >>   .~. 
> >>   /V\ Jan Groenewald 
> >>  /( )\www.aims.ac.za 
> >>  ^^-^^ 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
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> . 
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> > For more options, visit https://groups.google.com/d/optout. 
>

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Re: [sage-support] Computation just stops, no output or error message

[John Cremona]

My guess is that the output is buffered, i.e. it does not get actually
written out unti lthe buffer reaches some size.  You can get python to
flush the output after every output statement and then see what is
happening a bit better.

John

On 7 June 2017 at 16:33, Robin van der veer  wrote:
> Hi,
>
> I'm running a windows 10 host, and I have sage running in virtualbox; I just
> downloaded the .ova file from the website.
> I have virutalbox set up so it uses 6/8 of my cores, and 5GB of mem.
> It could be the case the 6 processes combined exceed this 5GB. Would this
> explain Sage quitting in the way I described?
>
> Op woensdag 7 juni 2017 17:30:37 UTC+2 schreef Jan Groenewald:
>>
>> Hi
>>
>>
>> On 7 June 2017 at 17:24, Robin van der veer  wrote:
>>>
>>> I'm running Sage on my local machine (so not the sage math cloud), and
>>> some of my computations just stop with no output or error message.
>>> My code looks essentially like this:
>>>
>>> @parallel
>>> def compute(revLex):
>>> long computations
>>> print some stuff
>>> write some stuff to files
>>> return
>>>
>>> r = compute(L)
>>> for x in r:
>>> x
>>>
>>> When I work with small cases, everything is fine. However for bigger
>>> cases the computations tend to take upwards of 2 hours, and then just stop.
>>> The only reason why I know one of the computations even stopped is
>>> because I'm staring at TOP in a console window and see the uptime jump from
>>> 110 orso minutes to 0 minutes, meaning that one job was finished, and it
>>> started working on the next.
>>> When this happens no output is printen, and the file to which some stuff
>>> should have been written is empty.
>>>
>>> What could cause this (besides a programming error on my part)? Is there
>>> some timeout even when running on your local machine? Or some resource
>>> limitations that just quit Sage if its using too much memory orso?
>>>
>>> I really hope that someone has an idea here, because each of these
>>> computations takes around 2 hours, so its very impracticle to just keep
>>> trying to see what works.
>>
>>
>> What is your OS and where can you check for out of memory messages?
>>
>> Regards,
>> Jan
>>
>>
>> --
>>   .~.
>>   /V\ Jan Groenewald
>>  /( )\www.aims.ac.za
>>  ^^-^^
>
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Re: [sage-support] Computation just stops, no output or error message

[Robin van der veer]

Hi,

I'm running a windows 10 host, and I have sage running in virtualbox; I 
just downloaded the .ova file from the website.
I have virutalbox set up so it uses 6/8 of my cores, and 5GB of mem. 
It could be the case the 6 processes combined exceed this 5GB. Would this 
explain Sage quitting in the way I described?

Op woensdag 7 juni 2017 17:30:37 UTC+2 schreef Jan Groenewald:
>
> Hi
>
> On 7 June 2017 at 17:24, Robin van der veer  > wrote:
>
>> I'm running Sage on my local machine (so not the sage math cloud), and 
>> some of my computations just stop with no output or error message.
>> My code looks essentially like this:
>>
>> @parallel
>> def compute(revLex):
>> long computations
>> print some stuff
>> write some stuff to files
>> return
>>
>> r = compute(L)
>> for x in r:
>> x
>>
>> When I work with small cases, everything is fine. However for bigger 
>> cases the computations tend to take upwards of 2 hours, and then just stop. 
>> The only reason why I know one of the computations even stopped is 
>> because I'm staring at TOP in a console window and see the uptime jump from 
>> 110 orso minutes to 0 minutes, meaning that one job was finished, and it 
>> started working on the next.
>> When this happens no output is printen, and the file to which some stuff 
>> should have been written is empty.
>>
>> What could cause this (besides a programming error on my part)? Is there 
>> some timeout even when running on your local machine? Or some resource 
>> limitations that just quit Sage if its using too much memory orso?
>>
>> I really hope that someone has an idea here, because each of these 
>> computations takes around 2 hours, so its very impracticle to just keep 
>> trying to see what works.
>>
>
> What is your OS and where can you check for out of memory messages? 
>
> Regards,
> Jan
>
>
> -- 
>   .~. 
>   /V\ Jan Groenewald
>  /( )\www.aims.ac.za
>  ^^-^^ 
>

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[sage-support] Computation just stops, no output or error message

[Robin van der veer]

I'm running Sage on my local machine (so not the sage math cloud), and some 
of my computations just stop with no output or error message.
My code looks essentially like this:

@parallel
def compute(revLex):
long computations
print some stuff
write some stuff to files
return

r = compute(L)
for x in r:
x

When I work with small cases, everything is fine. However for bigger cases 
the computations tend to take upwards of 2 hours, and then just stop. 
The only reason why I know one of the computations even stopped is because 
I'm staring at TOP in a console window and see the uptime jump from 110 
orso minutes to 0 minutes, meaning that one job was finished, and it 
started working on the next.
When this happens no output is printen, and the file to which some stuff 
should have been written is empty.

What could cause this (besides a programming error on my part)? Is there 
some timeout even when running on your local machine? Or some resource 
limitations that just quit Sage if its using too much memory orso?

I really hope that someone has an idea here, because each of these 
computations takes around 2 hours, so its very impracticle to just keep 
trying to see what works.

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