[sage-support] I can't access sage vertual machine from windows host by address `localhost:8000`.

[Wei, Huayi]

Hi, There

My windows is win 7.  I import  Sage-7.2.ova into  virtualbox (version 
5.1.4) with the default setting.


And I want to access the Sage-7.2 virtual machine, which has been 
booted,  from my host system by browser, for example, chrome.


I input `localhost:8000` into chrome, but I can't access the notebook.

Anyone ever got such problem? And How to fixed it?

Thanks

Huayi

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[sage-support] Re: huge virtual memory size when launching 7.3

[Volker Braun]

On Tuesday, August 30, 2016 at 11:03:39 PM UTC+2, leif wrote:
>
> 48 GB claimed by *every* Sage process here


Its a tiny fraction of the 128TB address space. We are not talking about 
used RAM here.

which is *total* (not free!) physical RAM + total (not free) swap space, 
> in bytes. 
>

Really, you need to take enough address space so that any computation that 
you can possibly do isn't artificially limited by the address space.

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[sage-support] Paper citing sagemath

[Montgomery-Smith, Stephen]

I just submitted a paper: https://arxiv.org/abs/1608.06314 that cites
sagemath.  Would you guys like to add it to your webpage?

http://www.sagemath.org/library-publications.html

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Re: [sage-support] Re: huge virtual memory size when launching 7.3

[William Stein]

On Tue, Aug 30, 2016 at 2:02 PM, Nils Bruin  wrote:
> On Tuesday, August 30, 2016 at 1:23:47 PM UTC-7, Volker Braun wrote:
>>
>>
>> ulimit -v is useless anyways
>
>
> In my experience it is quite useful on multi-user machines to limit the
> effects of runaway computer algebra processes. Many packages (maple,

More modern approaches involving containers and cgroups are much, much
better for solving this sort of problem...

-- 
William (http://wstein.org)

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[sage-support] Re: huge virtual memory size when launching 7.3

[leif]

leif wrote:
> William Stein wrote:
>> On Tue, Aug 30, 2016 at 9:56 AM, Thierry Dumont
>>  wrote:
>>> I have two computers, and sage installed on both:
>>>
>>> 1) Ubuntu 12.04 , sage-7.3 on an nfs mount,y
>>>
>>> 2) Ubuntu 16.04,  sage-7.3 on a local system, on a ssd.
>>>
>>> With the first one, sage starts slowly (as could be expected!), and I
>>> have time to look at sage starting with "top". And during the starting
>>> phase, before the prompt, sage uses more than 16 GB of virtual memory
>>> (VIRT: 16.380g); the same quantity is used when stopping sage (in the
>>> console interface).
>>> It seems quite large, no ?
>>>
>>> With the second machine, it's more difficult to see what happens with
>>> top, but it does not seems to use more than 7gb.
>>>
>>> Why such a large amount of memory ? (ok, it's  virtual, but it's large,
>>> no ?).
> 
> IMHO horrible (as *each* Sage subprocess is claiming that amount of
> memory, here usually ~28 to 50+ GB IIRC, as it depends on the physical
> memory installed) and dangerous, as this makes the usage of 'ulimit -v'
> nearly impossible and in practice requires to allow vm-overcommit.  With
> the latter, it's presumably quite easy to effectively crash many (if not
> most) machines, be it by just some bug in Sage, but also by a malicious
> user of course.  (I.e., at least the VM a Sage server / installation may
> run in.)
> 
> It also makes it more complicated to see how much memory a Sage process
> actually *uses*.
> 
> 
>> I think this is a hack that is used by PARI/GP, due to their
>> "interesting" primitive (but fast!) memory design.
> 
> And GAP / libgap.  In this recent case I guess the latter is (once
> again) to blame.

Nope, GAP / libgap by default "only" contribute about 10% to the (at
least!) 48 GB claimed by *every* Sage process here, while indeed the
PARI library in Sage takes /one fourth/ of

sage.misc.memory_info.MemoryInfo().virtual_memory_limit()

which is *total* (not free!) physical RAM + total (not free) swap space,
in bytes.

That's IMHO a regression, but dates back quite a couple of (beta)
releases AFAIK.  (The last *commit* regarding that is from January this
year, don't know when it got merged.)


-leif

P.S.:  The change regarding the PARI library was made in #19883;
according to the ticket's /milestone/ (which doesn't say much) it
presumably got merged into Sage 7.1.


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[sage-support] Re: huge virtual memory size when launching 7.3

[Nils Bruin]

On Tuesday, August 30, 2016 at 1:23:47 PM UTC-7, Volker Braun wrote:
>
>
> ulimit -v is useless anyways
>

In my experience it is quite useful on multi-user machines to limit the 
effects of runaway computer algebra processes. Many packages (maple, magma 
at least) will segfault earlier with a ulimit -v set than without. With a 
properly set limit, this will often prevent the machine from thrashing the 
swap (which tends to affect all users). My impression was that sage 
benefitted from similar protection.
 

>  
>
>> and in practice requires to allow vm-overcommit. 
>
>
> In the default mode (overcommit_memory==0) calls to mmap with 
> MAP_NORESERVE are not checked, so you don't have to do anything special. 
> Really, restricting virtual memory on a 64-bit system is only for 
> specialist applications.
>

Isn't that exactly what makes the above use of ulimit -v useful? 
Presumably, once pages DO get allocated, the operating system will check 
that the total virtual address space that is actually allocated (to swap or 
memory) fits within the "ulimit -v" bound. In that case we don't 
particularly need to care about the huge mappings that sage seems to 
request either.

In any case, I hope we can keep sage's memory management configured in such 
a way that one can set standard operating system limits in order to ensure 
that overeager memory-consuming processes will crash before they start 
affecting other processes too much.

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[sage-support] Re: huge virtual memory size when launching 7.3

[Volker Braun]

On Tuesday, August 30, 2016 at 8:26:29 PM UTC+2, leif wrote:
>
> IMHO horrible (as *each* Sage subprocess is claiming that amount of 
> memory, here usually ~28 to 50+ GB IIRC, as it depends on the physical 
> memory installed) and dangerous, as this makes the usage of 'ulimit -v' 
> nearly impossible 


ulimit -v is useless anyways
 

> and in practice requires to allow vm-overcommit. 


In the default mode (overcommit_memory==0) calls to mmap with MAP_NORESERVE 
are not checked, so you don't have to do anything special. Really, 
restricting virtual memory on a 64-bit system is only for specialist 
applications.
 

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[sage-support] Re: huge virtual memory size when launching 7.3

[leif]

William Stein wrote:
> On Tue, Aug 30, 2016 at 9:56 AM, Thierry Dumont
>  wrote:
>> I have two computers, and sage installed on both:
>>
>> 1) Ubuntu 12.04 , sage-7.3 on an nfs mount,y
>>
>> 2) Ubuntu 16.04,  sage-7.3 on a local system, on a ssd.
>>
>> With the first one, sage starts slowly (as could be expected!), and I
>> have time to look at sage starting with "top". And during the starting
>> phase, before the prompt, sage uses more than 16 GB of virtual memory
>> (VIRT: 16.380g); the same quantity is used when stopping sage (in the
>> console interface).
>> It seems quite large, no ?
>>
>> With the second machine, it's more difficult to see what happens with
>> top, but it does not seems to use more than 7gb.
>>
>> Why such a large amount of memory ? (ok, it's  virtual, but it's large,
>> no ?).

IMHO horrible (as *each* Sage subprocess is claiming that amount of
memory, here usually ~28 to 50+ GB IIRC, as it depends on the physical
memory installed) and dangerous, as this makes the usage of 'ulimit -v'
nearly impossible and in practice requires to allow vm-overcommit.  With
the latter, it's presumably quite easy to effectively crash many (if not
most) machines, be it by just some bug in Sage, but also by a malicious
user of course.  (I.e., at least the VM a Sage server / installation may
run in.)

It also makes it more complicated to see how much memory a Sage process
actually *uses*.


> I think this is a hack that is used by PARI/GP, due to their
> "interesting" primitive (but fast!) memory design.

And GAP / libgap.  In this recent case I guess the latter is (once
again) to blame.


I was quite surprised apparently nobody complained, but perhaps not many
at all noticed.


-leif


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Re: [sage-support] huge virtual memory size when launching 7.3

[Thierry Dumont]

Le 30/08/2016 à 19:06, William Stein a écrit :
> On Tue, Aug 30, 2016 at 9:56 AM, Thierry Dumont
>  wrote:
>> I have two computers, and sage installed on both:
>>
>> 1) Ubuntu 12.04 , sage-7.3 on an nfs mount,y
>>
>> 2) Ubuntu 16.04,  sage-7.3 on a local system, on a ssd.
>>
>> With the first one, sage starts slowly (as could be expected!), and I
>> have time to look at sage starting with "top". And during the starting
>> phase, before the prompt, sage uses more than 16 GB of virtual memory
>> (VIRT: 16.380g); the same quantity is used when stopping sage (in the
>> console interface).
>> It seems quite large, no ?
>>
>> With the second machine, it's more difficult to see what happens with
>> top, but it does not seems to use more than 7gb.
>>
>> Why such a large amount of memory ? (ok, it's  virtual, but it's large,
>> no ?).
> 
> I think this is a hack that is used by PARI/GP, due to their
> "interesting" primitive (but fast!) memory design.
> 
>  -- William
> 
>>
>> t.d.
>>

Mhhh, yes.And they certainly do something with what they allocate; I
tried this (c++):

---
#define DO_SOMETHING
int main()
{
  //allocate a 16 gb array.
  const long int n=2*10;
  long int *x=new long int[n];
#ifdef DO_SOMETHING
  for(long int i=0;i

Re: [sage-support] huge virtual memory size when launching 7.3

[William Stein]

On Tue, Aug 30, 2016 at 9:56 AM, Thierry Dumont
 wrote:
> I have two computers, and sage installed on both:
>
> 1) Ubuntu 12.04 , sage-7.3 on an nfs mount,y
>
> 2) Ubuntu 16.04,  sage-7.3 on a local system, on a ssd.
>
> With the first one, sage starts slowly (as could be expected!), and I
> have time to look at sage starting with "top". And during the starting
> phase, before the prompt, sage uses more than 16 GB of virtual memory
> (VIRT: 16.380g); the same quantity is used when stopping sage (in the
> console interface).
> It seems quite large, no ?
>
> With the second machine, it's more difficult to see what happens with
> top, but it does not seems to use more than 7gb.
>
> Why such a large amount of memory ? (ok, it's  virtual, but it's large,
> no ?).

I think this is a hack that is used by PARI/GP, due to their
"interesting" primitive (but fast!) memory design.

 -- William

>
> t.d.
>
>
>
>
> --
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-- 
William (http://wstein.org)

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[sage-support] huge virtual memory size when launching 7.3

[Thierry Dumont]

I have two computers, and sage installed on both:

1) Ubuntu 12.04 , sage-7.3 on an nfs mount,y

2) Ubuntu 16.04,  sage-7.3 on a local system, on a ssd.

With the first one, sage starts slowly (as could be expected!), and I
have time to look at sage starting with "top". And during the starting
phase, before the prompt, sage uses more than 16 GB of virtual memory
(VIRT: 16.380g); the same quantity is used when stopping sage (in the
console interface).
It seems quite large, no ?

With the second machine, it's more difficult to see what happens with
top, but it does not seems to use more than 7gb.

Why such a large amount of memory ? (ok, it's  virtual, but it's large,
no ?).

t.d.




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<>

[sage-support] Re: Can't download worksheet in case of non-ascii character in a cell (UnicodeDecodeError)

[kcrisman]

On Monday, March 10, 2014 at 4:29:06 PM UTC-4, Eugene wrote:
>
> Hello!
>
> I would like to report an issue: in case of non-ascii character exists in 
> a cell (like a utf-8 comment) the worksheet can not be downloaded:
>
>
This is now https://github.com/sagemath/sagenb/issues/410 

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[sage-support] Re: How should I determine if two strongly regular graphs are isomorphic?

[Paul Leopardi]

On Wednesday, 24 August 2016 02:00:03 UTC+10, Dima Pasechnik wrote:
>
> Also, do I get it right that you have a new "generic" construction of 
> strongly regular graphs?
> As you know, we are collecting them - would you be interested in adding it 
> into sage/graphs/generators/ ?
>

Sorry for the delay in replying.
I am pursuing the goal of classifying bent functions by their Cayley 
graphs.  
https://sites.google.com/site/paulleopardi/Leopardi-ACCMCC-2015-talk-revised.pdf?attredirects=0=1
To do this, at first I tried creating a large worksheet in SageMathCloud: 
https://cloud.sagemath.com/projects/80f4c9e7-8a37-4f59-82e7-aa179ec0b652/files/public/bent-functions-duals-Cayley-graphs-public.sagews
This turned out to be too slow even for the ternary bent functions in 8 
dimensions, so I am refactoring the code into smaller, faster pieces, and 
using Bliss: https://github.com/penguian/Boolean-Cayley-graphs

The construction is the simple one described by (e.g.) Bernasconi and 
Codenotti 1999: http://ieeexplore.ieee.org/document/755000/
One key difference is that I only consider those f such that f(0)=0, to 
yield a simple undirected strongly regular graph, as per Lemma 12 of 
Bernasconi and Codenotti.

Starting with a representative f of an Extended Affine (EA) equivalence 
class of bent functions in (Z_2)^{dim} -> Z_2, my code forms each 
g(x)=f(x+b)++f(b) for each b,c in (Z_2)^{dim},
and then lists the unique Cayley graphs found, yielding a list of Cayley 
graphs, and a matrix of indices.
The code that performs this search is in 
https://github.com/penguian/Boolean-Cayley-graphs/blob/master/boolean_function_cayley_graph_classification.sage

My starting point is known lists of representatives of EA equivalence 
classes of bent functions. So far, these are fully enumerated only up to 
ternary functions in dim=8.
See (e.g.) Tokareva, Bent Functions, 2015, Chapter 7. 
http://store.elsevier.com/Bent-Functions/Natalia-Tokareva/isbn-9780128023181/

The web site http://langevin.univ-tln.fr/project/quartics/quartics.html 
lists quartic forms in dim=8, but this is apparently not sufficient to 
enumerate the EA equivalence classes 
( Langevin and Leander 2011 
http://link.springer.com/article/10.1007/s10623-010-9455-z )
Maybe my code could help to count these classes?



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