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a big limit of mathematica?

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LumisROB

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Sep 10, 2005, 8:21:34 AM9/10/05
to
During this calculation:


m= Table[ (i-j)+3.*j^-4 +50*i , {i,1,10000} , {j,1,10000} ];
Det[m]

the kernel has jammed and the following message has been visualized

No more memory available.
Mathematica kernel has shut down.

It is not a banal problem, more times I encounter me with these
problems that really make unusable Mathematica for my purposes . In
such cases I am forced to pass to Matlab that is behaved better
always. But I love Mathematica and I want to look for a solution not
to abandon it
Precise that know Mathematica enough to fund and therefore I am not
scandalized me if in such problems the time of calculation lengthens
but really I don't understand because in reality it jams
Precise that have introduced more times this problem in numerous
occasions and anybody has ever known how to give me a satisfactory
explanation. Obviously I don't expect me that Mathematica is as fast
as a compiled program but that that expect me from a so valid program
it is that if it don't succeed in completing a calculation point out
me the reality motive.
Is it a wrong thing to pretend it?

The dimension of the in demand memory is not limited from windows xp
or my hardware-software(OS) configuration, in fact such error also
happens in xp 64 Bit with Mathematica 5.2 (64 Bit) Athlon 64 2 GB Ram.

Is it probably a big limit of mathematica in to manage data of big
dimensions ?
Are these problems the true limit of mathematica ?
Is it possible to overcome this obstacle? ……or Where am I being wrong?


Thanks for the help

Dana

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Sep 10, 2005, 10:47:21 AM9/10/05
to
Hi. Looks like as the size of your matrix gets bigger, the Determinant
tends towards zero.
However, I can't explain why with a size 100*100 (the first output), it
returns "0." and with the largest sizes, numbers that are very small.

In[1]:=
Simplify[(i-j)+3/j^4+50*i]

Out[1]=
51*i+3/j^4-j

In[2]:=
Table[Det[Table[51.*i+3/j^4-j,{i,n},{j,n}]],{n,100,400,100}]


Out[2]=
{0.,
-1.1058552925176574276594077*^-2291,
7.9451068970561274753784538*^-3316,
-2.0828859268407618803830820*^-4315
}


--
Dana DeLouis
Mathematica 5.2

"LumisROB" <lumisrob...@yahoo.com> wrote in message
news:loj5i15en27o6sqff...@4ax.com...

> Is it possible to overcome this obstacle? ..or Where am I being wrong?
>
>
> Thanks for the help


Richard Fateman

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Sep 10, 2005, 12:26:08 PM9/10/05
to
Dana wrote:
> Hi. Looks like as the size of your matrix gets bigger, the Determinant
> tends towards zero.
> However, I can't explain why with a size 100*100 (the first output), it
> returns "0." and with the largest sizes, numbers that are very small.
>
> In[1]:=
> Simplify[(i-j)+3/j^4+50*i]
>
> Out[1]=
> 51*i+3/j^4-j
>
> In[2]:=
> Table[Det[Table[51.*i+3/j^4-j,{i,n},{j,n}]],{n,100,400,100}]
>
>
> Out[2]=
> {0.,
> -1.1058552925176574276594077*^-2291,
> 7.9451068970561274753784538*^-3316,
> -2.0828859268407618803830820*^-4315
> }
>
>
>
>
In Mathematica 5.0.0 on an Intel Pentium 4,

{
-2.3072190778544011494885203792388`15.954589770191005\
*^-1432,
1.6138130601828444080943999966955787`15.9545897701910\
05*^-2817,
-2.17670639763548416057774043151`15.954589770191005*^\
-4180,
1.283924316663441664176128821`15.954589770191005*^-55\
02}

So the result "0.0" is a recent innovation. On my
system, the Precision of the first number is 15.9546
(decimal digits), not MachinePrecision, which makes
one wonder what is going to happen in version 5.3 or 5.4.
Mathematica's numerical model has been criticized by
several people (including me), since Mathematica 1.0.


If you do the calculation EXACTLY by using 51 instead of "51."
the determinant of the 100X100 matrix comes out exactly 0.
In fact, the determinant of the 10x10, 20x20 etc all come out
exactly 0.

The advantage of doing exact arithmetic (and using a CAS
like Mathematica, Maple,Macsyma etc) over Matlab, is that the results
can often be exactly right. In Matlab the result will
be exactly right only by coincidence.

For example, is there anything special about 51.0, 51.000000000000000 or
exactly 51? Well, why not just put in a symbol, like A instead
of 51. and compute the determinant. the 10X10 determinant
is exactly zero. I assume that knowing the answer you can prove
the determinant is zero always.

Try that in Matlab. Actually, matlab can be coerced to doing
it, but only by calling Maple. A much more versatile system
then would actually be sometime like Mathematica, which could,
if necessary for efficiency, call Matlab. The Mathematica
people claim to be doing that, or maybe they claim to have
already done that.

So, for the original poster: your complaint about mathematica
running out of memory has not been solved, but your reason for
trying that computation is probably no longer compelling.

RJF


Peter Pein

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Sep 10, 2005, 2:04:13 PM9/10/05
to
LumisROB schrieb:

Hi Roberto,

as Paul Abbott and me, we have written in comp.soft-sys.math.mathematica
in messages <dfovu8$ffs$1...@smc.vnet.net> (Paul) and
<dfov8q$f97$1...@smc.vnet.net> (me), where you posted a very similar matrix
with complex entries, the first 3 lines are not independent. The same is
true in this case:

In[1]:=
m = Table[(i - j) + 3/j^4 + 50*i, {i, 1, 10000}, {j, 1, 3}];
Solve[m . {x, y, z} == 0]
Out[2]=
{{x -> (497*z)/1647,
y -> -((2144*z)/1647)}}

If you've got such big matrices, try to play around with similar smaller
ones (like Dana did) using exact numbers, where possible (like Richard
did) and it is often easy to see simple relations (like Peter and Paul
;-) did).

Hope this helps,
Peter


--
Peter Pein, Berlin
GnuPG Key ID: 0xA34C5A82
http://people.freenet.de/Peter_Berlin/

Dana

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Sep 10, 2005, 2:31:35 PM9/10/05
to
Hi. Thanks. I didn't even think about testing the equation exactly. You're
right, the Det quickly drops to zero from 3 onward.
I looked at a small table matrix, but I'm not that good to quickly spot the
reason the Det is zero.

equ=Simplify[(i-j)+3/j^4+50*i]

51*i+3/j^4-j

Table[Det[Table[equ,{i,n},{j,n}]],{n,1,10}]

{53, 3111/16, 0, 0, 0, 0, 0, 0, 0, 0}

$Version
"5.2 for Microsoft Windows (June 20, 2005)"


Here's another technique for posting those small numbers. This breaks the
number into the Mantissa, and Exponent.

MantissaExponent[Table[Det[Table[equ,{i,n},{j,n}]],{n,100,600,100}]]

{{0.,-307},
{-0.1105855292517657,-2290},
{ 0.7945106897056127,-3315},
{-0.2082885926840762,-4314},
{-0.4993937307336691,-5285},
{-0.1384814122285155,-6265}
}

--
Dana DeLouis

"Richard Fateman" <fat...@cs.berkeley.edu> wrote in message
news:AODUe.5012$wk6....@newssvr11.news.prodigy.com...

Message has been deleted

car...@colorado.edu

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Sep 10, 2005, 2:49:45 PM9/10/05
to
In exact arithmetic such matrices have only rank 2 for orders n>=2,
so they are obvious singular for n>2. What is the point
of going to n=100000? That matrix will take >10^10*8 bytes if entries
are stored as 64-bit integers. Not many computers have 80 GB of RAM.

car...@colorado.edu

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Sep 10, 2005, 3:59:38 PM9/10/05
to
Oops, sorry "only" n=10000. (Thanks Richard) That should fit on a 1GB
machine.
In any case, the exercise is pointless beyond n=3.
A 10000 x 10000 instance is 9998 times singular.

LumisROB

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Sep 11, 2005, 9:15:02 AM9/11/05
to
On Sat, 10 Sep 2005 20:04:13 +0200, Peter Pein <pet...@dordos.net>
wrote:

>LumisROB schrieb:
>> During this calculation:
>>
>

>Hi Roberto,
>
>as Paul Abbott and me, we have written in comp.soft-sys.math.mathematica
>in messages <dfovu8$ffs$1...@smc.vnet.net> (Paul) and
><dfov8q$f97$1...@smc.vnet.net> (me), where you posted a very similar matrix
>with complex entries,

>Peter


Hi Peter,


Thanks to you and all the others for their help
I regret that on the comp.soft-sys.math.mathematica my answers are not
been published. I have sent more times the answers but they are always
lost. Very strange thing. I now write here these considerations of
mine:


I apologize for the error that however had immediately corrected. The
problem is that as has already happened me other times, when I
criticize Mathematica my message it doesn't reach destination (on
comp.soft-sys.math.mathematica). Now since I am not an expert of
neswgroup someone can say to me ……why this thing happens? who filters
the messages? Is it moderate by Wolfram !!?
I have also sent a complete message in which I said that to my notice
Mathematica could have a big defect of planning respect the management
of big data but also this has gone lost
Now dispatch this and again the other.
I apologize therefore to all those people that have helped me with
very deep answers but unfortunately they referred to a wrong problem
to cause my error (the exact valus is i and not the complex I . Even
if to the goals of the calculation nothing changes having set as
variable of iteration I (the error has been due in fact to an unlucky
copy and paste in whichi has been turned into I).

The my problem is ---- During this calculation:


m= Table[ (i-j)+3.*j^-4 +50*i , {i,1,10000} , {j,1,10000} ];
Det[m]

the kernel has jammed and the following message has been visualized

No more memory available.
Mathematica kernel has shut down.


For the poster RICHARD: Hi, Richard
Thanks for the answer but the problem is not the value of the Det (in
fact I have forced the calculation so that is effected in machine's
precision ) but the interruption of the calculation that would make
to think or to a bug or as me I think to a very bad planning of the
motor of numerical calculation of the management of big data.

You understand well that to say this is a different thing that to say:
Mathematica is a Cas with the merits typical of the arbitrary
precision but it is slow in numerical calculations. The problem is
that Wolfram is publicizing the vers. 5.2 saying that its limits are
alone those represented by the 64 Bit... but to me this seems not to
be true. In my calculation the limit if there is it is not in the
available resources but in a bug or in a planning... that they have to
explain me....or I am being wrong and then that calculation must have
completed

It is not a banal problem, more times I encounter me with these

problems that really make unusable Mathematica for my purposes and
they always occur in big calculations
In such cases I am forced to pass to Matlab (or a compiled C++
programs) that is behaved better always and this is a confirmation
that this problem is not due to lack of memory or if it is so it is
because mathematica manages badly it …… Or what I am wrong in my
reasoning
You try to calculate the matrix from me suitable that has 10^5 x 10^5
elements. Around 100 GBs are needed in total but Mathematica in
presence of such resources interrupts him.Matlab instead no, why? And
you mind well me I am not an estimator of Matlab... I love Mathematica


and I want to look for a solution not to abandon it
Precise that know Mathematica enough to fund and therefore I am not
scandalized me if in such problems the time of calculation lengthens
but really I don't understand because in reality it jams
Precise that have introduced more times this problem in numerous
occasions and anybody has ever known how to give me a satisfactory
explanation. Obviously I don't expect me that Mathematica is as fast
as a compiled program but that that expect me from a so valid program
it is that if it don't succeed in completing a calculation point out
me the reality motive.
Is it a wrong thing to pretend it?

The dimension of the in demand memory is not limited from windows xp
or my hardware-software(OS) configuration, in fact such error also
happens in xp 64 Bit with Mathematica 5.2 (64 Bit) Athlon 64 2 GB Ram.

Is it probably a big limit of mathematica in to manage data of big
dimensions ?
Are these problems the true limit of mathematica ?

I think that if the usual way of calculation is not worth resources to
understand if we will succeed in finishing a calculation (or rather if
all the rules of the numerical analysis are distorted) the Wolfram
should point out what in reality Mathematica does in these types of
calculations

Richard Fateman

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Sep 11, 2005, 1:07:25 PM9/11/05
to
LumisROB wrote:
<snip>

> when I
> criticize Mathematica my message it doesn't reach destination (on
> comp.soft-sys.math.mathematica). Now since I am not an expert of
> neswgroup someone can say to me ……why this thing happens? who filters
> the messages? Is it moderate by Wolfram !!?

No, Steve Christensen is the moderator.
Maybe your message is not getting through, (but you seem to be
able to send to this newsgroup!)

You do not know how much memory Mathematica uses up unless you
measure it. It may use several times as much memory as you think
it needs. In some cases it may use O(n^2) memory when you think it
needs only O(n). It may run out of memory on a stack which is allocated
a finite resource. ($RecursionLimit is 256. But the error message
you got is less informative.) Read about ByteCount and Memory Management.

If you habitually run out of memory in a computer algebra system,
you will have to find some way to be clever to reduce the size
of the problem, or find a different method.

You may very well have found a bug in Mathematica, but that may
not solve your problem. You may just convert a program that runs
out of memory into one that runs (almost) forever.

RJF

LumisROB

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Sep 11, 2005, 3:57:48 PM9/11/05
to

Hi richard,

thanks for the help

I don't think that it is a bug I think rather than the motor of
numerical calculation has not big limits of speed but of efficiency in
the use of the memory

However Thanks

car...@colorado.edu

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Sep 11, 2005, 5:51:10 PM9/11/05
to
IMHO a well implemented data structure for lists of repeating objects
should have a memory overhead of only O(1) for a 1D n-object list,
O(n) for a 2D n x n objects list, O(n^2) for a 3D n x n x n objects
list, and so on.

That was my experience in writing database systems 3 decades
ago. Are those orders of magnitude still considered correct? For
example, what would be the overhead in Lisp for a n x n table
of identical objects?

Richard Fateman

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Sep 11, 2005, 8:16:46 PM9/11/05
to

What makes you think that Mathematica is "well implemented"?

consider this program
Test[lim_] := Do[{a = Table[ i, {i, 10^n}];
Print[Timing[a[[1]] = a[[1]] + 1;]]},

{n, 1, lim}]

What this does is it allocates a vector of size 10, 100, 1000, etc.
and then it times the operation of incrementing just one element of the
vector. In a well-implemented system, the time to change one
element of a vector, especially the first element, should be a constant
regardless of the length of the vector. In Mathematica, the time
depends on the length of the vector. In my test, going from n=6 to
n=7, the time jumps by a factor of 100. In going from n=7 to n=8
the time jumps by a factor of 8.
Try Test[8], or if you dare, Test[9].

In Lisp, normally implemented arrays of size nXm of identical
objects (i.e. pointers to the same object) should be of size
proportional to nxm.

I do not know if the language definition requires this, however.


RJF

Lumis

unread,
Sep 12, 2005, 11:13:53 AM9/12/05
to
On Sun, 11 Sep 2005 17:07:25 GMT, Richard Fateman
<fat...@cs.berkeley.edu> wrote:

>LumisROB wrote:
><snip>
.....


>
>You may very well have found a bug in Mathematica, but that may
>not solve your problem. You may just convert a program that runs
>out of memory into one that runs (almost) forever.
>
>RJF

Hi Richard,
Thanks for the help. You have understood the truth my problem. Or
rather the impossibility with Mathematica to foresee if a numerical
problem can be completed developing a simple coarse calculation
regarding the occupation of memory Ram and Virtual (use often this
approach in calculations to the limit when I use Matlab or the C). I
rest, I abdicate numerical calculations on problems (I treat problems
of structural engineering with the FEM) of big dimensions.
Unfortunately some interactions with a program as Mathematica were
often me really useful

thanks of heart to everybody

Roberto

car...@colorado.edu

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Sep 12, 2005, 12:58:33 PM9/12/05
to
My guess (without proof) is that the internal Mathematica data
structures are
a combination of linked-list and paging. That would explain the
erratic timings.

Richard J. Fateman

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Sep 12, 2005, 1:32:13 PM9/12/05
to car...@colorado.edu

The primary reason is that when you change an element in a
vector, Mathematica believes it must re-evaluate all the
elements of the vector. This means that an assignment to
a vector of length n is not O(1), but O(n), even if only one element
changes. Of course paging can also add to the expense
for large vectors.

RJF

Daniel Lichtblau

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Sep 12, 2005, 2:52:08 PM9/12/05
to

This is primarily a first-time hit. Subsequent alterations do not seem
to incur this penalty. Indeed, one can modify all of the elements in
O(n). The test below illustrates.

test[lim_] := Do[
a = Range[10^n];
Print[n];
tt1 = Timing[a[[44]]++;];
tt2 = Timing[a[[1]]++;];
tt3 = Timing[a[[10^(n-1)-2]]++;];
tt4 = Timing[a+=4];
Print[Chop[Map[First,{tt1,tt2,tt3,tt4}]]/Second];
,{n, 5, lim}]

In[2]:= test[8]
5
{0.001, 0, 0, 0.001}
6
{0.011998, 0, 0, 0.020997}
7
{0.088987, 0, 0, 0.125981}
8
{0.679896, 0, 0, 1.12283}

This reevaluation semantics used in Mathematica is admittedly not
always optimal. But it is also, in this example, not so bad as one
might guess based only on knowing the first time behavior.

Daniel Lichtblau
Wolfram Research

car...@colorado.edu

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Sep 12, 2005, 3:41:02 PM9/12/05
to
A linked list with no heap overflow area would lead to that kind
of behavior. But it is erratic so it there must be another factor.

LumisROB

unread,
Sep 12, 2005, 6:04:03 PM9/12/05
to

Hi Carlos

These problems are all predictable ones if you study to fund the
kernel of Mathematica. What is magic and incomprehensible it is the
motive for which Mathematica in numerical problems that should be
resolved interrupts him for lack of memory

Cheers
Roberto

LumisROB

unread,
Sep 12, 2005, 6:23:06 PM9/12/05
to
On 12 Sep 2005 11:52:08 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

>

>
>In[2]:= test[8]
>5
>{0.001, 0, 0, 0.001}
>6
>{0.011998, 0, 0, 0.020997}
>7
>{0.088987, 0, 0, 0.125981}
>8
>{0.679896, 0, 0, 1.12283}
>
>This reevaluation semantics used in Mathematica is admittedly not
>always optimal. But it is also, in this example, not so bad as one
>might guess based only on knowing the first time behavior.
>
>Daniel Lichtblau
>Wolfram Research

Ok I have understood this concept
This behavior is predictable knowing as mathematica kernel is
implemented

The true problem is:

is it possible to foresee in advance having a computer,
an OS (32 or 64 Bit) and Mathematica(32 or 64 Bit) which dimensions of
a determined problem I succeed in resolving?
With Matlab or Maple or C I have always succeeded in banal way in
making this calculation (I work on problems treated with Finite
Element method).
With Mathematica no and anybody me ago a practical example

For instance because he doesn't succeed in calculating

m = Table[(i - j) + 3./j^4 + 50*i, {i, 1, 10^5}, {j, 1, 10^5}];
m[[1]].m[[1]]

ByteCount[1.0]=16

if I go to calculate this matrix

logic would like 10^5 * 10^5 *16 Bytes * 10^-9 = 160 GB


This problem on my hardware is interrupted for lack of memory (as
usual).
With Matlab or Maple on Same Hardware it is resolved (Ok!! with
exasperated slowness..... but they resolve )


Matlab (or a compiled program) performs this calculation because, I
beklieve, the data that have to contemporarily enter
the memory don't exceed the available Ram and the Virtual memory
handles the rest

Because nobody responds to this question?
is it perhaps the error that I commit so banal not to even receive an
answer?

Cheers

Roberto

Daniel Lichtblau

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Sep 12, 2005, 10:43:38 PM9/12/05
to

LumisROB wrote:
> On 12 Sep 2005 11:52:08 -0700, "Daniel Lichtblau" <da...@wolfram.com>
> wrote:
>
> [...]

I can respond to some of this; other parts I simply do not understand.

First, the matrix you create takes up a considerable amount of space.
If it is an array of machine doubles one would expect it to occupy
10^4*10^4*8 bytes. But let's have a quick look with a smaller version
of the matrix.

In[4]:=
tt[n_]:=Table[(i-j)+3./j^4+50*i,{i,n},{j,n}]

In[10]:=
t200=tt[200];
b200=ByteCount[t200];
b200/200.^2

Out[12]= 8.0015

Fine so far. Let's go ever so slightly larger, to 216 rows.

In[13]:=
t216=tt[216];
b216=ByteCount[t216];
b216/216.^2

Out[15]= 20.1301

Okay...we're now using over 20 bytes per entry on average. What
happened? Apparently we no longer get a packed array (One might verify
this using the predicate Developer`PackedArrayQ). This is quite likely
a bug and in any case we'll investigate further. Right now one can work
around this problem by explicit conversion of inputs to machine
doubles.

ttpack[n_] := Table[N[(i - j)] + 3./N[j]^4 + N[50*i], {i, n}, {j, n}]

(One might wonder where and why the breakdown occurs. It happens when
we go from 215 to 216 rows. Packed arrays can handle 2^31 elements in
total, and we are crossing the threshhold of 2^(31/2) elements here,
which I'm sure will figure into the diagnosis.)

Next question is what happens if you do obtain a packed array, and then
try to take the determinant. There are a few ways in which one can run
out of memory. One is that most 32 bit Mathematica platforms have a 2
Gb limit on total space. The determinant computation will require at
least one full sized copy of the matrix (using the Lapack functions
appropriate for computing such things). I'm not certain that only one
copy is utilized; there may be a need for more workspace. Also the
800,000,000 byte matrices each need contiguous storage, which may or
may not be available. Also Mathematica itself occupies space. The
upshot is it is not hard to see memory being an issue.

As of version 5.2 there is support for 64-bit platforms, with greater
memory capabilities. We have confirmed that on 64 bit systems with
sufficient RAM the example above can be handled (tested thus far on a
Linux and a Windows machine). Specifically, one can allocate the matrix
and compute its (possibly ill conditioned) determinant.

I'll mention that we tried creating a 8000 x 8000 matrix of random
reals in one of the other languages you indicate, in order to test the
claim that it can handle matrices in that size range. We got an
out-of-memory message. It is not clear to me what exactly you do to get
different behavior. Quite likely this, too, hinges on configuration
specifics such as available RAM.

For the record, whatever you may think you did, you did not do it on a
desktop machine with a matrix occupying 160 Gb of memory. Maybe you
meant 1.6 Gb?


Daniel Lichtblau
Wolfram Research

LumisROB

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Sep 13, 2005, 11:37:48 AM9/13/05
to
On 12 Sep 2005 19:43:38 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

>


>(One might wonder where and why the breakdown occurs. It happens when
>we go from 215 to 216 rows. Packed arrays can handle 2^31 elements in
>total, and we are crossing the threshhold of 2^(31/2) elements here,
>which I'm sure will figure into the diagnosis.)

Is this limit of the packedArrays worth for Mathem 5.2?

Where these accurate information can be retrieved on the limits of the
packeds array ...etc
If they are in the documentation what time I don't have available I
apologize me. In contrary case can you point out me where to be able
to deepen the kernel of mathematica?
On the texts I am sure that nothing of this doesn't exist. It serves
me because I would like to create a program fem that should undertake
itself to develop heavy numerical computations

>Next question is what happens if you do obtain a packed array, and then
>try to take the determinant. There are a few ways in which one can run
>out of memory. One is that most 32 bit Mathematica platforms have a 2
>Gb limit on total space.

Just for this motive I have not marveled when the calculation is
arrested on Mathematica 5.1 + XP(32Bit)
I have marveled instead when the calculation is arrested on
Mathematica 5.2 + WinXP(64Bit) 2GB Ram 400GB HD


> The determinant computation will require at
>least one full sized copy of the matrix (using the Lapack functions
>appropriate for computing such things). I'm not certain that only one
>copy is utilized; there may be a need for more workspace. Also the
>800,000,000 byte matrices each need contiguous storage, which may or
>may not be available. Also Mathematica itself occupies space. The
>upshot is it is not hard to see memory being an issue.
>
>As of version 5.2 there is support for 64-bit platforms, with greater
>memory capabilities. We have confirmed that on 64 bit systems with
>sufficient RAM the example above can be handled (tested thus far on a
>Linux and a Windows machine). Specifically, one can allocate the matrix
>and compute its (possibly ill conditioned) determinant.

Could I know how much RAM could be necessary to create a matrix (if it
is possible ) of 10^5 * 10^5 elements and to operate one single
products (Blas1) of the type m[[i]]. m[[j]] ? (Mathem 5.2 + XP(64) or
Linux Suse 64)

>I'll mention that we tried creating a 8000 x 8000 matrix of random
>reals in one of the other languages you indicate, in order to test the
>claim that it can handle matrices in that size range. We got an
>out-of-memory message. It is not clear to me what exactly you do to get
>different behavior. Quite likely this, too, hinges on configuration
>specifics such as available RAM.


Personally I have experimented in positive sense using Gnu gcc +
UbuntuLinux 5.04 (64Bit) + ACML (amd) (Blas+Lapack) 2GB RAM+ 400GB HD
+Athlon64


>
>
>For the record, whatever you may think you did, you did not do it on a
>desktop machine with a matrix occupying 160 Gb of memory. Maybe you
>meant 1.6 Gb?

Attention in this case I have well specified that I create only the
matrix and I don't calculate the determinant


However thanks of heart. I have finally understood the true essence of
the problem. I believe that without understanding well as the
technology packed array has been implemented both useless to try to
make analytical calculations on the dimension of memory used during
the calculation


Cheers
Rob

Daniel Lichtblau

unread,
Sep 13, 2005, 2:45:35 PM9/13/05
to

LumisROB wrote:
> On 12 Sep 2005 19:43:38 -0700, "Daniel Lichtblau" <da...@wolfram.com>
> wrote:
>
> >
> >(One might wonder where and why the breakdown occurs. It happens when
> >we go from 215 to 216 rows. Packed arrays can handle 2^31 elements in
> >total, and we are crossing the threshhold of 2^(31/2) elements here,
> >which I'm sure will figure into the diagnosis.)
>
> Is this limit of the packedArrays worth for Mathem 5.2?

Actually I found out it is correct behavior. There is an overflow of
machine integer arithmetic in computing j^4 when j>=216. Using explicit
conversion of j to a double (via N[]) is the appropriate thing to do in
order to avoid this pitfall.


> Where these accurate information can be retrieved on the limits of the
> packeds array ...etc

As of version 5.2 the maximum number of elements in a packed array is,
I believe, 2^30 (my claim of 2^31 was probably mistaken). To the best
of my knowledge this is not documented.


> [...]


> >Next question is what happens if you do obtain a packed array, and then
> >try to take the determinant. There are a few ways in which one can run
> >out of memory. One is that most 32 bit Mathematica platforms have a 2
> >Gb limit on total space.
>
> Just for this motive I have not marveled when the calculation is
> arrested on Mathematica 5.1 + XP(32Bit)
> I have marveled instead when the calculation is arrested on
> Mathematica 5.2 + WinXP(64Bit) 2GB Ram 400GB HD

As I noted, we are able to do the computation on 64 bit platforms. One
thing to note: I am told that if you are using a beta version of 64-bit
WinXP then your Mathematica installation will most likely be for the
32-bit version.


> > [...]


> >As of version 5.2 there is support for 64-bit platforms, with greater
> >memory capabilities. We have confirmed that on 64 bit systems with
> >sufficient RAM the example above can be handled (tested thus far on a
> >Linux and a Windows machine). Specifically, one can allocate the matrix
> >and compute its (possibly ill conditioned) determinant.
>
> Could I know how much RAM could be necessary to create a matrix (if it
> is possible ) of 10^5 * 10^5 elements and to operate one single
> products (Blas1) of the type m[[i]]. m[[j]] ? (Mathem 5.2 + XP(64) or
> Linux Suse 64)

That would be 10^10 (10 billion) elements. Mathematica will not support
matrices of that size. It does not matter how much RAM you have.


> >I'll mention that we tried creating a 8000 x 8000 matrix of random
> >reals in one of the other languages you indicate, in order to test the
> >claim that it can handle matrices in that size range. We got an
> >out-of-memory message. It is not clear to me what exactly you do to get
> >different behavior. Quite likely this, too, hinges on configuration
> >specifics such as available RAM.
>
>
> Personally I have experimented in positive sense using Gnu gcc +
> UbuntuLinux 5.04 (64Bit) + ACML (amd) (Blas+Lapack) 2GB RAM+ 400GB HD
> +Athlon64

We tested one of the Ma... languages you had mentioned. We were unable
to verify your claim that it handled a 10^4 x 10^4 matrix determinant
in any way other than to run out of memory.


> >For the record, whatever you may think you did, you did not do it on a
> >desktop machine with a matrix occupying 160 Gb of memory. Maybe you
> >meant 1.6 Gb?
>
> Attention in this case I have well specified that I create only the
> matrix and I don't calculate the determinant

(1) We were unable to create a random matrix of dimension 11000 x 11000
in the language we tried. Let alone 10^5 x 10^5.

(2) Why do you specifically fault Mathematica on memory capacity for
failing to find the determinant, if Matlab and Maple cannot find it
either? You rather strongly imply that the memory restriction you
encounter is specific to Mathematica. As best we can verify, this is
not correct. At least one of those others, on our installation, got
swamped even earlier (below 8000 x 8000).

On some 32-bit platforms Mathematica will compute the determinant of a
8000 x 8000 matrix, and on others it will run out of memory. So I would
suspect there are similar memory restrictions between languages in
regard to this type of computation, at least on 32 bit platforms.

In[1]:= mat = Table[Random[], {8000}, {8000}];

In[2]:= Timing[dd = Det[mat]]

9561
Out[2]= {69.79 Second, 2.731952583914477 10


> However thanks of heart. I have finally understood the true essence of
> the problem. I believe that without understanding well as the
> technology packed array has been implemented both useless to try to
> make analytical calculations on the dimension of memory used during
> the calculation
>
>
> Cheers
> Rob

It is not terribly difficult to make memory estimates involving packed
arrays in Mathematica. The only information not documented is total
array size of 2^30 elements. You certainly know that, when packed, they
occupy 8 bytes each for machine doubles. You can assume that a
workspace copy will be required for matrix manipulations that require
level 3 BLAS. There might be other considerations related to your
machine, installation, availability of contiguous memory, etc. But most
such issues will not be specific to Mathematica.


Daniel Lichtblau
Wolfram Research

Ronald Bruck

unread,
Sep 13, 2005, 4:34:24 PM9/13/05
to
In article <4324CB72...@cs.berkeley.edu>, Richard Fateman
<fat...@cs.berkeley.edu> wrote:

> car...@colorado.edu wrote:
> > IMHO a well implemented data structure for lists of repeating objects
> > should have a memory overhead of only O(1) for a 1D n-object list,
> > O(n) for a 2D n x n objects list, O(n^2) for a 3D n x n x n objects
> > list, and so on.
> >
> > That was my experience in writing database systems 3 decades
> > ago. Are those orders of magnitude still considered correct? For
> > example, what would be the overhead in Lisp for a n x n table
> > of identical objects?
> >
>
> What makes you think that Mathematica is "well implemented"?
>
> consider this program
> Test[lim_] := Do[{a = Table[ i, {i, 10^n}];
> Print[Timing[a[[1]] = a[[1]] + 1;]]},
>
> {n, 1, lim}]
>
> What this does is it allocates a vector of size 10, 100, 1000, etc.
> and then it times the operation of incrementing just one element of the
> vector. In a well-implemented system, the time to change one
> element of a vector, especially the first element, should be a constant
> regardless of the length of the vector. In Mathematica, the time

> depends on the length of the vector...

This can be infuriating. I remember writing a database program in UCSD
Pascal thirty years ago, only to discover that the time UCSD took to
look up a record in the database depended LINEARLY on the record number
n. Why? Because, to look up byte number n*sizeof(record), it ADDED
sizeof(record) to itself n times, instead of multiplying n times
sizeof(record). Completely useless. I had to write my own file
routines.

--Ron Bruck

car...@colorado.edu

unread,
Sep 13, 2005, 5:35:37 PM9/13/05
to
I agree; the kernel is well overdue for a thorough
rewrite. It should facilitate numerical mathematics with
zero-overhead MD arrays as primitive (atomic
types) and direct access to LAPACK and PETS.
But I cannot "fund" the study. Sorry, I dont have
that kind of money.

Daniel Lichtblau

unread,
Sep 13, 2005, 6:11:27 PM9/13/05
to

car...@colorado.edu wrote:
> I agree; the kernel is well overdue for a thorough
> rewrite. It should facilitate numerical mathematics with
> zero-overhead MD arrays as primitive (atomic
> types)

What exactly do you think a packed array is in Mathematica?


and direct access to LAPACK and PETS.
> But I cannot "fund" the study. Sorry, I dont have
> that kind of money.


A considerable amount of interface to Lapack and BLAS is there but not
documented. To get some idea of the functions involved, have a look at

??LinearAlgebra`*

and

??LinearAlgebra`*`*

None of this has anything much to do with "a full rewrite" of the
Mathematica kernel, whatever that might mean.


Daniel Lichtblau
Wolfram Research

LumisROB

unread,
Sep 13, 2005, 7:17:18 PM9/13/05
to
On 13 Sep 2005 11:45:35 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:


>>


>> Just for this motive I have not marveled when the calculation is
>> arrested on Mathematica 5.1 + XP(32Bit)
>> I have marveled instead when the calculation is arrested on
>> Mathematica 5.2 + WinXP(64Bit) 2GB Ram 400GB HD
>
>As I noted, we are able to do the computation on 64 bit platforms. One
>thing to note: I am told that if you are using a beta version of 64-bit
>WinXP then your Mathematica installation will most likely be for the
>32-bit version.
>

Mathematica 5.2 from you distributed in version try has limitations?
How do I do to know if the installation of Mathematica 5.2 on Win XP
64 are really working to 64 bit?


>>
>>
>> Personally I have experimented in positive sense using Gnu gcc +
>> UbuntuLinux 5.04 (64Bit) + ACML (amd) (Blas+Lapack) 2GB RAM+ 400GB HD
>> +Athlon64
>
>We tested one of the Ma... languages you had mentioned. We were unable
>to verify your claim that it handled a 10^4 x 10^4 matrix determinant
>in any way other than to run out of memory.
>
>

>


>(1) We were unable to create a random matrix of dimension 11000 x 11000
>in the language we tried. Let alone 10^5 x 10^5.
>
>(2) Why do you specifically fault Mathematica on memory capacity for
>failing to find the determinant, if Matlab and Maple cannot find it
>either? You rather strongly imply that the memory restriction you
>encounter is specific to Mathematica. As best we can verify, this is
>not correct. At least one of those others, on our installation, got
>swamped even earlier (below 8000 x 8000).
>

I have never said this, I have never said to have resolved the
calculation of the determinant with Matlab and I have specified this
more times. I have said instead that in a lot of occasions in which I
had interruptions of numerical calculation in Mathematica I succeeded
in Matlab or C in resolving the problem.
However the problem is not this, I have observed more times that I
love Mathematica and really for this I wanted to look for remedies to
be able to use it to fund


>
>It is not terribly difficult to make memory estimates involving packed
>arrays in Mathematica. The only information not documented is total
>array size of 2^30 elements. You certainly know that, when packed, they
>occupy 8 bytes each for machine doubles. You can assume that a
>workspace copy will be required for matrix manipulations that require
>level 3 BLAS. There might be other considerations related to your
>machine, installation, availability of contiguous memory, etc. But most
>such issues will not be specific to Mathematica.
>
>

Thanks so many as soon as the time to my disposition will allow me to
deepen these matters and to apply these jewels recommends I will
certainly do it.
So many graces for the jewel help

Roberto

car...@colorado.edu

unread,
Sep 13, 2005, 8:15:52 PM9/13/05
to
By "rewrite" I mean *a* kernel for computational mathematics,
and nothing else. Call it a toolbox if you want.
Sort of "reverse Matlab". In Matlab symbolic services f
orm a separate toolbox bridge Here the
computational kernel should be a largely a bridge to public
domain libraries, of which there are several excellent ones.

The symbolic kernel should be separate from the computational
one w/each interacting with the front end. One Cell property
would be the appropriate kernel it will execute.

Interweaving high performance numerics and symbolics in the
same pot risks the danger of "bug instability": fixing a bug
introduces 10 more. Beside the appropriate data structures are
different. Uncontrollable complexity has bothered many projects:
eventually the whole programming corps is busy just chasing bugs.

LumisROB

unread,
Sep 13, 2005, 8:52:18 PM9/13/05
to
Daniel wrote:

>>
>


>


I Apologize you, I make you an example that on my hardware-software
configuration ( WinXP 32+2Gb Ram ) it brings Mathematica to fail while
it is being resolved with other tool (of which don't do the name
because it seems that I want to make publicity to other tools while my
only purpose is to understand the motor of numerical calculation of
mathematica )


m = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
10^4}];
Norm[m, Infinity]

No more memory available.
Mathematica kernel has shut down.


I have created one of them now because as I told you often in past
has happened me this and therefore I think about being able to create
many others of it. This last problem as you can easily verify it
doesn't find limits in Lapack( or other numerical library) or in the
hardware or OS(32 bit) from me used

However thanks for your help. It has been conclusive to clarify me
some concepts even if the situation is not still me well clear I will
think it on a little

Kindest regards

Roberto

Daniel Lichtblau

unread,
Sep 14, 2005, 11:23:09 AM9/14/05
to

car...@colorado.edu wrote:
> By "rewrite" I mean *a* kernel for computational mathematics,
> and nothing else. Call it a toolbox if you want.
> Sort of "reverse Matlab". In Matlab symbolic services f
> orm a separate toolbox bridge Here the
> computational kernel should be a largely a bridge to public
> domain libraries, of which there are several excellent ones.

Thank you for clarifying what you had in mind.


> The symbolic kernel should be separate from the computational
> one w/each interacting with the front end. One Cell property
> would be the appropriate kernel it will execute.

I fail to see how this strategy would be useful, if the main purpose is
to allow symbolic and numeric computations.

I certainly understand that various libraries are powerful and useful.
But some e.g for dense and sparse linear algebra are already included
in the distribution of Mathematica, and others might be accessed by
external calls e.g. via MathLink.

One necessity is that there be adequate support for needed underlying
data structures, which differ between various libraries (for good
reason). This is in general supported by the capability of importing
from and exporting to various formats, in particular some sparse matrix
formats. Certainly there may be important ones (from the point of view
of specific purposes) missing. But supporting more formats is most
likely unrelated to what you have in mind. So I would still raise the
question of specifically what and how a "numerical kernel" strategy
that relies on arbitrary (or even specific) external libraries would
do, or how it would interact with the rest of Mathematica in terms of
passing back results.

If what you want is encorporation of more external libraries in the
Mathematica distribution, that is another matter. From what you wrote I
am assuming this is not really what you have in mind.


> Interweaving high performance numerics and symbolics in the
> same pot risks the danger of "bug instability": fixing a bug
> introduces 10 more. Beside the appropriate data structures are
> different. Uncontrollable complexity has bothered many projects:
> eventually the whole programming corps is busy just chasing bugs.

I find that to be often the case due to various types of "code
fragility". In particular it can arise when one function relies on
results from many others in such a way that small, defensible changes
down below lead to worsened behavior in the caller. Symbolic
integration appears to be particularly vulnerable to this phenomenon.

What is not so clear to me is how this sort of fragility problem, if I
correctly understand you, might particularly afflict either numeric or
symbolic computation simply from their coexistence in the same general
framework. Possibly if you could give an example or two...?

One thing I will note is there is a slowly growing area of "hybrid
symbolic-numeric computation" wherein methods and algorithms from one
field get applied to the other. This interplay provides some incentive
for keeping the two regimes yoked. I'm not sure this conflicts with
what you advocate, but it seems as though it might.

Let me make a general remark or two about what I think you are
proposing. Dedicated data structures certainly have their place. For
example, the SparseArray objects introduced in version 5 of Mathematica
were intended as providing reasonable means to do fast sparse linear
algebra. But certainly they will not provide sufficient flexibility to
accomodate any and all external library needs, which again implies the
need for import/export capabilities. On the flip side, there is not
always a good reason to form special data structures when a general one
will suffice. I think packed arrays, which are just efficiently
allocated/addressed tensor structures, provide an example of this in
that they are regarded just as lists (and basically indistinguishable
therefrom) in Mathematica.

By the way, I agree with the general sentiment that Mathematica is not
amenable to implementation and effective use of arbitrary data
structures. (Such can be done, but one has to know the magic
incantations...). I find that this sort of shortcoming can be an issue
when dealing with various algorithms from computer science, for
example. It can impede Mathematica efficiency as well in the numeric
realm, when, for example, use of Compile is precluded by a need for
non-tensorial data structures. But again I do not see how your
proposal, as I understand it, would address any of this.


Daniel Lichtblau
Wolfram Research

Daniel Lichtblau

unread,
Sep 14, 2005, 11:31:43 AM9/14/05
to

LumisROB wrote:
> Daniel wrote:
>
> I Apologize you, I make you an example that on my hardware-software
> configuration ( WinXP 32+2Gb Ram ) it brings Mathematica to fail while
> it is being resolved with other tool (of which don't do the name
> because it seems that I want to make publicity to other tools while my
> only purpose is to understand the motor of numerical calculation of
> mathematica )
>
>
> m = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
> 10^4}];
> Norm[m, Infinity]
>
> No more memory available.
> Mathematica kernel has shut down.

I suspect this is because the j^4 overflows machine integer arithmetic,
causing the matrix not to be packed. When I modify this slightly to use
only machine doubles (by computing N[j]^4 instead of j^4) I get a
result.

In[17]:= mat = Table[ i - j + 3./ N[j]^4 + 50*i, {i,10^4 },
{j,10^4}];

In[18]:=Developer`PackedArrayQ[mat]
Out[18]= True

In[19]:= ByteCount[mat]
Out[19]= 800000060

In[20]:= Norm[mat, Infinity]
9
Out[20]= 5.05 10

I would guess this is small enough to work with as a packed array but a
bit too large to handle in Mathematica, at least on 32-bit
installations, when not explicitly packed.


> [...]
> Kindest regards
>
> Roberto


Daniel Lichtblau
Wolfram Research

LumisROB

unread,
Sep 14, 2005, 5:58:09 PM9/14/05
to
On 14 Sep 2005 08:31:43 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

>


>LumisROB wrote:
>> Daniel wrote:
>>
>> I Apologize you, I make you an example that on my hardware-software
>> configuration ( WinXP 32+2Gb Ram ) it brings Mathematica to fail while
>> it is being resolved with other tool (of which don't do the name
>> because it seems that I want to make publicity to other tools while my
>> only purpose is to understand the motor of numerical calculation of
>> mathematica )
>>
>>
>> m = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
>> 10^4}];
>> Norm[m, Infinity]
>>
>> No more memory available.
>> Mathematica kernel has shut down.
>
>I suspect this is because the j^4 overflows machine integer arithmetic,
>causing the matrix not to be packed. When I modify this slightly to use
>only machine doubles (by computing N[j]^4 instead of j^4) I get a
>result.
>
>
>

>Daniel Lichtblau
>Wolfram Research

Indeed this motivation explains a lot of anomalies that I found only
in the numerical calculation. It serves me know something in more on
the packeds array. Where I can look ?. Could you point out a text that
explains the bonds among Ram Virtual Memory pagining flow of low-level
data ...et cetera to a general level that can give a general vision ?

Cheers
Roberto

LumisROB

unread,
Sep 15, 2005, 4:01:14 PM9/15/05
to
On 14 Sep 2005 08:31:43 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

I have verified the things that you have written me, let's see:


>It is not terribly difficult to make memory estimates involving packed
>arrays in Mathematica. The only information not documented is total
>array size of 2^30 elements. You certainly know that, when packed, they

>occupy 8 bytes each for machine doubles. .
>Daniel Lichtblau
>Wolfram Research

Sorry, This is not always true as I have verified in more occasions
The created object is an packedarray but the dimension of which the
memory is increased doesn't correspond to what you say. Is banal to
make an example (builds my matrix with an inferior dimension and you
will see)


>You can assume that a
>workspace copy will be required for matrix manipulations that require
>level 3 BLAS. There might be other considerations related to your
>machine, installation, availability of contiguous memory, etc. But most
>such issues will not be specific to Mathematica

Sorry,this occupation of memory is necessary not only for operations
of the type Blas3
This would be logical. In fact, if I build a matrix random and then do
I build another of it without cancelling the first Mathematica it
requires that both reside in the RAM despite me doesn't perform
calculations that involve both.. it seems that the virtual memory is
not exploited Because Mathematica doesn't set the first matrix in
virtual memory to make place to the creation of the second?
I keep on not understanding the way according to which Mathematica
certainly manages the memory and the manual it doesn't help to deepen

Cheers
Roberto

Daniel Lichtblau

unread,
Sep 15, 2005, 5:19:32 PM9/15/05
to

LumisROB wrote:
> On 14 Sep 2005 08:31:43 -0700, "Daniel Lichtblau" <da...@wolfram.com>
> wrote:
>
> I have verified the things that you have written me, let's see:
>
>
> >It is not terribly difficult to make memory estimates involving packed
> >arrays in Mathematica. The only information not documented is total
> >array size of 2^30 elements. You certainly know that, when packed, they
> >occupy 8 bytes each for machine doubles. .
> >Daniel Lichtblau
> >Wolfram Research
>
> Sorry, This is not always true as I have verified in more occasions
> The created object is an packedarray but the dimension of which the
> memory is increased doesn't correspond to what you say. Is banal to
> make an example (builds my matrix with an inferior dimension and you
> will see)

Show me an example of code that
(1) Creates a matrix of machine doubles in Mathematica, such that
(2) The matrix is packed, according to Developer`PackedArrayQ, and
(3) The space occupied by the matrix, according to ByteCount, deviates
notably from 8 x total number of elements.

I have seen no indication of any matrix created in Mathematica and
satisfying these three considerations. What I have seen are matrices
with byte count approximately 20 x number of elements, but they were
not packed (I explained this once or twice).


> >You can assume that a
> >workspace copy will be required for matrix manipulations that require
> >level 3 BLAS. There might be other considerations related to your
> >machine, installation, availability of contiguous memory, etc. But most
> >such issues will not be specific to Mathematica
>
> Sorry,this occupation of memory is necessary not only for operations
> of the type Blas3
> This would be logical.

I'm pretty sure I did not say that level 3 BLAS requirements are the
ONLY reason more memory might be required. But they are a major one. In
general operations that use Lapack and require manipulation of an
entire matrix will result in Mathematica making a copy of the input
matrix.


> In fact, if I build a matrix random and then do
> I build another of it without cancelling the first Mathematica it
> requires that both reside in the RAM despite me doesn't perform
> calculations that involve both.

It is not clear to me what you are claiming. If you do

mat1 = Table[Random[],{10^3},{10^3}];
mat2 = Table[Random[],{10^3},{10^3}];

then certainly you now have two matrices. Whether both reside in RAM
will be operating system dependent.

Is this what you mean?


> it seems that the virtual memory is
> not exploited Because Mathematica doesn't set the first matrix in
> virtual memory to make place to the creation of the second?
> I keep on not understanding the way according to which Mathematica
> certainly manages the memory and the manual it doesn't help to deepen
>
> Cheers
> Roberto

Mathematica does nothing special with memory allocation (it is handled
via C malloc). This is operating system dependent.


Daniel Lichtblau
Wolfram Research

Ronald Bruck

unread,
Sep 16, 2005, 12:33:42 AM9/16/05
to
In article <makji1d5efmn4fl3u...@4ax.com>, LumisROB
<lumisrob...@yahoo.com> wrote:
> .... it seems that the virtual memory is

> not exploited Because Mathematica doesn't set the first matrix in
> virtual memory to make place to the creation of the second?
> I keep on not understanding the way according to which Mathematica
> certainly manages the memory and the manual it doesn't help to deepen

Huh? How do you "exploit virtual memory"? VM should be TRANSPARENT to
the program.

Are you, perchance, using Windows? Then get a real OS! (Although
Windows VM behaves like any other, AFAIK.)

--Ron Bruck

LumisROB

unread,
Sep 16, 2005, 2:39:15 AM9/16/05
to
On Thu, 15 Sep 2005 21:33:42 -0700, Ronald Bruck <br...@math.usc.edu>
wrote:
Hi Ronald,


>Huh? How do you "exploit virtual memory"? VM should be TRANSPARENT to
>the program.

also I have always thought this
and this I have to say it is almost always happened when I "played"
with the computer

>
>Are you, perchance, using Windows? Then get a real OS! (Although
>Windows VM behaves like any other, AFAIK.)

I start to think that you are right
what I succeed in doing with ubuntu linux (64 bit) in comparison to
windows is... upsetting
and precise that am a profane of linux
I have to resolve numerical problems with great docks of data: does it
exist in linux a program similar to matlab or mathematica that it is
reliable?

Cheers
Rob

LumisROB

unread,
Sep 16, 2005, 3:55:42 AM9/16/05
to
On 15 Sep 2005 14:19:32 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

>


>Show me an example of code that
>(1) Creates a matrix of machine doubles in Mathematica, such that
>(2) The matrix is packed, according to Developer`PackedArrayQ, and
>(3) The space occupied by the matrix, according to ByteCount, deviates
>notably from 8 x total number of elements.
>
>I have seen no indication of any matrix created in Mathematica and
>satisfying these three considerations. What I have seen are matrices
>with byte count approximately 20 x number of elements, but they were
>not packed (I explained this once or twice).
>

In[1]:=
MaxMemoryUsed[ ] * 10^-6 MB
Out[1]=
2.214328 MB
In[2]:=
m=Table[(i-j)+3./N[j] ^4+50*i,{i,1,1000},{j,1,1000}];
In[3]:=
ByteCount[m[[1,1]] ]
Out[3]=
16
In[4]:=
Developer`PackedArrayQ[m]
Out[4]=
True
In[5]:=
MaxMemoryUsed[ ] * 10^-6 MB
Out[5]=
10.132752 MB
----------------------------- OK!!!!!!!
In[6]:=
1000* 1000* 8bytes /.bytes -> 10^-6 MB
Out[6]=
8. MB
In[14]:=
m2 = Table[ (i_ j) + 3. / N[j] ^4+ 50 * i, {i, 1, 1000}, {j, 1,
1000}];
Developer`PackedArrayQ[m2]
MaxMemoryUsed[ ] * 10^-6 MB
Out[15]=
True
Out[16]=
42.14968 MB
-------------------------------- WHY ??????..... tries to define more
than once the SAME object


>It is not clear to me what you are claiming. If you do
>
>mat1 = Table[Random[],{10^3},{10^3}];
>mat2 = Table[Random[],{10^3},{10^3}];
>
>then certainly you now have two matrices. Whether both reside in RAM
>will be operating system dependent.
>
>Is this what you mean?

OK But the problem that I set me is another
If I don't succeed in working because the space of addressing (in
windows) it limits me to 2Gb (max 3Gb) then I look for share-out my
job to try to reach the finishing line. In this procedure I have to
try to break the problem in so many small problems. Such small
problems owe however to effectively be managed in the virtual memory
Is this street practicable in mathematica?

it for example is not possible to climb over limitations of memory in
a matrix multiplication passing through block matrix multiplication ?


>
>Mathematica does nothing special with memory allocation (it is handled
>via C malloc). This is operating system dependent.

>Personally I don't believe that Mathematica manages the heap and the stack in usual way.

Surely it doesn't manage the memory in the same way according to which
the memory(Heap and Stack) is managed in a program c++..... but this
doesn't marvel me, mathematica is obviously a different tool
How does it manage it?
From the manual it is not understood. The indications are very generic

>Daniel Lichtblau
>Wolfram Research

LumisROB

unread,
Sep 16, 2005, 5:56:22 AM9/16/05
to
On Fri, 16 Sep 2005 07:55:42 GMT, LumisROB
<lumisrob...@yahoo.com> wrote:


>In[14]:=
>m2 = Table[ (i_ j) + 3. / N[j] ^4+ 50 * i, {i, 1, 1000}, {j, 1,
>1000}];
>Developer`PackedArrayQ[m2]
>MaxMemoryUsed[ ] * 10^-6 MB
>Out[15]=
>True
>Out[16]=
>42.14968 MB
>-------------------------------- WHY ??????..... tries to define more
>than once the SAME object
>

Sorry,I have committed a naivety.Since I activate in automatic
$HistoryLength I had not realized in reality that has not been loaded

Cheers Rob

Ronald Bruck

unread,
Sep 16, 2005, 11:37:12 AM9/16/05
to
In article <hhpki1lq7q127m3l1...@4ax.com>, LumisROB
<lumi...@yahoo.com> wrote:
...

> I have to resolve numerical problems with great docks of data: does it
> exist in linux a program similar to matlab or mathematica that it is
> reliable?

Well, both MATLAB and Mathematica have UNIX versions. And Linux
versions. They're note quite as nice as the Mac/Windows versions in
terms of licensing (the licenses are far more sensitive to hardware
changes; both companies are responsive to requests for new passwords,
but I learned to dislike this method when Macsyma went belly-up and I
lost everything).

My impression is both programs are FASTER in Linux.

--Ron Bruck

car...@colorado.edu

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Sep 16, 2005, 12:36:07 PM9/16/05
to
The performance of VM, if implemented at all, is OS and hardware
dependent. Even for different Unix flavors (that includes Mac OSX)
your mileage may vary.

The best implementation I can recall was VAX-VMS (it had to be, given
their OS name). For the Cray I had to write my own using the idea of
a "RAM device" and was a hell of a tune up. Any comments on Windows?
I know they have used some soft comps from VMS after 2000.

LumisROB

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Sep 16, 2005, 4:34:40 PM9/16/05
to
On 16 Sep 2005 09:36:07 -0700, car...@colorado.edu wrote:

Hi Carlos
on these matters I believe that in few knows the things to
fund.Personally as soon as I think about having understood something
it arrives the test that makes to jump everything. An account is to
manage heap stack in a program and an account it is to understand the
low-level operation.
As it is possible to resolve a problem of limit of memory? if I have
to create a great matrix and the system it doesn't allow me this I
thought about breaking the problem and to resolve him... but it is not
so simple and the documentations are often poor (and if this can be
justified in a free library really I don't understand because this
happens in commercial products of elevated cost. )
I have an admiration towards the Vax-VMSs if nothing else because I
think that they forced to use the head and not to make the robots.
Do you know some book that faces these matters and is valid?
Thanks of heart

LumisROB

unread,
Sep 17, 2005, 10:54:14 AM9/17/05
to
On 15 Sep 2005 14:19:32 -0700, "Daniel Lichtblau" <da...@wolfram.com>
wrote:

>> m = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,


>> 10^4}];
>> Norm[m, Infinity]
>>
>> No more memory available.
>> Mathematica kernel has shut down.
>
>I suspect this is because the j^4 overflows machine integer arithmetic,
>causing the matrix not to be packed. When I modify this slightly to use
>only machine doubles (by computing N[j]^4 instead of j^4) I get a
>result.
>
>
>

>Daniel Lichtblau
>Wolfram Research

Indeed this motivation explains a lot of anomalies that I found only

in the numerical calculation but I think that this motive doesn't
exclude others of it.
I explain you:
I have performed the calculation under on the configuration WinXP(64)
Bit + Mathematica 5.2 + 2GB Ram + 400GB HardDisks. Working with other
tools I succeed in resolving without not even worrying me about the
virtual memory, everything it is managed in transparent way as I have
thought it always had to happen. What happens in Mathematica ?(also
assuring himself that the packed-array are built.... In this problem I
don't overcome the limit of the packeds array and not even the limit
of the space of addressing of the operating system )

m1 = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
10^4}];
m2 = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
10^4}];
m3 = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
10^4}];
m4 = Table[ i - j + 3./ j^4 + 50 * i , {i, 1, 10^ 4 }, {j, 1,
10^4}];

No more memory available.


Mathematica kernel has shut down.

>It is not terribly difficult to make memory estimates involving packed
>arrays in Mathematica. The only information not documented is.....


>There might be other considerations related to your
>machine, installation, availability of contiguous memory, etc. But most

>such issues will not be specific to Mathematica.

>Daniel Lichtblau
>Wolfram Research

I keep on thinking that you are too much optimist on Mathematica
Please explain me with some numbers because the interruption dictates
above it happens so that can understand well where I am (or my
computer + Mathematica !!! ) wrong
Thanks of your time

Rob

Richard Fateman

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Sep 17, 2005, 12:18:54 PM9/17/05
to

Dear Rob:

1. Yes, it is a poor behavior of the system if it gives you
no indication that you are approaching the limit of available memory.
Especially bad if it reaches that limit and then crashes
with loss of all work.

Mathematica should address
this issue. Some Lisp systems have a better
engineered approach to dealing with such problems,
and Mathematica could be improved.

But how many times must you post the same message?

2. The fact that you can find out how much space
is used by a particular object in Mathematica
(ignoring sharing), by ByteCount should make it
possible for you to study the phenomenon without
posting more questions.

3. The size of your computer hard disk is irrelevant,
as Daniel L. has pointed out. Please read the responses
to your questions. Perhaps find someone who is
more fluent in English to translate to your native
language.

car...@colorado.edu

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Sep 17, 2005, 2:56:20 PM9/17/05
to

28. Ronald Bruck   Sep 15, 10:33 pm     show options
Newsgroups: sci.math.symbolic
From: Ronald Bruck <b...@math.usc.edu> - Find messages by this author
Date: Thu, 15 Sep 2005 21:33:42 -0700
Local: Thurs, Sep 15 2005 10:33 pm
Subject: Re: a big limit of mathematica?

> Huh?  How do you "exploit virtual memory"?  VM should be TRANSPARENT to
> the program.

Not necessarily. In a modular and well documented OS (that is BTW
the case with most Unix flavors) you should be able to turn off the
system VM
and write your own VM pager, customized to your application
"granularity".
For example, your application might specify the page size.

LumisROB

unread,
Sep 17, 2005, 3:18:15 PM9/17/05