pysparse-users

Re: [Pysparse-users] item iterators

[Dominique O. <dom...@gm...>]

On Fri, Sep 4, 2009 at 8:09 AM, Jose Blanca<jb...@bt...> wrote:
> Hi:
> I'm new to pyparse, thanks for doing this tool open source.
> I'm trying to  store an sparse vector and to get the results. My requirements
> a quite simple I just need to store some items and to get them at the end of
> the analysis.
> I've created the matrix with:
> vect = pysparse.spmatrix.ll_mat(nelements, 1, size_hint)
>
> And now I want to get the items from the matrix. I could do:
> items = vect.items()
>
> The problem is that the created items is a list not an iterator. That consumes
> a lot of extra memory just to access the matrix. Is this the expected
> behaviour or am I missing something?

Hi Jose,

Sorry for the late reply. Pysparse objects are not iterable and
weren't really designed to store vectors (although they obviously can)
but large sparse matrices. As Lukasz suggested, you can use find() to
get the values in triple format as Numpy arrays and iterate through
those. However, you may find it more convenient to simply store your
sparse vector in a dictionary and iterate through the list of items.

-- 
Dominique

Re: [Pysparse-users] item iterators

[<lu...@o2...>]

Jose Blanca <jb...@bt...> writes:

> Hi:
> I'm new to pyparse, thanks for doing this tool open source.
> I'm trying to  store an sparse vector and to get the results. My requirements 
> a quite simple I just need to store some items and to get them at the end of 
> the analysis.
> I've created the matrix with:
> vect = pysparse.spmatrix.ll_mat(nelements, 1, size_hint)
>
> And now I want to get the items from the matrix. I could do:
> items = vect.items()

Not exactly what you ask, but you may try

values, rows, cols = vect.find()

which returns numpy arrays instead of tuples.

>
> The problem is that the created items is a list not an iterator. That consumes 
> a lot of extra memory just to access the matrix. Is this the expected 
> behaviour or am I missing something?
> Best Regards,

[Pysparse-users] item iterators

[Jose B. <jb...@bt...>]

Hi:
I'm new to pyparse, thanks for doing this tool open source.
I'm trying to  store an sparse vector and to get the results. My requirements 
a quite simple I just need to store some items and to get them at the end of 
the analysis.
I've created the matrix with:
vect = pysparse.spmatrix.ll_mat(nelements, 1, size_hint)

And now I want to get the items from the matrix. I could do:
items = vect.items()

The problem is that the created items is a list not an iterator. That consumes 
a lot of extra memory just to access the matrix. Is this the expected 
behaviour or am I missing something?
Best Regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)

Re: [Pysparse-users] [Pysparse-developers] Bug from Debian user

[Adam C P. IV <haz...@de...>]

Thanks very much Dan!  I'll package it soon.

-Adam

On Mon, 2009-08-31 at 18:47 -0400, Daniel Wheeler wrote:
> Hi,
> 
> I did a release of version 1.1 of pysparse, which involved:
> 
>   - bumping version number to 1.1
>   - creating tags/version-1_1 branch
>   - releasing using the tags/version-1_1 branch
>   - bumping version number to 1.2a1 (just a way to say that you don't
> have version 1,1 but a later revision on trunk)
> 
> Future bug fixes should be done on "branches/version-1_1".
> "tags/version-1_1" is just a place holder to remember which revision
> version 1.1 was, it shouldn't be touched.
> 
> There are a lot of changes from 1.0 and I don't know what all of them
> are.I think the main difference between 1.1 and 1,0 is the vastly
> superior indexing capabilities thanks to Dominque's wonderful effort
> to get fancy type indexing working in pysparse.
> 
> Cheers
> 
> On Wed, Aug 5, 2009 at 3:29 PM, Adam C Powell IV<haz...@de...> wrote:
> > On Wed, 2009-08-05 at 15:09 -0400, Daniel Wheeler wrote:
> >> On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote:
> >> > Hi Dan,
> >> >
> >> > Yes, an official release would be helpful.  Using SVN is generally a
> >> > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a
> >> > complex package, so I wanted to use SVN to iron out the bugs before
> >> > release.
> >>
> >> I see. You just need to iron out dependencies and stuff like that
> >
> > Yeah, that's not a problem.
> >
> >> > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that.
> >>
> >> I'll do it soon and give you a heads up when it is done. This is going
> >> into the Debian repositories correct? What about Ubuntu?
> >
> > Yes, into Debian.  Ubuntu slurps Debian packages into their "universe"
> > soon after release.  So the Karmic universe is already well-established
> > by now, and they'll only update packages if they are core to their
> > release plans -- which pysparse almost certainly is not.
> >
> >> One other thing. Now that pysparse will be in the repositories (and
> >> also trilinos in lenny and karmic), I don't think there is anything
> >> stopping us going ahead with getting fipy in there. How should I
> >> proceed with that?
> >
> > Indeed, that was my original motivation for packaging PySparse. :-)
> >
> > I'll revisit that after packaging the new PySparse release.
> >
> > -Adam
-- 
GPG fingerprint: D54D 1AEE B11C CE9B A02B  C5DD 526F 01E8 564E E4B6

Engineering consulting with open source tools
http://www.opennovation.com/

Re: [Pysparse-users] [Pysparse-developers] Bug from Debian user

[Daniel W. <dan...@gm...>]

Hi,

I did a release of version 1.1 of pysparse, which involved:

  - bumping version number to 1.1
  - creating tags/version-1_1 branch
  - releasing using the tags/version-1_1 branch
  - bumping version number to 1.2a1 (just a way to say that you don't
have version 1,1 but a later revision on trunk)

Future bug fixes should be done on "branches/version-1_1".
"tags/version-1_1" is just a place holder to remember which revision
version 1.1 was, it shouldn't be touched.

There are a lot of changes from 1.0 and I don't know what all of them
are.I think the main difference between 1.1 and 1,0 is the vastly
superior indexing capabilities thanks to Dominque's wonderful effort
to get fancy type indexing working in pysparse.

Cheers

On Wed, Aug 5, 2009 at 3:29 PM, Adam C Powell IV<haz...@de...> wrote:
> On Wed, 2009-08-05 at 15:09 -0400, Daniel Wheeler wrote:
>> On Wed, Aug 5, 2009 at 2:02 PM, Adam C Powell IV<haz...@de...> wrote:
>> > Hi Dan,
>> >
>> > Yes, an official release would be helpful.  Using SVN is generally a
>> > temporary thing, e.g. Elmer is hoping to release 6.0 this Fall, and is a
>> > complex package, so I wanted to use SVN to iron out the bugs before
>> > release.
>>
>> I see. You just need to iron out dependencies and stuff like that
>
> Yeah, that's not a problem.
>
>> > So if there's a 1.1.0 pysparse soon, I'll go ahead and package that.
>>
>> I'll do it soon and give you a heads up when it is done. This is going
>> into the Debian repositories correct? What about Ubuntu?
>
> Yes, into Debian.  Ubuntu slurps Debian packages into their "universe"
> soon after release.  So the Karmic universe is already well-established
> by now, and they'll only update packages if they are core to their
> release plans -- which pysparse almost certainly is not.
>
>> One other thing. Now that pysparse will be in the repositories (and
>> also trilinos in lenny and karmic), I don't think there is anything
>> stopping us going ahead with getting fipy in there. How should I
>> proceed with that?
>
> Indeed, that was my original motivation for packaging PySparse. :-)
>
> I'll revisit that after packaging the new PySparse release.
>
> -Adam
> --
> GPG fingerprint: D54D 1AEE B11C CE9B A02B  C5DD 526F 01E8 564E E4B6
>
> Engineering consulting with open source tools
> http://www.opennovation.com/
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> Pysparse-developers mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-developers
>
>



-- 
Daniel Wheeler

Re: [Pysparse-users] example

[Dominique O. <dom...@gm...>]

On Fri, Aug 7, 2009 at 2:42 PM, Jaim Bucay <Jai...@ra...> wrote:

> Hi, I have never used Pysparse before. I would like to use it to create a
> very large Sparse Matrix and find its Eigenvalues. Do you know where I can
> get some simple examples of how to implement something like this. Thank you.


If you look at http://pysparse.sf.net
 and follow the documentation, you will find several examples that
will help you understand how to populate a sparse matrix with
Pysparse. For the computation of eigenvalues, look into the jdsym
module:
http://pysparse.sourceforge.net/jdsym.html
Be aware that this is a very expensive operation, especially if you
need *all* eigenvalues. Often,
you only need to find a few.

-- 
Dominique

[Pysparse-users] example

[Jaim B. <Jai...@ra...>]

Hi, I have never used Pysparse before. I would like to use it to create a 
very large Sparse Matrix and find its Eigenvalues. Do you know where I can 
get some simple examples of how to implement something like this. Thank 
you.

Jaim Bucay
Post-Grad Student Tech.
(520) 665-5837

Re: [Pysparse-users] Using find() function for spmatrix

[Dominique O. <dom...@gm...>]

On Wed, Jul 1, 2009 at 4:33 PM, Oz Nahum <na...@gm...> wrote:

> Hi Everyone,
> I find pysparse a very nice tool.
> I've been playing around with it for a couple of days.
> I was wondering how use the find() function.
>
> it try this:
>
> >>> from pysparse import *
> >>> m = 5
> >>> n = 5
> >>>
> >>> A = spmatrix.ll_mat(m*n, m*n)
> >>>
> >>> H = 3
> >>> V = 2
> >>> a = [0,0,] #row index
> >>> b = [0,1,] #column index
> >>> val = [H+V, -H,] #node value
> >>> A.put(val,a,b)
> >>>
> >>> val1, a1,b1 = A.find()
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> AttributeError: find
>
> It seems the object does not have this function, or most likely I am doing
> something wrong...
>
> I am using the latest debian package of pysparse, any help would be
> appreciated.
>

Hi Oz,

You are not doing anything wrong, but I am not sure we still have anyone to
maintain a deb for Pysparse. The one you have is for an outdated version of
Pysparse. You will have access to the find() method if you use the svn
version of Pysparse. Your script works as is for me.

Cheers,
Dominique

[Pysparse-users] Using find() function for spmatrix

[Oz N. <na...@gm...>]

Hi Everyone,
I find pysparse a very nice tool.
I've been playing around with it for a couple of days.
I was wondering how use the find() function.

it try this:

>>> from pysparse import *
>>> m = 5
>>> n = 5
>>>
>>> A = spmatrix.ll_mat(m*n, m*n)
>>>
>>> H = 3
>>> V = 2
>>> a = [0,0,] #row index
>>> b = [0,1,] #column index
>>> val = [H+V, -H,] #node value
>>> A.put(val,a,b)
>>>
>>> val1, a1,b1 = A.find()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: find

It seems the object does not have this function, or most likely I am doing
something wrong...

I am using the latest debian package of pysparse, any help would be
appreciated.

Thanks,

Oz

-- 
----
           Imagine there's no countries
           It isn't hard to do
           Nothing to kill or die for
           And no religion too
           Imagine all the people
           Living life in peace

[Pysparse-users] cvs2svn

[Daniel W. <dan...@gm...>]

This is a note to inform pysparse users that the pysparse CVS
repository was today migrated to subversion. To checkout pysparse's
trunk use

   $ svn co https://pysparse.svn.sourceforge.net/svnroot/pysparse/trunk

Cheers

-- 
Daniel Wheeler

Re: [Pysparse-users] questions about pysparse versions

[Daniel W. <dan...@gm...>]

On Fri, Sep 26, 2008 at 9:42 PM,  <dx...@my...> wrote:
> Hi,
>
> I understand pysparse is updated to work with numpy (vs. old numeric)
> since version 1.0. My question is,
>
> 1. Will ver 1.01 has the same syntax as ver 0.34?

Essential, yes. The main difference is that everything is imported
under the "pysparse" umbrella. You will have to change your code form

   >>> import pysparse_module

to

   >>> import pysparse.pysparse_module as pysparse_module

This change eradicated the name space pollution and cleaned up site-packages.

> 2. Do I have to change my old code that works with ver 0.34 in order
> to use ver 1.01 ?

Yes as outlined above.

> 3. Does ver 1.01 still work with numeric?

Yes, at least it is designed to. You need to specify that you want to
use Numeric in setup.py.

> I've been using 0.34.032 and pretty happy with it, so I'm a little
> worried the compatibility issues that may take place after upgrading
> pysparse to ver 1.01.

There is no added functionality so it may not be worth it. The changes
were required to stay current with the rest of the scientific python
community.

-- 
Daniel Wheeler

[Pysparse-users] questions about pysparse versions

[<dx...@my...>]

Hi,

I understand pysparse is updated to work with numpy (vs. old numeric)
since version 1.0. My question is,

1. Will ver 1.01 has the same syntax as ver 0.34?

2. Do I have to change my old code that works with ver 0.34 in order
to use ver 1.01 ?

3. Does ver 1.01 still work with numeric?

I've been using 0.34.032 and pretty happy with it, so I'm a little
worried the compatibility issues that may take place after upgrading
pysparse to ver 1.01.

Thanks,

-DX

Re: [Pysparse-users] Comlpex numbers

[Roman G. <rom...@gm...>]

Hello

pysparse only deals with double precision real numbers. The was a 
followup project called pysparse2, implemented with C++ templates that 
was intended to support arbitrary matrix element types. Unfortunately 
pysparse2 was never completed. So it's just doubles now.

Regards,
Roman

Daniel Wheeler wrote:
> Hi,
>
> As far as I know, I don't believe that pysparse was ever written to
> deal with complex numbers. The original author of the code would
> probably know better. I certainly am not aware that anyone has tried
> making pysparse work with complex numbers. I do hear a lot of
> discussion on the scipy list regarding sparse matrices and complex
> numbers. Scipy sparse matrices almost certainly are fully configured
> to deal with complex numbers so you might want to try that. Cheers
>
> On Sun, Sep 21, 2008 at 10:23 AM, 1 1 <gsh...@gm...> wrote:
>   
>> ---------- Forwarded message ----------
>> From: 1 1 <gsh...@gm...>
>> Date: 2008/9/21
>> Subject: Comlpex numbers
>> To: if...@ma...
>>
>>
>> This code:
>>     from pysparse import spmatrix
>>     print spmatrix.LLMatType # print complex
>>     a = spmatrix.ll_mat(1,1)
>>     a[0,0]=12j
>> not work. Error: can't conver complex to float.
>> Complex numbers do not work?
>> Thanks.
>>
>>
>>
>>
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Pysparse-users mailing list
>> Pys...@li...
>> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>>
>>
>>     
>
>
>
>   

Re: [Pysparse-users] Comlpex numbers

[Daniel W. <dan...@gm...>]

Hi,

As far as I know, I don't believe that pysparse was ever written to
deal with complex numbers. The original author of the code would
probably know better. I certainly am not aware that anyone has tried
making pysparse work with complex numbers. I do hear a lot of
discussion on the scipy list regarding sparse matrices and complex
numbers. Scipy sparse matrices almost certainly are fully configured
to deal with complex numbers so you might want to try that. Cheers

On Sun, Sep 21, 2008 at 10:23 AM, 1 1 <gsh...@gm...> wrote:
>
>
> ---------- Forwarded message ----------
> From: 1 1 <gsh...@gm...>
> Date: 2008/9/21
> Subject: Comlpex numbers
> To: if...@ma...
>
>
> This code:
>     from pysparse import spmatrix
>     print spmatrix.LLMatType # print complex
>     a = spmatrix.ll_mat(1,1)
>     a[0,0]=12j
> not work. Error: can't conver complex to float.
> Complex numbers do not work?
> Thanks.
>
>
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
>



-- 
Daniel Wheeler

[Pysparse-users] Comlpex numbers

[1 1 <gsh...@gm...>]

---------- Forwarded message ----------
From: 1 1 <gsh...@gm...>
Date: 2008/9/21
Subject: Comlpex numbers
To: if...@ma...


This code:
    from pysparse import spmatrix
    print spmatrix.LLMatType # print complex
    a = spmatrix.ll_mat(1,1)
    a[0,0]=12j
not work. Error: can't conver complex to float.
Complex numbers do not work?
Thanks.

Re: [Pysparse-users] Compiling pysparse on a 64 bit machine

[Daniel W. <dan...@gm...>]

I had a similar problem with pytrilinos that required the swig
interface to be fixed. It should work whatever int type is chosen. I
might look into this at some point. Cheers.

On Thu, Jul 10, 2008 at 6:11 AM, Artur Palha <art...@gm...> wrote:
> Hello Daniel
>
> Once again I manage to solve the problem.
>
> When I was trying to make a simple program that mimics the problem I
> have, to send you, as you asked, I found the problem. Maybe there is a
> bug with pysparse or the problem is mine.
>
> The simplest program is:
>
> import numpy
> import pysparse
>
> GN = numpy.array([0,1,2,3])
>
> B = pysparse.spmatrix.ll_mat(10, 10, 10)
>
> for i in range(0,2):
>    B[GN[i], GN[i]] += 10
>
> print B
>
>
> If you do this it works. But if you use:
>
> GN = numpy.array([0,1,2,3], dtype="int32")
>
> It gives the error I stated.
>
> If one prints the dtype of GN of the first code, it states that it is
> int64. Hence the problem is that one cannot give in32 as an index to a
> ll_mat on a 64bit machine, or at least on mine.
>
> Once again thank you for your help!
>
> -artur palha
>
> On Wed, Jul 9, 2008 at 3:16 PM, Artur Palha <art...@gm...> wrote:
>> Thank you for the help, again.
>>
>> The error it gives is:
>>
>> IndexError: first index is invalid
>>
>> And the error comes up when I try to assign a value to an entry of the
>> B matrix in this way:
>>
>> B[ GN[e,n,m], GN[e,i,j] ] += something
>>
>> B is the sparse matrix and GN is a 3d array.
>>
>> I have checked that the values of GN are correct. The exact same code
>> works on another machine. I even tried a simpler code and it gives the
>> same error. The strange thing is that if I try to do it in ipython,
>> line by line, it works. Even if I assign a the value of GN to another
>> variable, as:
>>
>> a = GN[e,n,m]
>> b = GN[e,i,j]
>>
>> and then try:
>>
>> B[a,b] += something
>>
>> it does not work also, or if I assing to a and b constant values as:
>>
>> a = 1
>> b = 2
>>
>> B[a,b] += something
>>
>> It only works if I do:
>>
>> B[1,2] += something
>>
>> Any help?
>>
>> Thank you
>>
>> -artur palha
>>
>> On Thu, Jul 3, 2008 at 6:06 PM, Daniel Wheeler
>> <dan...@gm...> wrote:
>>> On Thu, Jul 3, 2008 at 8:50 AM, Artur Palha <art...@gm...> wrote:
>>>> I hope someone can help me
>>>>
>>>> I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.
>>>>
>>>> It compiles but gives an error acessing the sparse arrays.
>>>
>>> What is the error? I use pysparse on a 64 bit machine without problems.
>>>
>>>> I read on
>>>> the README file that there is an incompatibility issue with pysparse
>>>> and numpy on 64bit machines and that a patch is needed.
>>>
>>> According to the CVS log, the message was there from the initial
>>> import of pysparse. I'll remove it.
>>>
>>>> I have
>>>> installed version 1.1.0 of Numpy do I need the patch or the problem is
>>>> somewhere else?
>>>
>>> Can you give some more details?
>>>
>>> --
>>> Daniel Wheeler
>>>
>>
>



-- 
Daniel Wheeler

Re: [Pysparse-users] Compiling pysparse on a 64 bit machine

[Artur P. <art...@gm...>]

Hello Daniel

Once again I manage to solve the problem.

When I was trying to make a simple program that mimics the problem I
have, to send you, as you asked, I found the problem. Maybe there is a
bug with pysparse or the problem is mine.

The simplest program is:

import numpy
import pysparse

GN = numpy.array([0,1,2,3])

B = pysparse.spmatrix.ll_mat(10, 10, 10)

for i in range(0,2):
    B[GN[i], GN[i]] += 10

print B


If you do this it works. But if you use:

GN = numpy.array([0,1,2,3], dtype="int32")

It gives the error I stated.

If one prints the dtype of GN of the first code, it states that it is
int64. Hence the problem is that one cannot give in32 as an index to a
ll_mat on a 64bit machine, or at least on mine.

Once again thank you for your help!

-artur palha

On Wed, Jul 9, 2008 at 3:16 PM, Artur Palha <art...@gm...> wrote:
> Thank you for the help, again.
>
> The error it gives is:
>
> IndexError: first index is invalid
>
> And the error comes up when I try to assign a value to an entry of the
> B matrix in this way:
>
> B[ GN[e,n,m], GN[e,i,j] ] += something
>
> B is the sparse matrix and GN is a 3d array.
>
> I have checked that the values of GN are correct. The exact same code
> works on another machine. I even tried a simpler code and it gives the
> same error. The strange thing is that if I try to do it in ipython,
> line by line, it works. Even if I assign a the value of GN to another
> variable, as:
>
> a = GN[e,n,m]
> b = GN[e,i,j]
>
> and then try:
>
> B[a,b] += something
>
> it does not work also, or if I assing to a and b constant values as:
>
> a = 1
> b = 2
>
> B[a,b] += something
>
> It only works if I do:
>
> B[1,2] += something
>
> Any help?
>
> Thank you
>
> -artur palha
>
> On Thu, Jul 3, 2008 at 6:06 PM, Daniel Wheeler
> <dan...@gm...> wrote:
>> On Thu, Jul 3, 2008 at 8:50 AM, Artur Palha <art...@gm...> wrote:
>>> I hope someone can help me
>>>
>>> I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.
>>>
>>> It compiles but gives an error acessing the sparse arrays.
>>
>> What is the error? I use pysparse on a 64 bit machine without problems.
>>
>>> I read on
>>> the README file that there is an incompatibility issue with pysparse
>>> and numpy on 64bit machines and that a patch is needed.
>>
>> According to the CVS log, the message was there from the initial
>> import of pysparse. I'll remove it.
>>
>>> I have
>>> installed version 1.1.0 of Numpy do I need the patch or the problem is
>>> somewhere else?
>>
>> Can you give some more details?
>>
>> --
>> Daniel Wheeler
>>
>

Re: [Pysparse-users] Compiling pysparse on a 64 bit machine

[Daniel W. <dan...@gm...>]

Put the simplest script that you can together that demonstrates the
problem and I'll try running it on a variety machines that we have
here and perhaps see what is going on.

Cheers.

On Wed, Jul 9, 2008 at 9:16 AM, Artur Palha <art...@gm...> wrote:
> Thank you for the help, again.
>
> The error it gives is:
>
> IndexError: first index is invalid
>
> And the error comes up when I try to assign a value to an entry of the
> B matrix in this way:
>
> B[ GN[e,n,m], GN[e,i,j] ] += something
>
> B is the sparse matrix and GN is a 3d array.
>
> I have checked that the values of GN are correct. The exact same code
> works on another machine. I even tried a simpler code and it gives the
> same error. The strange thing is that if I try to do it in ipython,
> line by line, it works. Even if I assign a the value of GN to another
> variable, as:
>
> a = GN[e,n,m]
> b = GN[e,i,j]
>
> and then try:
>
> B[a,b] += something
>
> it does not work also, or if I assing to a and b constant values as:
>
> a = 1
> b = 2
>
> B[a,b] += something
>
> It only works if I do:
>
> B[1,2] += something
>
> Any help?
>
> Thank you
>
> -artur palha
>
> On Thu, Jul 3, 2008 at 6:06 PM, Daniel Wheeler
> <dan...@gm...> wrote:
>> On Thu, Jul 3, 2008 at 8:50 AM, Artur Palha <art...@gm...> wrote:
>>> I hope someone can help me
>>>
>>> I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.
>>>
>>> It compiles but gives an error acessing the sparse arrays.
>>
>> What is the error? I use pysparse on a 64 bit machine without problems.
>>
>>> I read on
>>> the README file that there is an incompatibility issue with pysparse
>>> and numpy on 64bit machines and that a patch is needed.
>>
>> According to the CVS log, the message was there from the initial
>> import of pysparse. I'll remove it.
>>
>>> I have
>>> installed version 1.1.0 of Numpy do I need the patch or the problem is
>>> somewhere else?
>>
>> Can you give some more details?
>>
>> --
>> Daniel Wheeler
>>
>



-- 
Daniel Wheeler

Re: [Pysparse-users] Compiling pysparse on a 64 bit machine

[Artur P. <art...@gm...>]

Thank you for the help, again.

The error it gives is:

IndexError: first index is invalid

And the error comes up when I try to assign a value to an entry of the
B matrix in this way:

B[ GN[e,n,m], GN[e,i,j] ] += something

B is the sparse matrix and GN is a 3d array.

I have checked that the values of GN are correct. The exact same code
works on another machine. I even tried a simpler code and it gives the
same error. The strange thing is that if I try to do it in ipython,
line by line, it works. Even if I assign a the value of GN to another
variable, as:

a = GN[e,n,m]
b = GN[e,i,j]

and then try:

B[a,b] += something

it does not work also, or if I assing to a and b constant values as:

a = 1
b = 2

B[a,b] += something

It only works if I do:

B[1,2] += something

Any help?

Thank you

-artur palha

On Thu, Jul 3, 2008 at 6:06 PM, Daniel Wheeler
<dan...@gm...> wrote:
> On Thu, Jul 3, 2008 at 8:50 AM, Artur Palha <art...@gm...> wrote:
>> I hope someone can help me
>>
>> I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.
>>
>> It compiles but gives an error acessing the sparse arrays.
>
> What is the error? I use pysparse on a 64 bit machine without problems.
>
>> I read on
>> the README file that there is an incompatibility issue with pysparse
>> and numpy on 64bit machines and that a patch is needed.
>
> According to the CVS log, the message was there from the initial
> import of pysparse. I'll remove it.
>
>> I have
>> installed version 1.1.0 of Numpy do I need the patch or the problem is
>> somewhere else?
>
> Can you give some more details?
>
> --
> Daniel Wheeler
>

Re: [Pysparse-users] Compiling pysparse on a 64 bit machine

[Daniel W. <dan...@gm...>]

On Thu, Jul 3, 2008 at 8:50 AM, Artur Palha <art...@gm...> wrote:
> I hope someone can help me
>
> I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.
>
> It compiles but gives an error acessing the sparse arrays.

What is the error? I use pysparse on a 64 bit machine without problems.

> I read on
> the README file that there is an incompatibility issue with pysparse
> and numpy on 64bit machines and that a patch is needed.

According to the CVS log, the message was there from the initial
import of pysparse. I'll remove it.

> I have
> installed version 1.1.0 of Numpy do I need the patch or the problem is
> somewhere else?

Can you give some more details?

-- 
Daniel Wheeler

[Pysparse-users] Compiling pysparse on a 64 bit machine

[Artur P. <art...@gm...>]

I hope someone can help me

I am trying to compile pysparse on a 64 bit machine with openSuse 10.3.

It compiles but gives an error acessing the sparse arrays. I read on
the README file that there is an incompatibility issue with pysparse
and numpy on 64bit machines and that a patch is needed. I have
installed version 1.1.0 of Numpy do I need the patch or the problem is
somewhere else?

Thanking in advance.

Best regards

-artur palha

Re: [Pysparse-users] Adding a column of a sparse matrix to a dense vector

[gorkiana m. <gor...@gm...>]

Dominique,

Yes, I noticed that, I also made some changes because it asked numerix which
was inside Fipy. Thank you. But yet I could not use it.

Nevertheless I managed to solve my problem during this weekend.

Basically pysparse.spmatrix.ll_mat objects have two methods: keys() and
values()

With this two it is possible to do what I want. This is what I did:

A = pysparse.spmatrix.ll_mat(10,10)   # a 10 x 10 sparse matrix
X = numpy.arange(0,10)                       # a dense vector of length 10

A[0,1] = 10; A[0,2] = 10; A[0,3] = 10

To add the first row of A to X one just needs to do the following:

A_indices = numpy.array(A[0,:].keys())[:,1]     # keys is a list of tuples,
so converting to numpy.array yelds a matrix
                                                                         #
the first column is the row index and the second column the column index
                                                                         #
we just need the column index
                                                                         #
we get a vector with the indices where A has nonzero values at row 0
A_values = numpy.array(A[0,:].values())         # the nonzero values of row
0

X[A_indices] = X[A_indices] + A_values

Simple!

Thank you very much Dominique and Daniel for your help. Probably I will have
more looks at FiPy because I will have more problems for sure!

-artur palha

On Sat, Jun 21, 2008 at 2:58 PM, Dominique Orban <dom...@gm...>
wrote:

> Artur,
>
> On top of the file that Daniel sent, you also need sparseMatrix.py
> which you can download from the repository Daniel mentioned earlier. I
> also attach it below.
>
> Good luck,
> Dominique
>
> On Fri, Jun 20, 2008 at 10:09 AM, Daniel Wheeler
> <dan...@gm...> wrote:
> > On Fri, Jun 20, 2008 at 6:50 AM, Artur Palha <art...@gm...>
> wrote:
> >> Thank you for your help Daniel
> >
> > No problem.
> >
> >> I have downloaded it but it is asking for more modules from your
> project.
> >
> > Yes. I realized that Dominique Orban created a version of this that
> > works with pysparse alone. See attachment. It really needs to be
> > integrated into pysparse properly. I just haven't had a chance yet.
> >
> >> I will try to have a look and see if I can do something based on what
> >> you did. In the meantime I will also have a look a pyTrilinos.
> >
> > Try scipy as well.
> >
> > --
> > Daniel Wheeler
> >
> > -------------------------------------------------------------------------
> > Check out the new SourceForge.net Marketplace.
> > It's the best place to buy or sell services for
> > just about anything Open Source.
> > http://sourceforge.net/services/buy/index.php
> > _______________________________________________
> > Pysparse-users mailing list
> > Pys...@li...
> > https://lists.sourceforge.net/lists/listinfo/pysparse-users
> >
> >
>

Re: [Pysparse-users] Adding a column of a sparse matrix to a dense vector

[Dominique O. <dom...@gm...>]

Artur,

On top of the file that Daniel sent, you also need sparseMatrix.py
which you can download from the repository Daniel mentioned earlier. I
also attach it below.

Good luck,
Dominique

On Fri, Jun 20, 2008 at 10:09 AM, Daniel Wheeler
<dan...@gm...> wrote:
> On Fri, Jun 20, 2008 at 6:50 AM, Artur Palha <art...@gm...> wrote:
>> Thank you for your help Daniel
>
> No problem.
>
>> I have downloaded it but it is asking for more modules from your project.
>
> Yes. I realized that Dominique Orban created a version of this that
> works with pysparse alone. See attachment. It really needs to be
> integrated into pysparse properly. I just haven't had a chance yet.
>
>> I will try to have a look and see if I can do something based on what
>> you did. In the meantime I will also have a look a pyTrilinos.
>
> Try scipy as well.
>
> --
> Daniel Wheeler
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
>

Re: [Pysparse-users] Adding a column of a sparse matrix to a dense vector

[Daniel W. <dan...@gm...>]

On Fri, Jun 20, 2008 at 6:50 AM, Artur Palha <art...@gm...> wrote:
> Thank you for your help Daniel

No problem.

> I have downloaded it but it is asking for more modules from your project.

Yes. I realized that Dominique Orban created a version of this that
works with pysparse alone. See attachment. It really needs to be
integrated into pysparse properly. I just haven't had a chance yet.

> I will try to have a look and see if I can do something based on what
> you did. In the meantime I will also have a look a pyTrilinos.

Try scipy as well.

-- 
Daniel Wheeler

Re: [Pysparse-users] Adding a column of a sparse matrix to a dense vector

[Artur P. <art...@gm...>]

Thank you for your help Daniel

I have downloaded it but it is asking for more modules from your project.

I will try to have a look and see if I can do something based on what
you did. In the meantime I will also have a look a pyTrilinos.

Thank you once again.

-artur palha

On Tue, Jun 17, 2008 at 11:33 AM, Artur Palha <art...@gm...> wrote:
> Hi to you all, I hope someone can help me.
>
> I am trying to do the following with pysparse but I am having problems doing it.
>
> I have a dense vector, say:
>
> x = numpy.arange(0,10)
>
> and a sparse matrix:
>
> A = pysparse.spmatrix.ll_mat(10,10)
>
> What I wish to do is:
>
> x = x + A[:, 2]
>
> But this gives the following error:
> TypeError: unsupported operand type(s) for +: 'float' and 'll_mat'
>
> Then I tried like this:
>
> x = numpy.arange(0,10)
>
> A = pysparse.sparray.sparray((10,10))
>
> With this it works ok but then, when I try to do a slice:
>
> A_reduced = A[0:5, 0:5]
>
> It gives an error:
> TypeError: unsupported operand type(s) for +: 'int' and 'slice'
>
> Anybody can give a help?
>
> Also, what is the main difference between spmatrix and sparray?
>
> Thanking in advance
>
> Best regards
>
> -artur palha
>