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numarray speed question

P: n/a
grv
So it is supposed to be very fast to have an array of say 5 million
integers stored in a binary file and do

a = numarray.fromfile('filename', (2, 2, 2))
numarray.add(a, 9, a)

but how is that faster than reading the entire file into memory and then
having a for loop in C:
(loop over range) {
*p++ += 9 }

or is that essentially what's going on?
Jul 18 '05 #1
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11 Replies


P: n/a
On Wed, 4 Aug 2004, grv wrote:
So it is supposed to be very fast to have an array of say 5 million
integers stored in a binary file and do

a = numarray.fromfile('filename', (2, 2, 2))
numarray.add(a, 9, a)

but how is that faster than reading the entire file into memory and then
having a for loop in C:
(loop over range) {
*p++ += 9 }

or is that essentially what's going on?


That's essentially what's going on ;) The point of numarray isn't to be
hyper-fast, but to be as fast as the equivalent C (or Fortran, or
what-have-you) implementation. In many cases, it's faster, because
numarray is designed with several speed hacks in mind, but it's nothing
you can't do (without a little work) in C.

Jul 18 '05 #2

P: n/a
grv
sq******@WPI.EDU (Christopher T King) wrote in
<Pi**************************************@ccc6.wpi .edu>:
On Wed, 4 Aug 2004, grv wrote:
So it is supposed to be very fast to have an array of say 5 million
integers stored in a binary file and do

a = numarray.fromfile('filename', (2, 2, 2))
numarray.add(a, 9, a)

but how is that faster than reading the entire file into memory and
then having a for loop in C:
(loop over range) {
*p++ += 9 }

or is that essentially what's going on?


That's essentially what's going on ;) The point of numarray isn't to be
hyper-fast, but to be as fast as the equivalent C (or Fortran, or
what-have-you) implementation. In many cases, it's faster, because
numarray is designed with several speed hacks in mind, but it's nothing
you can't do (without a little work) in C.


Yes but see I'm interested in what speed hacks can actually be done to
improve the above code. I just don't see anything that can iterate and add
over that memory region faster.
Jul 18 '05 #3

P: n/a
At some point, gr****@hotmail.com (grv) wrote:
sq******@WPI.EDU (Christopher T King) wrote in
<Pi**************************************@ccc6.wpi .edu>:
On Wed, 4 Aug 2004, grv wrote:
So it is supposed to be very fast to have an array of say 5 million
integers stored in a binary file and do

a = numarray.fromfile('filename', (2, 2, 2))
numarray.add(a, 9, a)

but how is that faster than reading the entire file into memory and
then having a for loop in C:
(loop over range) {
*p++ += 9 }

or is that essentially what's going on?


That's essentially what's going on ;) The point of numarray isn't to be
hyper-fast, but to be as fast as the equivalent C (or Fortran, or
what-have-you) implementation. In many cases, it's faster, because
numarray is designed with several speed hacks in mind, but it's nothing
you can't do (without a little work) in C.


Yes but see I'm interested in what speed hacks can actually be done to
improve the above code. I just don't see anything that can iterate and add
over that memory region faster.


Well, numarray probably isn't faster for this case (adding a scalar to
a vector). In fact, the relevant numarray code looks like this:

static int add_Float64_vector_scalar(long niter, long ninargs, long noutargs, vo
id **buffers, long *bsizes) {
long i;
Float64 *tin1 = (Float64 *) buffers[0];
Float64 tscalar = *(Float64 *) buffers[1];
Float64 *tout = (Float64 *) buffers[2];

for (i=0; i<niter; i++, tin1++, tout++) {
*tout = *tin1 + tscalar;
}
return 0;
}

What you *do* get with numarray is:

1) transparent handling of byteswapped, misaligned, discontiguous,
type-mismatched data (say, from a memory-mapped file generated on a
system with a different byte order as single-precision instead of
double-precision).

2) ease-of-use. That two lines of python code above is _it_ (except
for an 'import numarray' statement). Your C code isn't anywhere
nearly complete enough to use. You would need to add routines to
read the file, etc.

3) interactive use. You can do all this in the Python command line. If
you want to multiply instead of add, an up-arrow and some editing
will do that. With C, you'd have to recompile.

If you need the best possible speed (after doing it in numarray and
finding it isn't fast enough), you can write an extension module to
do that bit in C, or look into scipy.weave for inlining C code, or into
f2py for linking Fortran code to Python.

--
|>|\/|<
/--------------------------------------------------------------------------\
|David M. Cooke
|cookedm(at)physics(dot)mcmaster(dot)ca
Jul 18 '05 #4

P: n/a
co**********@physics.mcmaster.ca (David M. Cooke) wrote in message news:<qn*************@arbutus.physics.mcmaster.ca> ...
Well, numarray probably isn't faster for this case (adding a scalar to
a vector). In fact, the relevant numarray code looks like this:

static int add_Float64_vector_scalar(long niter, long ninargs, long noutargs, vo
id **buffers, long *bsizes) {
long i;
Float64 *tin1 = (Float64 *) buffers[0];
Float64 tscalar = *(Float64 *) buffers[1];
Float64 *tout = (Float64 *) buffers[2];

for (i=0; i<niter; i++, tin1++, tout++) {
*tout = *tin1 + tscalar;
}
return 0;
}
OK good. So doing it in C isn't really that much of a headache when
it comes to optimization.
What you *do* get with numarray is:

1) transparent handling of byteswapped, misaligned, discontiguous,
type-mismatched data (say, from a memory-mapped file generated on a
system with a different byte order as single-precision instead of
double-precision).
Heh. Try timing the example I gave (a += 5) using byteswapped vs.
byteswap(). It's fairly fast to do the byteswap. If you go the
interpretation way (byteswapped) then all subsequent array operations
are at least an order of magnitude slower (5 million elements test
example).
2) ease-of-use. That two lines of python code above is _it_ (except
for an 'import numarray' statement). Your C code isn't anywhere
nearly complete enough to use. You would need to add routines to
read the file, etc.
Can't argue here.
3) interactive use. You can do all this in the Python command line. If
you want to multiply instead of add, an up-arrow and some editing
will do that. With C, you'd have to recompile.
As much as I hate the .edu push for interpreted languages like lisp
and ml, having a python interpreter to test code out real quickly
before it goes into the source script is real nice.
If you need the best possible speed (after doing it in numarray and
finding it isn't fast enough), you can write an extension module to
do that bit in C, or look into scipy.weave for inlining C code, or into
f2py for linking Fortran code to Python.


Well re speed what really bothers me is the slowness in which numarray
is improving in this area. If I have to take 1000 FFT's over 32
element arrays, then it's useless. I'll have to install both numarray
and numeric :/
Jul 18 '05 #5

P: n/a
At some point, gr****@hotmail.com (grv575) wrote:
What you *do* get with numarray is:

1) transparent handling of byteswapped, misaligned, discontiguous,
type-mismatched data (say, from a memory-mapped file generated on a
system with a different byte order as single-precision instead of
double-precision).


Heh. Try timing the example I gave (a += 5) using byteswapped vs.
byteswap(). It's fairly fast to do the byteswap. If you go the
interpretation way (byteswapped) then all subsequent array operations
are at least an order of magnitude slower (5 million elements test
example).


You mean something like
a = arange(0, 5000000, type=Float64).byteswapped()
a += 5

vs.
a = arange(0, 5000000, type=Float64)
a.byteswap()
a += 5

? I get the same time for the a+=5 in each case -- and it's only twice
as slow as operating on a non-byteswapped version. Note that numarray
calls the ufunc add routine with non-byteswapped numbers; it takes a
block, orders it correctly, then adds 5 to that, does the byteswap on
the result, and stores that back. (You're not making a full copy of
the array; just a large enough section at a time to do useful work.)
If you need the best possible speed (after doing it in numarray and
finding it isn't fast enough), you can write an extension module to
do that bit in C, or look into scipy.weave for inlining C code, or into
f2py for linking Fortran code to Python.


Well re speed what really bothers me is the slowness in which numarray
is improving in this area. If I have to take 1000 FFT's over 32
element arrays, then it's useless. I'll have to install both numarray
and numeric :/


Maybe what you need is a package designed for *small* arrays ( < 1000).
Simple C wrappers; just C doubles and ints, no byteswap, non-aligned.
Maybe a fixed number of dimensions. Probably easy to throw something
together using Pyrex. Or, wrap blitz++ with boost::python.

--
|>|\/|<
/--------------------------------------------------------------------------\
|David M. Cooke
|cookedm(at)physics(dot)mcmaster(dot)ca
Jul 18 '05 #6

P: n/a
grv
co**********@physics.mcmaster.ca (David M. Cooke) wrote in
<qn*************@arbutus.physics.mcmaster.ca>:
At some point, gr****@hotmail.com (grv575) wrote:
Heh. Try timing the example I gave (a += 5) using byteswapped vs.
byteswap(). It's fairly fast to do the byteswap. If you go the
interpretation way (byteswapped) then all subsequent array operations
are at least an order of magnitude slower (5 million elements test
example).


You mean something like
a = arange(0, 5000000, type=Float64).byteswapped()
a += 5

vs.
a = arange(0, 5000000, type=Float64)
a.byteswap()
a += 5

? I get the same time for the a+=5 in each case -- and it's only twice
as slow as operating on a non-byteswapped version. Note that numarray
calls the ufunc add routine with non-byteswapped numbers; it takes a
block, orders it correctly, then adds 5 to that, does the byteswap on
the result, and stores that back. (You're not making a full copy of
the array; just a large enough section at a time to do useful work.)


It must be using some sort of cache for the multiplication. Seems like on
the first run it takes 6 seconds and subsequently .05 seconds for either
version.
Maybe what you need is a package designed for *small* arrays ( < 1000).
Simple C wrappers; just C doubles and ints, no byteswap, non-aligned.
Maybe a fixed number of dimensions. Probably easy to throw something
together using Pyrex. Or, wrap blitz++ with boost::python.


I'll check out Numeric first. Would rather have a drop-in solution (which
hopefully will get more optimized in future releases) rather than hacking
my own wrappers. Is it some purist mentality that's keeping numarray from
dropping to C code for the time-critical routines? Or can a lot of the
speed issues be attributed to the overhead of using objects for the library
(numarray does seem more general)?
Jul 18 '05 #7

P: n/a
At some point, gr****@hotmail.com (grv) wrote:
co**********@physics.mcmaster.ca (David M. Cooke) wrote in
<qn*************@arbutus.physics.mcmaster.ca>:
At some point, gr****@hotmail.com (grv575) wrote:

Heh. Try timing the example I gave (a += 5) using byteswapped vs.
byteswap(). It's fairly fast to do the byteswap. If you go the
interpretation way (byteswapped) then all subsequent array operations
are at least an order of magnitude slower (5 million elements test
example).


You mean something like
a = arange(0, 5000000, type=Float64).byteswapped()
a += 5

vs.
a = arange(0, 5000000, type=Float64)
a.byteswap()
a += 5

? I get the same time for the a+=5 in each case -- and it's only twice
as slow as operating on a non-byteswapped version. Note that numarray
calls the ufunc add routine with non-byteswapped numbers; it takes a
block, orders it correctly, then adds 5 to that, does the byteswap on
the result, and stores that back. (You're not making a full copy of
the array; just a large enough section at a time to do useful work.)


It must be using some sort of cache for the multiplication. Seems like on
the first run it takes 6 seconds and subsequently .05 seconds for either
version.


There is. The ufunc for the addition gets cached, so the first time
takes longer (but not that much???)
Maybe what you need is a package designed for *small* arrays ( < 1000).
Simple C wrappers; just C doubles and ints, no byteswap, non-aligned.
Maybe a fixed number of dimensions. Probably easy to throw something
together using Pyrex. Or, wrap blitz++ with boost::python.


I'll check out Numeric first. Would rather have a drop-in solution (which
hopefully will get more optimized in future releases) rather than hacking
my own wrappers. Is it some purist mentality that's keeping numarray from
dropping to C code for the time-critical routines? Or can a lot of the
speed issues be attributed to the overhead of using objects for the library
(numarray does seem more general)?


It's the object overhead in numarray. The developers moved stuff up to
Python, where it's more flexible to handle. Numeric is faster for
small arrays (say < 3000), but numarray is much better at large
arrays. I have some speed comparisions at
http://arbutus.mcmaster.ca/dmc/numpy/

I did a simple wrapper using Pyrex the other night for a vector of
doubles (it just does addition, so it's not much good :-) It's twice
as fast as Numeric, so I might give it a further try.

--
|>|\/|<
/--------------------------------------------------------------------------\
|David M. Cooke
|cookedm(at)physics(dot)mcmaster(dot)ca
Jul 18 '05 #8

P: n/a
Is it true that python uses doubles for all it's internal floating
point arithmetic even if you're using something like numarray's
Complex32? Is it possible to do single precision ffts in numarray or
no?

co**********@physics.mcmaster.ca (David M. Cooke) wrote in message news:<qn*************@arbutus.physics.mcmaster.ca> ...
At some point, gr****@hotmail.com (grv) wrote:
co**********@physics.mcmaster.ca (David M. Cooke) wrote in
<qn*************@arbutus.physics.mcmaster.ca>:
At some point, gr****@hotmail.com (grv575) wrote: Heh. Try timing the example I gave (a += 5) using byteswapped vs.
byteswap(). It's fairly fast to do the byteswap. If you go the
interpretation way (byteswapped) then all subsequent array operations
are at least an order of magnitude slower (5 million elements test
example).

You mean something like
a = arange(0, 5000000, type=Float64).byteswapped()
a += 5

vs.
a = arange(0, 5000000, type=Float64)
a.byteswap()
a += 5

? I get the same time for the a+=5 in each case -- and it's only twice
as slow as operating on a non-byteswapped version. Note that numarray
calls the ufunc add routine with non-byteswapped numbers; it takes a
block, orders it correctly, then adds 5 to that, does the byteswap on
the result, and stores that back. (You're not making a full copy of
the array; just a large enough section at a time to do useful work.)


It must be using some sort of cache for the multiplication. Seems like on
the first run it takes 6 seconds and subsequently .05 seconds for either
version.


There is. The ufunc for the addition gets cached, so the first time
takes longer (but not that much???)
Maybe what you need is a package designed for *small* arrays ( < 1000).
Simple C wrappers; just C doubles and ints, no byteswap, non-aligned.
Maybe a fixed number of dimensions. Probably easy to throw something
together using Pyrex. Or, wrap blitz++ with boost::python.


I'll check out Numeric first. Would rather have a drop-in solution (which
hopefully will get more optimized in future releases) rather than hacking
my own wrappers. Is it some purist mentality that's keeping numarray from
dropping to C code for the time-critical routines? Or can a lot of the
speed issues be attributed to the overhead of using objects for the library
(numarray does seem more general)?


It's the object overhead in numarray. The developers moved stuff up to
Python, where it's more flexible to handle. Numeric is faster for
small arrays (say < 3000), but numarray is much better at large
arrays. I have some speed comparisions at
http://arbutus.mcmaster.ca/dmc/numpy/

I did a simple wrapper using Pyrex the other night for a vector of
doubles (it just does addition, so it's not much good :-) It's twice
as fast as Numeric, so I might give it a further try.

Jul 18 '05 #9

P: n/a
grv575 wrote:
Is it true that python uses doubles for all it's internal floating
point arithmetic
Yes.

even if you're using something like numarray's Complex32?
No. Numarray is an extension module and can use whatever numeric types
it feels like. Float32 for instance is an array of C floats (assuming
floats are 32 bits on your box, which they almost certainly are).
Is it possible to do single precision ffts in numarray or no?
I believe so, but I'm not sure off the top of my head. I recommend that
you ask on numpy-discussion <nu**************@lists.sourceforge.net> or
peek at the implementation. It's possible that all FFTs are done double
precision, but I don't think so.

-tim

co**********@physics.mcmaster.ca (David M. Cooke) wrote in message news:<qn*************@arbutus.physics.mcmaster.ca> ...
At some point, gr****@hotmail.com (grv) wrote:

co**********@physics.mcmaster.ca (David M. Cooke) wrote in
<qn*************@arbutus.physics.mcmaster.ca> :
At some point, gr****@hotmail.com (grv575) wrote:

>Heh. Try timing the example I gave (a += 5) using byteswapped vs.
>byteswap(). It's fairly fast to do the byteswap. If you go the
>interpretation way (byteswapped) then all subsequent array operations
>are at least an order of magnitude slower (5 million elements test
>example).

You mean something like
a = arange(0, 5000000, type=Float64).byteswapped()
a += 5

vs.
a = arange(0, 5000000, type=Float64)
a.byteswap()
a += 5

? I get the same time for the a+=5 in each case -- and it's only twice
as slow as operating on a non-byteswapped version. Note that numarray
calls the ufunc add routine with non-byteswapped numbers; it takes a
block, orders it correctly, then adds 5 to that, does the byteswap on
the result, and stores that back. (You're not making a full copy of
the array; just a large enough section at a time to do useful work.)

It must be using some sort of cache for the multiplication. Seems like on
the first run it takes 6 seconds and subsequently .05 seconds for either
version.


There is. The ufunc for the addition gets cached, so the first time
takes longer (but not that much???)

Maybe what you need is a package designed for *small* arrays ( < 1000).
Simple C wrappers; just C doubles and ints, no byteswap, non-aligned.
Maybe a fixed number of dimensions. Probably easy to throw something
together using Pyrex. Or, wrap blitz++ with boost::python.

I'll check out Numeric first. Would rather have a drop-in solution (which
hopefully will get more optimized in future releases) rather than hacking
my own wrappers. Is it some purist mentality that's keeping numarray from
dropping to C code for the time-critical routines? Or can a lot of the
speed issues be attributed to the overhead of using objects for the library
(numarray does seem more general)?


It's the object overhead in numarray. The developers moved stuff up to
Python, where it's more flexible to handle. Numeric is faster for
small arrays (say < 3000), but numarray is much better at large
arrays. I have some speed comparisions at
http://arbutus.mcmaster.ca/dmc/numpy/

I did a simple wrapper using Pyrex the other night for a vector of
doubles (it just does addition, so it's not much good :-) It's twice
as fast as Numeric, so I might give it a further try.


Jul 18 '05 #10

P: n/a
At some point, Tim Hochberg <ti**********@ieee.org> wrote:
grv575 wrote:

Is it possible to do single precision ffts in numarray or
no?


I believe so, but I'm not sure off the top of my head. I recommend
that you ask on numpy-discussion
<nu**************@lists.sourceforge.net> or peek at the
implementation. It's possible that all FFTs are done double precision,
but I don't think so.


Looks like the numarray.fft package uses doubles.

If you really need floats, SciPy wraps the single- and
double-precision versions of FFTW. (Although SciPy uses Numeric, not
numarray).

Or, you can make your own version of numarray.fft using floats
(actually looks to relatively simple to do).

--
|>|\/|<
/--------------------------------------------------------------------------\
|David M. Cooke
|cookedm(at)physics(dot)mcmaster(dot)ca
Jul 18 '05 #11

P: n/a
Great that cleared up that discrepancy between the source and the code
I'm translating to. I think I've tried all the libraries though,
numarray.fft, numarray.fftpack, scipi's fft module. I've even got the
install script for scipi to tell me it found fftw modules so I'm
pretty sure it was using them, but I'm getting the same speeds for
each module...and the code _should_ be about 10x faster (compared to
C/fortran/etc.) They really should better document exactly how to get
fast ffts up and running under these number packages.

co**********@physics.mcmaster.ca (David M. Cooke) wrote in message news:<qn*************@arbutus.physics.mcmaster.ca> ...
At some point, Tim Hochberg <ti**********@ieee.org> wrote:
grv575 wrote:

Is it possible to do single precision ffts in numarray or
no?


I believe so, but I'm not sure off the top of my head. I recommend
that you ask on numpy-discussion
<nu**************@lists.sourceforge.net> or peek at the
implementation. It's possible that all FFTs are done double precision,
but I don't think so.


Looks like the numarray.fft package uses doubles.

If you really need floats, SciPy wraps the single- and
double-precision versions of FFTW. (Although SciPy uses Numeric, not
numarray).

Or, you can make your own version of numarray.fft using floats
(actually looks to relatively simple to do).

Jul 18 '05 #12

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