Re: Slight recode of gsll/data/permutations.lisp (Re: Bugfix for gsll/data/permutations.lisp)
This is a follow-up on the previous patch.
I applied the same principles on data/combination.lisp and recoded using GSL's combination functions only. Again this cleared up some errors or failures on my end.
I hope that I did not mangle major pieces of your design intent.
Mirko
On Fri, Nov 27, 2015 at 10:43 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Liam,
I am not trying to bludgeon this issue to death nor convince the you that I am right and you are wrong.
In a nutshell, I started on this path because of exception errors when trying to load GSLL on Windows (SBCL or CCL) using GSL compiled MinGW64. I traced this to the initialization of the permutation structures and the size of the requested memory (see recent post on CFFI mailing list).
I decided to rewrite a small part of permutation.lisp to use GSL's code to directly initialize and query permutation structure. The attached patch contains the rewrite and some minor edits. All the permutation and qrpt tests pass.
The patch should be considered a proof-of-concept (or failure of concept).
For me, this patch has cleared the exception errors that have started me on this trek. Even if it is not accepted, I learned something, and it was fun. And I can keep it on my GSLL so that it runs for me.
Best,
Mirko
On Thu, Nov 26, 2015 at 10:24 AM, Liam Healy lhealy@common-lisp.net wrote:
Added thought: you can lookup any GSL (C) function to find the CL equivalent by using gsl-lookup. So for example
(gsl:gsl-lookup "gsl_permute_vector") PERMUTE T
tells you #'permute is the function you want. If there is no equivalent (there are some C functions with no interface in CL), you will get NIL as the return value of this function.
Liam
On Wed, Nov 25, 2015 at 11:20 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Thanks for the explanations - I missed the :generic and :method
specifiers.
I'll study the macro-expansions.
Sorry for the noise.
Mirko
On Tue, Nov 24, 2015 at 10:16 PM, Liam Healy lhealy@common-lisp.net
wrote:
The original code looks right to me.
You have taken the generic function and the associated foreign vector methods #'permute and gratuitously renamed them #'permute-vector, leaving the method for raw C pointer with the original name and no generic function. Then you completely delete the generic function and vector methods for #'permute-inverse for no apparent reason, leaving a method for the raw C pointer only.
There is no duplicated code here. There is certainly the equivalent of gsl_permute_vector, it is the GRID:VECTOR-DOUBLE-FLOAT (second arg) method of #'permute (which you renamed).
I recommend macroexpansion as a way of seeing what's being defined. If you use emacs, place the cursor on the defmfun line and do C-c C-m. Then you will see all the generic functions and methods, and you will see there is no error in the original code.
On Tue, Nov 24, 2015 at 5:43 PM, Mirko Vukovic <
mirko.vukovic@gmail.com>
wrote:
Because of a typo, GSLL did not have the equivalent of GSL_PERMUTE_VECTOR.
There was also a section of duplicated code.
This patch should fix these errors.
NOTE: I did not test this patch - My GSLL system is not behaving super-cleanly on MSYS2 and GSL2.1. Proceed with care.
Mirko
Thanks for these patches. I think that GSLL should use the GSL functions for permutations and combinations rather than relying on the foreign representation as vectors (and the wrong type, too, as you discovered). There is some loss of use of grid functions for manipulation, but I never used that anyway (and I doubt anyone else did).
However, I would make some changes. Please use defmobject to define the permutation and combination classes. It defines the interface to GSL following GSL's standard way of naming functions. Second, GSLL does not define interfaces to any _calloc functions, relying instead on separate functions for clearing/resetting the data (and GSL always defines a function for doing that). I'm not sure of the value of the _calloc functions, but if they are thought useful, they should be defined for every mobject and thus need a change in defmobject. So, I would eliminate the :initialize keyword for now.
The best way to learn how to use defmobject is to look at the other uses of it in GSLL. When you write something, you can macroexpand it to see that what comes out looks correct. Try macroexpanding the defmobject histogram form and see how the interface to the foreign object and functions is defined.
I have created an issue at https://gitlab.common-lisp.net/antik/gsll/issues/2. If you want to register as a user on gitlab.common-lisp.net, I can assign it to you and we can continue discussion and patches there. Thanks again.
Liam
On Sun, Nov 29, 2015 at 10:02 AM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
This is a follow-up on the previous patch.
I applied the same principles on data/combination.lisp and recoded using GSL's combination functions only. Again this cleared up some errors or failures on my end.
I hope that I did not mangle major pieces of your design intent.
Mirko
On Fri, Nov 27, 2015 at 10:43 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Liam,
I am not trying to bludgeon this issue to death nor convince the you that I am right and you are wrong.
In a nutshell, I started on this path because of exception errors when trying to load GSLL on Windows (SBCL or CCL) using GSL compiled MinGW64. I traced this to the initialization of the permutation structures and the size of the requested memory (see recent post on CFFI mailing list).
I decided to rewrite a small part of permutation.lisp to use GSL's code to directly initialize and query permutation structure. The attached patch contains the rewrite and some minor edits. All the permutation and qrpt tests pass.
The patch should be considered a proof-of-concept (or failure of concept).
For me, this patch has cleared the exception errors that have started me on this trek. Even if it is not accepted, I learned something, and it was fun. And I can keep it on my GSLL so that it runs for me.
Best,
Mirko
On Thu, Nov 26, 2015 at 10:24 AM, Liam Healy lhealy@common-lisp.net wrote:
Added thought: you can lookup any GSL (C) function to find the CL equivalent by using gsl-lookup. So for example
(gsl:gsl-lookup "gsl_permute_vector") PERMUTE T
tells you #'permute is the function you want. If there is no equivalent (there are some C functions with no interface in CL), you will get NIL as the return value of this function.
Liam
On Wed, Nov 25, 2015 at 11:20 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Thanks for the explanations - I missed the :generic and :method specifiers. I'll study the macro-expansions.
Sorry for the noise.
Mirko
On Tue, Nov 24, 2015 at 10:16 PM, Liam Healy lhealy@common-lisp.net wrote:
The original code looks right to me.
You have taken the generic function and the associated foreign vector methods #'permute and gratuitously renamed them #'permute-vector, leaving the method for raw C pointer with the original name and no generic function. Then you completely delete the generic function and vector methods for #'permute-inverse for no apparent reason, leaving a method for the raw C pointer only.
There is no duplicated code here. There is certainly the equivalent of gsl_permute_vector, it is the GRID:VECTOR-DOUBLE-FLOAT (second arg) method of #'permute (which you renamed).
I recommend macroexpansion as a way of seeing what's being defined. If you use emacs, place the cursor on the defmfun line and do C-c C-m. Then you will see all the generic functions and methods, and you will see there is no error in the original code.
On Tue, Nov 24, 2015 at 5:43 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Because of a typo, GSLL did not have the equivalent of GSL_PERMUTE_VECTOR.
There was also a section of duplicated code.
This patch should fix these errors.
NOTE: I did not test this patch - My GSLL system is not behaving super-cleanly on MSYS2 and GSL2.1. Proceed with care.
Mirko
Hi Liam,
thanks for the feedback. I will get an account on gitlab.
Mirko
On Fri, Jan 1, 2016 at 1:12 PM, Liam Healy lhealy@common-lisp.net wrote:
Thanks for these patches. I think that GSLL should use the GSL functions for permutations and combinations rather than relying on the foreign representation as vectors (and the wrong type, too, as you discovered). There is some loss of use of grid functions for manipulation, but I never used that anyway (and I doubt anyone else did).
However, I would make some changes. Please use defmobject to define the permutation and combination classes. It defines the interface to GSL following GSL's standard way of naming functions. Second, GSLL does not define interfaces to any _calloc functions, relying instead on separate functions for clearing/resetting the data (and GSL always defines a function for doing that). I'm not sure of the value of the _calloc functions, but if they are thought useful, they should be defined for every mobject and thus need a change in defmobject. So, I would eliminate the :initialize keyword for now.
The best way to learn how to use defmobject is to look at the other uses of it in GSLL. When you write something, you can macroexpand it to see that what comes out looks correct. Try macroexpanding the defmobject histogram form and see how the interface to the foreign object and functions is defined.
I have created an issue at https://gitlab.common-lisp.net/antik/gsll/issues/2. If you want to register as a user on gitlab.common-lisp.net, I can assign it to you and we can continue discussion and patches there. Thanks again.
Liam
On Sun, Nov 29, 2015 at 10:02 AM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
This is a follow-up on the previous patch.
I applied the same principles on data/combination.lisp and recoded using GSL's combination functions only. Again this cleared up some errors or failures on my end.
I hope that I did not mangle major pieces of your design intent.
Mirko
On Fri, Nov 27, 2015 at 10:43 PM, Mirko Vukovic <mirko.vukovic@gmail.com
wrote:
Liam,
I am not trying to bludgeon this issue to death nor convince the you
that
I am right and you are wrong.
In a nutshell, I started on this path because of exception errors when trying to load GSLL on Windows (SBCL or CCL) using GSL compiled MinGW64. I traced this to the initialization of the permutation structures and the size of the requested memory (see recent post on CFFI mailing list).
I decided to rewrite a small part of permutation.lisp to use GSL's code
to
directly initialize and query permutation structure. The attached patch contains the rewrite and some minor edits. All the permutation and qrpt tests pass.
The patch should be considered a proof-of-concept (or failure of
concept).
For me, this patch has cleared the exception errors that have started me on this trek. Even if it is not accepted, I learned something, and it was fun. And I can keep it on my GSLL so that it runs for me.
Best,
Mirko
On Thu, Nov 26, 2015 at 10:24 AM, Liam Healy lhealy@common-lisp.net wrote:
Added thought: you can lookup any GSL (C) function to find the CL equivalent by using gsl-lookup. So for example
(gsl:gsl-lookup "gsl_permute_vector") PERMUTE T
tells you #'permute is the function you want. If there is no equivalent (there are some C functions with no interface in CL), you will get NIL as the return value of this function.
Liam
On Wed, Nov 25, 2015 at 11:20 PM, Mirko Vukovic <
mirko.vukovic@gmail.com>
wrote:
Thanks for the explanations - I missed the :generic and :method specifiers. I'll study the macro-expansions.
Sorry for the noise.
Mirko
On Tue, Nov 24, 2015 at 10:16 PM, Liam Healy <lhealy@common-lisp.net
wrote:
The original code looks right to me.
You have taken the generic function and the associated foreign
vector
methods #'permute and gratuitously renamed them #'permute-vector, leaving the method for raw C pointer with the original name and no generic function. Then you completely delete the generic function
and
vector methods for #'permute-inverse for no apparent reason,
leaving a
method for the raw C pointer only.
There is no duplicated code here. There is certainly the equivalent
of
gsl_permute_vector, it is the GRID:VECTOR-DOUBLE-FLOAT (second arg) method of #'permute (which you renamed).
I recommend macroexpansion as a way of seeing what's being defined.
If
you use emacs, place the cursor on the defmfun line and do C-c C-m. Then you will see all the generic functions and methods, and you
will
see there is no error in the original code.
On Tue, Nov 24, 2015 at 5:43 PM, Mirko Vukovic mirko.vukovic@gmail.com wrote: > Because of a typo, GSLL did not have the equivalent of > GSL_PERMUTE_VECTOR. > > There was also a section of duplicated code. > > This patch should fix these errors. > > NOTE: I did not test this patch - My GSLL system is not behaving > super-cleanly on MSYS2 and GSL2.1. Proceed with care. > > Mirko
I got an account on gitlab. I need to find a time slot to work on this, so no progress in next few days.
Thanks for the coding suggestions.
Mirko
On Mon, Jan 4, 2016 at 7:18 AM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
Hi Liam,
thanks for the feedback. I will get an account on gitlab.
Mirko
On Fri, Jan 1, 2016 at 1:12 PM, Liam Healy lhealy@common-lisp.net wrote:
Thanks for these patches. I think that GSLL should use the GSL functions for permutations and combinations rather than relying on the foreign representation as vectors (and the wrong type, too, as you discovered). There is some loss of use of grid functions for manipulation, but I never used that anyway (and I doubt anyone else did).
However, I would make some changes. Please use defmobject to define the permutation and combination classes. It defines the interface to GSL following GSL's standard way of naming functions. Second, GSLL does not define interfaces to any _calloc functions, relying instead on separate functions for clearing/resetting the data (and GSL always defines a function for doing that). I'm not sure of the value of the _calloc functions, but if they are thought useful, they should be defined for every mobject and thus need a change in defmobject. So, I would eliminate the :initialize keyword for now.
The best way to learn how to use defmobject is to look at the other uses of it in GSLL. When you write something, you can macroexpand it to see that what comes out looks correct. Try macroexpanding the defmobject histogram form and see how the interface to the foreign object and functions is defined.
I have created an issue at https://gitlab.common-lisp.net/antik/gsll/issues/2. If you want to register as a user on gitlab.common-lisp.net, I can assign it to you and we can continue discussion and patches there. Thanks again.
Liam
On Sun, Nov 29, 2015 at 10:02 AM, Mirko Vukovic mirko.vukovic@gmail.com wrote:
This is a follow-up on the previous patch.
I applied the same principles on data/combination.lisp and recoded using GSL's combination functions only. Again this cleared up some errors or failures on my end.
I hope that I did not mangle major pieces of your design intent.
Mirko
On Fri, Nov 27, 2015 at 10:43 PM, Mirko Vukovic <
mirko.vukovic@gmail.com>
wrote:
Liam,
I am not trying to bludgeon this issue to death nor convince the you
that
I am right and you are wrong.
In a nutshell, I started on this path because of exception errors when trying to load GSLL on Windows (SBCL or CCL) using GSL compiled MinGW64. I traced this to the initialization of the permutation structures and the size of the requested memory (see recent post on CFFI mailing list).
I decided to rewrite a small part of permutation.lisp to use GSL's
code to
directly initialize and query permutation structure. The attached patch
contains
the rewrite and some minor edits. All the permutation and qrpt tests pass.
The patch should be considered a proof-of-concept (or failure of
concept).
For me, this patch has cleared the exception errors that have started
me
on this trek. Even if it is not accepted, I learned something, and it was fun. And I can keep it on my GSLL so that it runs for me.
Best,
Mirko
On Thu, Nov 26, 2015 at 10:24 AM, Liam Healy lhealy@common-lisp.net wrote:
Added thought: you can lookup any GSL (C) function to find the CL equivalent by using gsl-lookup. So for example
(gsl:gsl-lookup "gsl_permute_vector") PERMUTE T
tells you #'permute is the function you want. If there is no equivalent (there are some C functions with no interface in CL), you will get NIL as the return value of this function.
Liam
On Wed, Nov 25, 2015 at 11:20 PM, Mirko Vukovic <
mirko.vukovic@gmail.com>
wrote:
Thanks for the explanations - I missed the :generic and :method specifiers. I'll study the macro-expansions.
Sorry for the noise.
Mirko
On Tue, Nov 24, 2015 at 10:16 PM, Liam Healy <
lhealy@common-lisp.net>
wrote: > > The original code looks right to me. > > You have taken the generic function and the associated foreign
vector
> methods #'permute and gratuitously renamed them #'permute-vector, > leaving the method for raw C pointer with the original name and no > generic function. Then you completely delete the generic function
and
> vector methods for #'permute-inverse for no apparent reason,
leaving a
> method for the raw C pointer only. > > There is no duplicated code here. There is certainly the
equivalent of
> gsl_permute_vector, it is the GRID:VECTOR-DOUBLE-FLOAT (second arg) > method of #'permute (which you renamed). > > I recommend macroexpansion as a way of seeing what's being
defined. If
> you use emacs, place the cursor on the defmfun line and do C-c C-m. > Then you will see all the generic functions and methods, and you
will
> see there is no error in the original code. > > On Tue, Nov 24, 2015 at 5:43 PM, Mirko Vukovic > mirko.vukovic@gmail.com > wrote: > > Because of a typo, GSLL did not have the equivalent of > > GSL_PERMUTE_VECTOR. > > > > There was also a section of duplicated code. > > > > This patch should fix these errors. > > > > NOTE: I did not test this patch - My GSLL system is not behaving > > super-cleanly on MSYS2 and GSL2.1. Proceed with care. > > > > Mirko
-
Liam Healy -
Mirko Vukovic