November 2015 - gsll-devel - mailman3.common-lisp.net

Re: Slight recode of gsll/data/permutations.lisp (Re: Bugfix for gsll/data/permutations.lisp)
by Mirko Vukovic 22 Jan '16

22 Jan '16

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(a)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(a)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(a)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(a)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(a)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 >> > >> > >> > >

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Re: [patch] fix gsl-config-pathname
by Munawar Cheema 29 Dec '15

29 Dec '15

I tried to check this on my OS X Mavericks system with CCL but I am getting readtable errors. Just to make sure this is what I did. I git cloned both antik and gsll to my local-projects directory from https://gitlab.common-lisp.net/groups/antik If I git log I see the commit of antik is:63fa8e0a0c04090... and for gsll it is: ad5409ec81f4af... When I try either (ql:quickload :antik) or (ql:quickload :gsll) i get errors like: Reader error on #<BASIC-FILE-CHARACTER-INPUT-STREAM ("/Users/mcheema/quicklisp/local-projects/antik/tests/physical-quantities-grid.lisp"/4 UTF-8) #x3020023E839D>, near position 2047, within "m)) #(1.0d0 5.0d": Undefined character #\( in a #\# dispatch macro. Reader error on #<BASIC-FILE-CHARACTER-INPUT-STREAM ("/Users/mcheema/quicklisp/local-projects/gsll/polynomial.lisp"/4 UTF-8) #x3020024DCCBD>, near position 1730, within "t x.\") #+fsbv (defm": Undefined character #\+ in a #\# dispatch macro. I see there was a commit relating to a named-readtable recently and maybe that is causing the problem or I am just not doing this correctly. -- Kind Regards Munawar

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gsll+msys2, gsl2.0, antik patches
by Mirko Vukovic 06 Dec '15

06 Dec '15

For GSLL I am attaching two git patches that accomplish several things: - Loading of GSL that is part of MSYS2 on Windows - Removed dependency on Osicat library - Enable loading of GSL 2.0 by fixing a bit of code in nonlinear least squares fitter. - Disabled loading of basis-spline.lisp - Cosmetic fixes. I could not figure out the problem with basis-spline. I thus removed it. There may be a much better solution than that. I checked the above on latest CCL and SBCL on Windows 7. Warning: the two commits required some git surgery (splitting a commit into two). I hope that I did not introduce additional problems with the splits. For Antik I am attaching one patch that fixes the readtable problem on CCL: (named-readtables:defreadtable :antik (:merge :standard) #-ccl(:macro-char #\# :dispatch)) Without the patch all #... reader macros (CL and Antik) were deleted. With this patch both CL and Antik's reader macros work in CCL. I also tried the patch with SBCL, and I don't see a need for it. But since the macro-char redefinition did not hurt in SBCL, I left it in. Mirko

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Slight recode of gsll/data/permutations.lisp (Re: Bugfix for gsll/data/permutations.lisp)
by Mirko Vukovic 28 Nov '15

28 Nov '15

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(a)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(a)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(a)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(a)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 > > > > >

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Bugfix for gsll/data/permutations.lisp
by Mirko Vukovic 26 Nov '15

26 Nov '15

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

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Trying to write the interface to gsl_multifit_fdfsolver_jac
by Mirko Vukovic 13 Nov '15

13 Nov '15

I am trying to write the interface to this gsl function: gsl_multifit_fdfsolver_jac (I believe introduced in gsl 2.0) that is necessary for nonlinear-least-squares.lisp (It is returns the Jacobian) See documentation <https://www.gnu.org/software/gsl/manual/html_node/Computing-the-covariance-…> and example usage: gsl_multifit_fdfsolver_jac(s, J); gsl_multifit_covar (J, 0.0, covar); This is my failed attempt after looking at gsll code and documentation (defmfun jacobian (solver) "gsl_multifit_fdfsolver_jac" (((mpointer solver) :pointer) (*jacobian :pointer) :definition :function :inputs (solver) :outputs (*jacobian) :c-return :success-failure :return ((make-foreign-array-from-mpointer *jacobian)) :documentation "Query the solver for the Jacobian, a pointer") Can someone tell me how to make this work? Thanks, Mirko

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GSL 2.x news
by Mirko Vukovic 11 Nov '15

11 Nov '15

This email is related to recent releases of GSL and (not GSLL): GSL 2.0 and 2.1 have been released (see http://www.gnu.org/software/gsl/ and http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS) 2.0 is now distributed by msys2 on Windows. 2.0 brought new functionality, changes to the interface and some new bugs. As far as I know gsll has not been updated yet (and that is not a critique). 2.0 compiles on Windows on CCL and SBCL with the exception of two issues: - solve-minimize-fit\solver-struct__grovel.c - There is no class named GSLL::BASIS-SPLINE. I am not sure if these errors are related to the bugs discussed in this email thread: http://lists.gnu.org/archive/html/help-gsl/2015-11/msg00006.html) On SBCL 1.30 the test summary is: Unit Test Summary | 3722 assertions total | 3658 passed | 64 failed | 19 execution errors | 0 missing tests #<TEST-RESULTS-DB Total(3722) Passed(3658) Failed(64) Errors(19)> All execution errors have to do with exception_access_violation. Mirko

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A question about numerical-integration.lisp
by Alasdair McAndrew 02 Nov '15

02 Nov '15

Hello, I am using the excellent gsll package (in the first instance), to provide an interface to quadpack for the mathematics system FriCAS. I'm slowly going through calculus/numerical-integration.lisp one function at a time and writing each one into FriCAS as I go. This means writing functions in FriCAS's own language SPAD which interface with gsll. This is made harder by me being a lisp newbie. However, I've come to integration-QAGP, and I've tried to run the test command (having first defined the function it calls). However, all I get is errors. I'm using SBCL in emacs-slime, and I have installed gsll with quicklisp, so that I can call an integration routine with * (gsll:integration-qng (lambda (x) (exp (- (* x x)))) 0.0 1.0) But the commands * (defun integration-test-f454 (x) (* (expt x 3) (* (log (abs (* (- (expt x 2) 1.0d0) (- (expt x 2) 2.0d0))))))) * (gsll:integration-QAGp 'integration-test-f454 (grid:copy-to (vector 0.0d0 1.0d0 (sqrt 2.0d0) 3.0d0)) 0.0d0 1.0d-3 1000) just produces a long list of errors. Is "grid" a standard library, or does it need to be loaded first? (Told you I was a newbie...) Thanks Alasdair -- [image: http://www.facebook.com/alasdair.mcandrew] <http://www.facebook.com/alasdair.mcandrew> [image: https://plus.google.com/+AlasdairMcAndrew/posts] <https://plus.google.com/+AlasdairMcAndrew/posts> [image: https://www.linkedin.com/pub/alasdair-mcandrew/a/178/108] <https://www.linkedin.com/pub/alasdair-mcandrew/a/178/108> [image: https://twitter.com/amca01] <https://twitter.com/amca01> [image: http://numbersandshapes.net] <http://numbersandshapes.net>

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