October 2013 - gsll-devel - mailman3.common-lisp.net

[GSLL-devel] Fixing up make-grid-data for clisp (was making copy-to working in clisp+grid: fix to element-type)
by Mirko Vukovic 26 Dec '13

26 Dec '13

This is a follow up on my posted fix to copy-to. For some reason this has triggered another error. I do not understand how that other error is triggered. The error and the fix are discussed at the bottom of the email On Fri, Jan 4, 2013 at 10:39 AM, Mirko Vukovic <mirko.vukovic(a)gmail.com>wrote: > The following works in sbcl+grid: > > (copy-to (make-array 2 :element-type 'double-float :initial-contents > '(1.0d0 2.0d0)) 'grid:foreign-array) > > But it does not work in clisp+grid. > > The root cause lies in the function grid/array.lisp/element-type. It uses > `(array-element-type grid)'. > > But this can present a problem. Quoting hyperspec: > > (Because of *array* <http://26_glo_a.htm#array> *upgrading*, this *type > specifier* <http://26_glo_t.htm#type_specifier> can in some cases denote > a *supertype* <http://26_glo_s.htm#supertype> of the *expressed array > element type* <http://26_glo_e.htm#expressed_array_element_type> of the * > array*.) > > In CLISP, array-element-type returns `T' when passed #(1d0 2d0) > > It returns T even when passed a simple array: > > (array-element-type (make-array 2 :element-type 'double-float > :initial-contents > '(1.0d0 2.0d0) > :adjustable nil > :fill-pointer nil > :displaced-to nil) ) > > The proposed fix is > > (defmethod element-type ((grid array)) > (type-of (row-major-aref grid 0)) > #+skip(array-element-type grid)) > > Now copy-to works in clisp as well. > > Mirko > > > After finishing this, I recompiled afresh, and got another error that I traced to make-grid-data and make-array In clisp, make-array will return an array of NIL's even if the element-type is specified as double float. In SBCL make-array will return an array filled with 1d0. I had to add some clisp specific code to make-grid-data in order for it to initialize properly. First, a helper function: (defun default-element (element-type) "Return a default element depending on element-type " (let ((a-list '((double-float . 1d0) (symbol . T)))) (let ((match (cdr (assoc element-type a-list)))) (assert match () "Default element type undefined for element-type ~a" element-type) match))) And second, a bit of set-up code in make-grid-data. I broke apart the (let* statement to provide an explicit initial element if it has not been specified already: (defmethod make-grid-data ((type (eql 'array)) dimensions rest-spec &key (initial-element nil initial-element-p) (initial-contents nil initial-contents-p)) (let ((element-type (top-spec-type rest-spec))) #+clisp (unless (or initial-element-p initial-contents-p) (setf initial-element (default-element element-type) initial-element-p t)) (let ((array ... UNCHANGED Summary: To fix to copy-to, I modified (defmethod element-type ((grid array)) For some unknown reason, that triggered an error in the array initialization routine. To fix that, I had to add code to make-grid-data, so that it fills double-float arrays with 0d0 instead of NIL's I will continue using this code to see if there are additional problems. BTW, I realize that CLISP is not a preferred platform for speedy computation, but that is what I use on Windows, until SBCL gets officially ported to it. And in addition, it is a nice cross-check on portability. Mirko

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[GSLL-devel] making copy-to working in clisp+grid: fix to element-type
by Mirko Vukovic 26 Dec '13

26 Dec '13

The following works in sbcl+grid: (copy-to (make-array 2 :element-type 'double-float :initial-contents '(1.0d0 2.0d0)) 'grid:foreign-array) But it does not work in clisp+grid. The root cause lies in the function grid/array.lisp/element-type. It uses `(array-element-type grid)'. But this can present a problem. Quoting hyperspec: (Because of *array* <26_glo_a.htm#array> *upgrading*, this *type specifier*<26_glo_t.htm#type_specifier>can in some cases denote a *supertype* <26_glo_s.htm#supertype> of the *expressed array element type*<26_glo_e.htm#expressed_array_element_type>of the *array*.) In CLISP, array-element-type returns `T' when passed #(1d0 2d0) It returns T even when passed a simple array: (array-element-type (make-array 2 :element-type 'double-float :initial-contents '(1.0d0 2.0d0) :adjustable nil :fill-pointer nil :displaced-to nil) ) The proposed fix is (defmethod element-type ((grid array)) (type-of (row-major-aref grid 0)) #+skip(array-element-type grid)) Now copy-to works in clisp as well. Mirko

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transposed matrix multiplication (in blas2,3) bugfixes
by Mirko Vukovic 25 Dec '13

25 Dec '13

matrix-product in blas3.lisp calls the gsl_blas gemm routine. It has optional parameters TransA and TransB to specify whether the matrices A and/or B should be transposed prior to multiplying. These two take values :trans or :notrans. The bug is twofold. matrix-product calls matrix-product-dimensions (defined in blas2). To do its job properly, matrix-product-dimensions should have TransA and TransB as parameters, and matrix-product should call it with those as arguments. Here is the modified matrix-product-dimensions: (defun matrix-product-dimensions (a b &optional (TRANSA :NOTRANS) (TRANSB :NOTRANS)) (if (typep b 'grid:matrix) (list (funcall (case transa (:notrans #'first) (:trans #'second) (t (error "Invalid tranposition keyword, ~a" transa))) (grid:dimensions a)) (funcall (case transb (:notrans #'second) (:trans #'first) (t (error "Invalid tranposition keyword, ~a" transb))) (grid:dimensions b))) (first (funcall (case transa (:notrans #'first) (:trans #'second) (t (error "Invalid tranposition keyword, ~a" transa))) (grid:dimensions a))))) This can probably be improved. I applied the same fix to the case when b is not a matrix, since matrix-product in blas2 which works on matrix x vector, also accepts that TransB argument. Finally matrix-product has to be fixed. It is defined in both blas2 (for matrix vector multiplication) and in blas3 (for matrix matrix multiplication). The modifications consist of modifying the call to matrix-product-dimensions to include TransA (and TransB) ;; blas2 (defmfun matrix-product ((A grid:matrix) (x vector) &optional y (alpha 1) (beta 1) (TransA :notrans) TransB &aux (yarr (grid:ensure-foreign-array y (matrix-product-dimensions A x TransA) element-type 0))) ("gsl_blas_" :type "gemv") ((transa cblas-transpose) (alpha :element-c-type) ((mpointer A) :pointer) ((mpointer x) :pointer) (beta :element-c-type) ((mpointer yarr) :pointer)) :definition :generic :element-types #+fsbv :float-complex #-fsbv :float :inputs (A x) :outputs (yarr) :documentation ; FDL "If the second and third arguments are vectors, compute the matrix-vector product and sum y = alpha op(A) x + beta y, where op(A) = A, A^T, A^H for TransA = :notrans, :trans, :conjtrans. If the second and third arguments are matrices, compute the matrix-matrix product and sum C = alpha op(A) op(B) + beta C where op(A) = A, A^T, A^H for TransA = :notrans, :trans, :conjtrans and similarly for the parameter TransB.") ;; blas3 (defmfun matrix-product ((A grid:matrix) (B grid:matrix) &optional C (alpha 1) (beta 1) (TransA :notrans) (TransB :notrans) &aux (Carr (or C (grid:make-foreign-array element-type :dimensions (matrix-product-dimensions A B TransA TransB) :initial-element 0)))) ("gsl_blas_" :type "gemm") ((TransA cblas-transpose) (TransB cblas-transpose) (alpha :element-c-type) ((mpointer A) :pointer) ((mpointer B) :pointer) (beta :element-c-type) ((mpointer Carr) :pointer)) :definition :methods :element-types #+fsbv :float-complex #-fsbv :float :inputs (A B Carr) :outputs (Carr)) I did not test this exhaustively, but the modifications did work my a few matrix multiplications that I needed. Mirko

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Symbol "*BUILT-IN-FLOAT-TYPES*" not found in the CFFI package.
by Adam Jensen 04 Oct '13

04 Oct '13

Hi, I've encountered some problems while having a look at GSLL (well, attempting to have a look at GSLL anyway). I can't seem to get started on an OpenBSD machine or a Xubuntu Linux machine. Any ideas about what the problem may be? ------------------------------------------------------------------- Problems on an OpenBSD machine ------------------------------------------------------------------- lucidrine:/home/hanzer$ dmesg | head -1 OpenBSD 5.3 (GENERIC.MP) #58: Tue Mar 12 18:43:53 MDT 2013 lucidrine:/home/hanzer$ sbcl --version SBCL 1.0.58.openbsd -- Installed from /usr/ports -- gsl-1.15 libffi-3.0.9 -- lucidrine:/home/hanzer$ curl -O http://beta.quicklisp.org/quicklisp.lisp lucidrine:/home/hanzer$ sbcl --load quicklisp.lisp ... * (quicklisp-quickstart:install) ... * (ql:add-to-init-file) ... * (ql:quickload "gsll") --a bunch of fetching then-- ; Loading "gsll" [package alexandria.0.dev]........................ [package babel-encodings]......................... [package babel]................................... .................................................. [package cffi-sys]................................ [package cffi].................................... .................................................. [package cffi-features]........................... [package cffi-grovel]........... debugger invoked on a ASDF:LOAD-SYSTEM-DEFINITION-ERROR: Error while trying to load definition for system gsll from pathname /home/hanzer/quicklisp/dists/quicklisp/software/gsll-20130615-git/gsll.asd: Unable to load any of the alternatives: ("libffi.so.6" "libffi32.so.6" "libffi.so.5" "libffi32.so.5") Type HELP for debugger help, or (SB-EXT:QUIT) to exit from SBCL. ------------------------------------------------------------------- Problems on a xubuntu Linux machine ------------------------------------------------------------------- #30-Ubuntu SMP Wed May 1 16:36:13 UTC 2013 (Ubuntu 3.8.0-19.30-generic 3.8.8) helix:~$ sbcl --version SBCL 1.1.1.0.debian -- Installed from Synaptic -- libgsl0-dev libgsl0ldbl libffi6 libffi-dev -- helix:~$ curl -O http://beta.quicklisp.org/quicklisp.lisp ... helix:~$ sbcl --load quicklisp.lisp ... * (quicklisp-quickstart:install) ... ==== quicklisp installed ==== ... * (ql:quickload "gsll") ... --a bunch of fetching then-- ; Loading "gsll" ..; cc -m32 -I/usr/share/common-lisp/source/cl-cffi/ -fPIC -o /home/dmagus/.cache/common-lisp/sbcl-1.1.1.0.debian-linux-x86/home/dmagus/quicklisp/dists/quicklisp/software/cffi_0.11.2/libffi/libffi-unix /home/dmagus/.cache/common-lisp/sbcl-1.1.1.0.debian-linux-x86/home/dmagus/quicklisp/dists/quicklisp/software/cffi_0.11.2/libffi/libffi-unix.c ; /home/dmagus/.cache/common-lisp/sbcl-1.1.1.0.debian-linux-x86/home/dmagus/quicklisp/dists/quicklisp/software/cffi_0.11.2/libffi/libffi-unix /home/dmagus/.cache/common-lisp/sbcl-1.1.1.0.debian-linux-x86/home/dmagus/quicklisp/dists/quicklisp/software/cffi_0.11.2/libffi/libffi-unix.grovel-tmp.lisp .; ; caught ERROR: ; READ error during COMPILE-FILE: ; ; Symbol "*BUILT-IN-FLOAT-TYPES*" not found in the CFFI package. ; ; Line: 36, Column: 49, File-Position: 1632 ; ; Stream: #<SB-SYS:FD-STREAM ; for "file /home/dmagus/quicklisp/dists/quicklisp/software/cffi_0.11.2/libffi/built-in-types.lisp" ; {C2C57B9}> debugger invoked on a LOAD-SYSTEM-DEFINITION-ERROR in thread #<THREAD "main thread" RUNNING {AB16819}>: Error while trying to load definition for system gsll from pathname /home/dmagus/quicklisp/dists/quicklisp/software/gsll-20130615-git/gsll.asd: Error while invoking #<COMPILE-OP NIL {B978391}> on #<CL-SOURCE-FILE "cffi-libffi" "libffi" "built-in-types"> Type HELP for debugger help, or (SB-EXT:EXIT) to exit from SBCL.

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