From c231924ab9a72979001640d866db1988f8fd3bde Mon Sep 17 00:00:00 2001 From: "B. Wilson" Date: Sun, 16 May 2021 19:02:29 +0900 Subject: [PATCH] gnu: Add j. To: guix-patches@gnu.org * gnu/packages/jsoftware.scm: New file. * gnu/packages/patches/jsoftware-j901-f-fixes.patch: New file. * gnu/local.mk: (GNU_SYSTEM_MODULES, dist_patch_DATA): Add them. --- gnu/local.mk | 2 + gnu/packages/jsoftware.scm | 432 ++++++++++++++++++ .../patches/jsoftware-j901-f-fixes.patch | 80 ++++ 3 files changed, 514 insertions(+) create mode 100644 gnu/packages/jsoftware.scm create mode 100644 gnu/packages/patches/jsoftware-j901-f-fixes.patch diff --git a/gnu/local.mk b/gnu/local.mk index c3b0274945..b706ec4e86 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -305,6 +305,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/javascript.scm \ %D%/packages/jemalloc.scm \ %D%/packages/jrnl.scm \ + %D%/packages/jsoftware.scm \ %D%/packages/jose.scm \ %D%/packages/julia.scm \ %D%/packages/julia-xyz.scm \ @@ -1270,6 +1271,7 @@ dist_patch_DATA = \ %D%/packages/patches/jfsutils-add-sysmacros.patch \ %D%/packages/patches/jfsutils-include-systypes.patch \ %D%/packages/patches/jsoncpp-fix-inverted-case.patch \ + %D%/packages/patches/jsoftware-j901-f-fixes.patch \ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \ %D%/packages/patches/libffi-3.3-powerpc-fixes.patch \ diff --git a/gnu/packages/jsoftware.scm b/gnu/packages/jsoftware.scm new file mode 100644 index 0000000000..f6f6099e42 --- /dev/null +++ b/gnu/packages/jsoftware.scm @@ -0,0 +1,432 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2021 B. Wilson +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages jsoftware) + #:use-module (guix records) + #:use-module (guix packages) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix git-download) + #:use-module (guix build-system gnu) + #:use-module (guix build-system trivial) + #:use-module (guix build utils) + #:use-module (guix utils) + #:use-module (gnu packages) + #:use-module (gnu packages libedit) + #:use-module (gnu packages llvm) + #:use-module (gnu packages maths) + #:use-module (guix gexp) + #:use-module (ice-9 match)) + + +(define (jname prefix jtype) + "Return a package name for the given prefix and jtype, e.g. `jlib', + `jlib-beta', `j', and `j-beta'." + (let ((postfix (if (eq? jtype 'release) "" + (string-append "-" (symbol->string jtype))))) + (string-append prefix postfix))) + +(define (jversion->string version revision) + "Return a string representation of a J version and (optional) revision pair." + (let ((postfix (if (not revision) "" + (string-append "-" revision)))) + (string-append version postfix))) + +(define (jinfo->git-tag jversion jtype jrevision) + "Given version parameters, construct a git tag for upstream releases." + (let ((postfix (if (not jrevision) "" + (string-append "-" jrevision)))) + (string-append "j" jversion "-" (symbol->string jtype) postfix))) + +(define-record-type* + jlib-build-configuration make-jlib-build-configuration + jlib-build-configuration? + (builder jlib-build-configuration-builder (default "guix.gnu.org")) + (version jlib-build-configuration-version (default #f)) + (revision jlib-build-configuration-revision (default #f)) + (hash jlib-build-configuration-hash (default #f)) + (type jlib-build-configuration-type (default 'release)) + (patches jlib-build-configuration-patches (default '())) + (extra-inputs jlib-build-configuration-extra-inputs (default '())) + (extra-envars jlib-build-configuration-extra-envars (default '()))) + +(define make-jlib + (match-lambda + (($ + builder jversion revision hash type patches extra-inputs extra-envars) + (package + (name (jname "jlib" type)) + (version (jversion->string jversion revision)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jsoftware/jsource") + (commit (jinfo->git-tag jversion type revision)))) + (sha256 (base32 hash)) + (file-name (git-file-name name version)) + (patches patches))) + (properties `((jversion . ,jversion) + (jrevision . ,revision) + (jtype . ,type))) + (build-system gnu-build-system) + (native-inputs `(("clang-toolchain" ,clang-toolchain))) + (inputs (cons* `("libedit" ,libedit) + `("libomp" ,libomp) + extra-inputs)) + (arguments + `(#:modules (((ice-9 ftw) #:select (scandir)) + ((ice-9 popen) #:select (open-pipe* close-pipe)) + ((ice-9 regex) #:select (match:substring string-match)) + ((ice-9 threads) #:select (parallel par-for-each)) + ((srfi srfi-26) #:select (cut)) + ((srfi srfi-1) #:select (fold)) + ,@%gnu-build-system-modules) + #:phases + ;; Upstream's build system consists of ad-hoc scripts that build + ;; build up (very complicated) environment variables to pass to make. + ;; The basic build process looks like this: + ;; + ;; 1) Copy jsrc/jversion-x.h to jsrc/jversion.h and edit values; + ;; 2) Set jplatform and j64x environment variables; + ;; 3) Run make2/build_jconsole.sh and make2/build_libj.sh; + ;; + ;; However, upstream expects users to run J directly from the source + ;; directory; they do not supply a make `install' target. Thus it + ;; takes some massaging to install files in FHS-style directories. + (modify-phases %standard-phases + ;; In particular, we have to set up + ;; + ;; 1) jsrc/jversion.h as in a typical build; + ;; 2) jlibrary/bin/profilex.ijs to point to writable directories; + ;; 3) make2/build_*.sh to respect standard build conventions; + ;; 4) jsrc/jconsole.c to fix libedit dlopen; and + ;; 5) Hard coded references to addons directory. + (replace 'configure + (lambda* (#:key target inputs outputs #:allow-other-keys) + (let* ((clang-toolchain (assoc-ref inputs "clang-toolchain")) + (clang (string-append clang-toolchain "/bin/clang")) + (libedit (assoc-ref inputs "libedit")) + (out (assoc-ref outputs "out")) + (share (string-append out "/share/j"))) + ;; Set up build constants + (copy-file "jsrc/jversion-x.h" "jsrc/jversion.h") + (substitute* "jsrc/jversion.h" + (("^#define jversion.*$") + (format #f "#define jversion ~s\n" ,version)) + (("^#define jtype.*$") + (format #f "#define jtype ~s\n" (symbol->string ',type))) + (("^#define jbuilder.*$") + (format #f "#define jbuilder ~s\n" ,builder))) + ;; Create profilex.ijs overrides to point to the correct + ;; store items. Note that we set ~install and ~addons + ;; directories to reside under ~user to allow installing + ;; and loading addons. TODO: Guix-ify J addons as well. + (call-with-output-file "jlibrary/bin/profilex.ijs" + (lambda (port) + (display + (string-join + (list + (format #f "system=. '~a/system'" share) + (format #f "tools=. '~a/tools'" share) + ;; Upstream defaults to spamming $HOME with + ;; unhidden userdata directories. Set this to be + ;; $HOME/.j// instead + "'jtype jversion'=. (3&{,{.) <;._2 ,&'/' 9!:14''" + "jversion=. ({.~ i.&'-') jversion" + "jsuffix=. >@{&('';'-beta') jtype -: 'beta'" + "user=. home,'/.j/',jversion,jsuffix" + "addons=. user,'/addons'" + "break=. user,'/break'" + "config=. user,'/config'" + "install=. user,'/install'" + "snap=. user,'/snap'" + "temp=. user,'/temp'" + "\n") + "\n") + port))) + ;; Munge the build scripts into reason: + ;; 1. Short-circuit the fragile compiler detection; + ;; 2. Make sure to include our CFLAGS and LFLAGS; and + ;; 3. Propagate script errors to top level. + (for-each + (lambda (file) + (with-directory-excursion "make2" + (substitute* file + ;; The `compiler' variable doesn't point to the actual + ;; compiler. It is just a switch to tell the build + ;; scripts whether to use gcc- or clang-specific + ;; flags. + (("^compiler=.*$") "compiler=clang\n") + (("^LDFLAGS=\"" def) (string-append def "$LDFLAGS ")) + (("^(common=\")(\\$USETHREAD.*)$" _ def rest) + (string-append def "$CFLAGS " rest)) + (("^#!.*" shebang) + (string-append shebang "set -o errexit\n"))))) + '("build_jconsole.sh" "build_libj.sh")) + ;; The jconsole manually loads libedit with dlopen. The path + ;; must be absolute to correctly point to our input. + (substitute* "jsrc/jconsole.c" + (("libedit\\.so\\.[0-9]" so-file) + (format #f "~a/lib/~a" libedit so-file))) + ;; The ~addons/dev directory supplies tentative J-script + ;; definitions of new J engine functionality. Since we point + ;; ~addons under the ~user directory, we move it under + ;; ~system instead, which sits as-is in the output. + (with-directory-excursion "jsrc" + (for-each + (lambda (file) + (substitute* file (("~addons/dev") "~system/dev"))) + (scandir "." + (lambda (f) (eq? (stat:type (stat f)) 'regular))))) + ;; Implementation of 9!:14 records build time which breaks + ;; build reproducibility. Note that upstream code depends on + ;; the exact format of these strings, so we need to mimic the + ;; standard. + (substitute* "jsrc/j.c" + (("__DATE__") "\"Jan 01 1970\"") + (("__TIME__") "\"00:00:00\"")) + ;; Upstream recommends using clang, with GCC support being + ;; second-class, often resulting in build failures. + (setenv "CC" clang)))) + ;; The build output depends primarily on the values of the + ;; `jplatform' and `j64x' environment variables. If the target is + ;; ARM, then `jplatform' is "raspberry", otherwise it is `linux'. + ;; In addition to 32- and 64- bit versions, `j64x' controlls + ;; whether AVX or AVX2 variants of libj are built. + ;; + ;; However, build targets are not fine-grained enough to + ;; distinguish between CPU features. Thus we build and install all + ;; variants of libj, expecting jconsole to be called with a wrapper + ;; script that detects AVX features and loads the appropriate libj + ;; at runtime. + (replace 'build + (lambda _ + (setenv "USE_OPENMP" "1") + (setenv "USE_THREAD" "1") + (for-each (lambda (var-val) (apply setenv var-val)) + (quote ,extra-envars)) + ;; The build scripts assume that PWD is make2. + (with-directory-excursion "make2" + (let* ((platform ,(if (target-arm?) "raspberry" "linux")) + (jplat (string-append "jplatform=" platform)) + (target-bit ,(if (target-64bit?) "64" "32")) + (jbit (string-append "j64x=" "j" target-bit)) + (jbit-avx (string-append jbit "avx")) + (jbit-avx2 (string-append jbit "avx2"))) + (parallel + ;; Since jconsole doesn't depend on AVX features, we just + ;; build it once. + (invoke "env" jplat jbit "./build_jconsole.sh") + (invoke "env" jplat jbit "./build_libj.sh") + (if ,(target-64bit?) + (parallel + (invoke "env" jplat jbit-avx "./build_libj.sh") + (invoke "env" jplat jbit-avx2 + "./build_libj.sh")))))))) + ;; The test suite is expected to be run as follows for each variant + ;; of libj that we build: + ;; + ;; $ echo 'RUN ddall' | jconsole test/tsu.ijs + ;; + ;; This requires a working jconsole with accessible jlibrary files. + ;; We simply place these all under test/bin. + (replace 'check + (lambda _ + (let ((jplatform ,(if (target-arm?) "raspberry" "linux"))) + (mkdir-p "test/bin") + (for-each + (lambda (dir) + (let ((source (string-append "jlibrary/" dir)) + (dest (string-append "test/bin/" dir))) + (begin + (mkdir-p dest) + (copy-recursively source dest)))) + '("system" "tools" "addons")) + ;; The jlibrary/dev directory only sometimes exists, but + ;; needs to be copied into the ~system directory when it + ;; does. + (if (access? "jlibrary/dev" R_OK) + (copy-recursively "jlibrary/dev" "test/bin/system/dev")) + (par-for-each + (lambda (dir) + (let* ((jbin (string-append "bin/" jplatform)) + (jbit ,(if (target-64bit?) "j64" "j32")) + (jconsole (string-append jbin "/" jbit + "/jconsole")) + (source (string-append jbin "/" dir)) + (dest (string-append "test/bin/" dir))) + (begin + (mkdir-p dest) + (copy-recursively source dest) + (install-file "jlibrary/bin/profile.ijs" dest) + (install-file jconsole dest) + (let* ((jc (string-append dest "/jconsole")) + (tests "test/tsu.ijs") + (port (open-pipe* OPEN_WRITE jc tests))) + (display "RUN ddall\n" port) + (when (not (zero? (status:exit-val + (close-pipe port)))) + (error "Some J build tests failed.")))))) + (scandir (string-append "bin/" jplatform) + (negate (cut member <> '("." ".."))))) + #t))) + ;; Now that everything is built, installation is fairly + ;; straightforward, following FHS conventions. The only quirk is + ;; that we install jconsole under /libexec to make room for the + ;; wrapper replacement under /bin. + (replace 'install + (lambda* (#:key outputs inputs #:allow-other-keys) + (let* ((jplat ,(if (target-arm?) "raspberry" "linux")) + (jbit ,(if (target-64bit?) "j64" "j32")) + (jconsole (string-join + `("bin" ,jplat ,jbit "jconsole") "/")) + (out (assoc-ref outputs "out")) + (etc (string-append out "/etc/j")) + (lib (string-append out "/lib/j")) + (libexec (string-append out "/libexec")) + (share (string-append out "/share/j")) + (system (string-append share "/system")) + (dev (string-append system "/dev"))) + (mkdir-p lib) + (for-each + (lambda (jarch) + (let* ((jbin (string-join `("bin" ,jplat ,jarch) "/")) + (javx-match (string-match "avx.*" jarch)) + (javx (if (not javx-match) "" + (match:substring javx-match))) + (sep (if javx-match "-" "")) + (source (string-append jbin "/libj.so")) + (dest (format #f "~a/libj~a~a.so" lib sep javx))) + (copy-file source dest))) + (scandir (string-append "bin/" jplat) + (negate (cut member <> '("." ".."))))) + (install-file jconsole libexec) + (copy-recursively "jlibrary/system" system) + (if (access? "jlibrary/dev" R_OK) + (copy-recursively "jlibrary/dev" dev)) + (install-file "jlibrary/bin/profile.ijs" etc) + (install-file "jlibrary/bin/profilex.ijs" etc))))))) + (home-page "https://www.jsoftware.com/") + (synopsis "Ascii-only, array programming language in the APL family") + (description + "J is a high-level, general-purpose programming language that is +particularly suited to the mathematical, statistical, and logical analysis of +data. It is a powerful tool for developing algorithms and exploring problems +that are not already well understood.") + (license license:gpl3+))))) + + +(define jlib-901 + (make-jlib + (jlib-build-configuration + (version "901") + (revision "f") + (hash "1776021m0j1aanzwg60by83n53pw7i6afd5wplfzczwk8bywax4p") + (patches (search-patches "jsoftware-j901-f-fixes.patch"))))) + + +(define jlib-build-configuration-with-sleef + (jlib-build-configuration + (extra-inputs `(("sleef" ,sleef))) + (extra-envars `(("USE_SLEEF_SRC" "0") + ("LDFLAGS" "-lsleef"))))) + +(define jlib-902 + (make-jlib + (jlib-build-configuration + (inherit jlib-build-configuration-with-sleef) + (version "902") + (revision "b") + (hash "0j67vgikqflwjqacsdicasvyv1k54s2c8vjgwmf0ix7l41p4xqz0")))) + +(define jlib-903-beta + (make-jlib + (jlib-build-configuration + (inherit jlib-build-configuration-with-sleef) + (version "903") + (revision "h") + (type 'beta) + (hash "13sw2ffgx6pm699qfi50drlp8y1vmzj4swzx82g6vhyjpjci1w4h")))) + + +(define (make-ijconsole jlib) + "Generate a G-exp wrapper script that detects AVX/AVX2 support at runtime and + executes jconsole with the appropriate libj.so and profile.ijs." + (program-file (string-append "ijconsole-" (package-version jlib)) + #~(begin + (use-modules ((ice-9 rdelim) #:select (read-line)) + ((ice-9 regex) #:select (regexp-match? string-match))) + + (define (cpu-feature-line? string) + (string-prefix? "flags" string)) + + (define (contains-word? word string) + (regexp-match? + (string-match (string-join `("\\<" ,word "\\>") "") + string))) + + (define (has-cpu-feature? feature) + (with-input-from-file "/proc/cpuinfo" + (lambda () + (catch 'found + (lambda () + (let loop ((line (read-line))) + (cond ((eof-object? line) #f) + ((and (cpu-feature-line? line) + (contains-word? feature line)) + (throw 'found)) + (else (loop (read-line)))))) + (const #t))))) + + (let* ((jconsole (string-append #$jlib "/libexec/jconsole")) + (libj (format #f "~a/lib/j/libj-~a.so" #$jlib + (cond ((has-cpu-feature? "avx2") "avx2") + ((has-cpu-feature? "avx") "avx") + (else "")))) + (jprofile (string-append #$jlib "/etc/j/profile.ijs"))) + (apply execl jconsole "ijconsole" "-lib" libj "-jprofile" jprofile + (cdr (command-line))))))) + +(define (make-j jlib) + "Generate a J package containing /bin/ijconsole- linked against the + given jlib library package. Note that the ijconsole executable is versioned + since it is typical for J users to have multiple versions installed on the + same system." + (let ((jversion (assq-ref (package-properties jlib) 'jversion)) + (jtype (assq-ref (package-properties jlib) 'jtype))) + (package (inherit jlib) + (name (jname "j" jtype)) + (source #f) + (inputs `(("jlib" ,jlib) + ("ijconsole" ,(make-ijconsole jlib)))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((ijconsole (assoc-ref %build-inputs "ijconsole")) + (out (assoc-ref %outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (symlink ijconsole + (string-append bin "/ijconsole-" ,jversion))))))))) + +(define-public j-901 (make-j jlib-901)) +(define-public j-902 (make-j jlib-902)) +(define-public j-903-beta (make-j jlib-903-beta)) diff --git a/gnu/packages/patches/jsoftware-j901-f-fixes.patch b/gnu/packages/patches/jsoftware-j901-f-fixes.patch new file mode 100644 index 0000000000..0ac7e94de4 --- /dev/null +++ b/gnu/packages/patches/jsoftware-j901-f-fixes.patch @@ -0,0 +1,80 @@ +This patch fixes two separate issues with ustream sources: + +* Normalize import paths in jsrc/cip.c + +Upstream claims to have some build requirements that force them to use strange +import paths. However, these paths do not exist inside our build chroot. + +* Fix unititialized variable warning + +Clang 9 issues some warnings which cause the build to fail since upstream +compiles with -Werror. + + +diff --git a/jsrc/cip.c b/jsrc/cip.c +index 61da4088..fb3c03b6 100644 +--- a/jsrc/cip.c ++++ b/jsrc/cip.c +@@ -3,9 +3,9 @@ + /* */ + /* Conjunctions: Inner Product */ + +-#include "../../jsource/jsrc/j.h" +-#include "../../jsource/jsrc/vasm.h" +-#include "../../jsource/jsrc/gemm.h" ++#include "j.h" ++#include "vasm.h" ++#include "gemm.h" + + #define MAXAROWS 384 // max rows of a that we can process to stay in L2 cache a strip is m*CACHEHEIGHT, z strip is m*CACHEWIDTH this is wired to 128*3 - check if you chage + +@@ -1057,15 +1057,15 @@ static A jtipbx(J jt,A a,A w,C c,C d){A g=0,x0,x1,z;B*av,*av0,b,*v0,*v1,*zv;C c0 + switch(c){ + case CPLUSDOT: + #define F |= +-#include "../../jsource/jsrc/cip_t.h" ++#include "cip_t.h" + break; + case CSTARDOT: + #define F &= +-#include "../../jsource/jsrc/cip_t.h" ++#include "cip_t.h" + break; + case CNE: + #define F ^= +-#include "../../jsource/jsrc/cip_t.h" ++#include "cip_t.h" + break; + } + R z; +diff --git a/jsrc/gemm.c b/jsrc/gemm.c +index 51fe306e..b105dfc1 100644 +--- a/jsrc/gemm.c ++++ b/jsrc/gemm.c +@@ -318,7 +318,7 @@ dgemm_nn (I m, + _B); + + // loop 3 +- I i; ++ I i=0; + #pragma omp parallel for default(none),private(i),shared(j,l,A,C,mb,nc,kc,alpha,_beta,_mc,_B,rs_a,cs_a,rs_c,cs_c) + for (i=0; i