From nobody Sat Dec 17 01:54:23 2022 X-Original-To: ports-bugs@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4NYptR3D23z1Cfql for ; Sat, 17 Dec 2022 01:54:23 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4NYptR0qrWz3FT7 for ; Sat, 17 Dec 2022 01:54:23 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1671242063; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; 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Sat, 17 Dec 2022 01:54:22 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.5]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id 2BH1sMXs053000 for ; Sat, 17 Dec 2022 01:54:22 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id 2BH1sM45052998 for ports-bugs@FreeBSD.org; Sat, 17 Dec 2022 01:54:22 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 268422] math/atlas alapack is not a full lapack after update to 3.10.3 Date: Sat, 17 Dec 2022 01:54:23 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Some People X-Bugzilla-Who: alt2600@icloud.com X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: ports-bugs@FreeBSD.org X-Bugzilla-Flags: X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter attachments.created Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated List-Id: Ports bug reports List-Archive: https://lists.freebsd.org/archives/freebsd-ports-bugs List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-ports-bugs@freebsd.org X-BeenThere: freebsd-ports-bugs@freebsd.org MIME-Version: 1.0 X-ThisMailContainsUnwantedMimeParts: N https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D268422 Bug ID: 268422 Summary: math/atlas alapack is not a full lapack after update to 3.10.3 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Some People Priority: --- Component: Individual Port(s) Assignee: ports-bugs@FreeBSD.org Reporter: alt2600@icloud.com Created attachment 238852 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D238852&action= =3Dedit git-Makefile_full_lapack.diff So ran into some issues after Atlas update with some errors indicating miss= ing symbols notably from py-numpy when configuring opencv, or py-netCDF4 ImportError: /usr/local/lib/python3.9/site-packages/numpy/linalg/_umath_linalg.cpython-3= 9.so: Undefined symbol "sgesdd_" so after poking around the backup package of Atlas and the current ones I confirmed the old one did provide that symbol, and I recall that becoming default a while ago to build full lapack.=20 So I starting digging and saw what upstream did with eliminating specifying just the static library reference to use. I basically manually did in the do-build section things that configure would have done if if had built its = own lapack.a and set it up to use it. This included passing some options to xconfig, stripping some objects from our reference lapack and copying it in= to ${opt}/lib where the build expects it. it appears passing flapack to xconfig doesn't really do anything, all the business setting things up now seems to= be in configure, but can be worked around. I confirmed this now provides the library, opencv doesn't fail to import the symbol loading numpy, all the things that use atlas build. I even re-built py-scipy with atlas using this: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D257400 and the scikit packages I have that use it. I've attached my patch --=20 You are receiving this mail because: You are the assignee for the bug.=