From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 22 01:46:13 2021 Received: (at submit) by debbugs.gnu.org; 22 Jun 2021 05:46:13 +0000 Received: from localhost ([127.0.0.1]:37543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZEi-0000b8-UX for submit@debbugs.gnu.org; Tue, 22 Jun 2021 01:46:13 -0400 Received: from lists.gnu.org ([209.51.188.17]:44988) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZEg-0000b0-Fm for submit@debbugs.gnu.org; Tue, 22 Jun 2021 01:46:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42558) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lvZEg-0002oQ-2L for guix-patches@gnu.org; Tue, 22 Jun 2021 01:46:10 -0400 Received: from mail.arctype.co ([138.68.9.245]:46094) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lvZEb-00082Z-DR for guix-patches@gnu.org; Tue, 22 Jun 2021 01:46:09 -0400 Received: from authenticated-user (mail.arctype.co [138.68.9.245]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by mail.arctype.co (Postfix) with ESMTPSA id DC57711F07F; Mon, 21 Jun 2021 22:45:30 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=arctype.co; s=mail; t=1624340731; bh=oyzAQ8zhrrjxGVpABUQtkf9h2j+smOmAdouyEMZJVRk=; h=From:To:Cc:Subject:Date:From; b=MJ0oNxhnkyIylVaqPLBh/quHVC/3yQ8yumdMiLM1JdjhXOjbQipQ6QBzT6B84JM3Y YDqo0lcknbS7HqbG3cfwesu+hqJcRg3a/9Wc2ukmiJIGdGsVjRti4w2CpUODF7NXPH Ao75Ag1BbSK+8J2ij2kjpRyDMHVXcsZBBYUPna345729ZDDqqgeBb2ZpSI3gQMDeu2 F8uKAiNtl5Xffhr3pspx8wVa+cCRtR/WcHDPOYZX4hzSSulZWDm0Hhq7Cm6IMi4wcV 4t2tFfOYVEmfO5UndFwzlxMg8k3vHuTkOX5vj/RVOS/VlWyx4qNk/yWQp92Qeq0bZe RCFOuQQjT8u1Q== From: Ryan Sundberg To: guix-patches@gnu.org Subject: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls Date: Mon, 21 Jun 2021 22:44:24 -0700 Message-Id: <20210622054423.31851-1-ryan@arctype.co> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=138.68.9.245; envelope-from=ryan@arctype.co; helo=mail.arctype.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Ryan Sundberg X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.4 (--) Disable the thread local storage model in jemalloc 5 to prevent shared libraries linked to libjemalloc from crashing on dlopen(). https://github.com/jemalloc/jemalloc/issues/937 This bug affects both Java JNI and python libraries which link to jemalloc 5, such as RocksDB, which will crash the program when loaded. * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-exec-tls configure flag. --- gnu/packages/jemalloc.scm | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index c4b87b540d..67a1ca8e14 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017 Eric Bavier +;;; Copyright © 2021 Ryan Sundberg ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,10 +30,10 @@ #:use-module (gnu packages perl) #:use-module (guix build-system gnu)) -(define-public jemalloc +(define jemalloc-4.5.0 (package (name "jemalloc") - (version "5.2.1") + (version "4.5.0") (source (origin (method url-fetch) (uri (string-append @@ -40,7 +41,7 @@ version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl")))) + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl")))) (build-system gnu-build-system) (arguments `(#:phases @@ -58,7 +59,7 @@ ;; Transparent huge pages are only enabled by default on Intel processors '() '(#:configure-flags (list "--disable-thp"))))) - (inputs `(("perl" ,perl))) + (inputs '()) ;; Install the scripts to a separate output to avoid referencing Perl and ;; Bash in the default output, saving ~75 MiB on the closure. (outputs '("out" "bin")) @@ -69,10 +70,10 @@ fragmentation avoidance and scalable concurrency support.") (license bsd-2))) -(define-public jemalloc-4.5.0 +(define-public jemalloc (package - (inherit jemalloc) - (version "4.5.0") + (inherit jemalloc-4.5.0) + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency support.") version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl")))) - (inputs '()))) + "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl")))) + (arguments + (substitute-keyword-arguments (package-arguments jemalloc-base) + ;; Disable the thread local storage model in jemalloc 5 to prevent + ;; shared libraries linked to libjemalloc from crashing on dlopen() + ;; https://github.com/jemalloc/jemalloc/issues/937 + ((#:configure-flags base-configure-flags '()) + `(cons "--disable-initial-exec-tls" ,base-configure-flags)))) + (inputs `(("perl" ,perl))))) -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 22 01:52:32 2021 Received: (at 49167) by debbugs.gnu.org; 22 Jun 2021 05:52:32 +0000 Received: from localhost ([127.0.0.1]:37563 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZKp-0000kx-Jz for submit@debbugs.gnu.org; Tue, 22 Jun 2021 01:52:32 -0400 Received: from mail.arctype.co ([138.68.9.245]:33745) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZKn-0000kd-61 for 49167@debbugs.gnu.org; Tue, 22 Jun 2021 01:52:30 -0400 Received: from authenticated-user (mail.arctype.co [138.68.9.245]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by mail.arctype.co (Postfix) with ESMTPSA id 38DC111F07F for <49167@debbugs.gnu.org>; Mon, 21 Jun 2021 22:52:23 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=arctype.co; s=mail; t=1624341143; bh=NNnjDbjjGtnyKpyOku/gwnGSpTUDZHzYje9T3OnV5hw=; h=Subject:To:References:From:Date:In-Reply-To:From; b=TdNvmCNtghFZADpRetvDHBDZX2uiHWe42z5raQ9r45ul/9hJo7wVIAQjZpCwOD3C4 OACOvpdjQp5c4YLZZeN4h1pp5JG9hmCFZW/HsHjomJUDdehurh5bpkc8ZLnOAvc9E4 xWDdwSv+ph/4iL+w80pDtrPtGZxWRU8s1Ux1nolUYhByFErMjetSZ6etPdN9p+/PoO zJr+WUuyOziavSb+nARV357KOHcbniXHDs5CH9L+rrqDnU0J6GMaR76hGblreqLXZo 4bhIQjF6DbX6oiZDlndz3TEuRgxRdg+FYv3yQbS0cgqr5HtDMmpOOmHszGxv/MG57u lUIIFRuPNJlAA== Subject: Re: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls To: 49167@debbugs.gnu.org References: <20210622054423.31851-1-ryan@arctype.co> From: Ryan Sundberg Message-ID: Date: Mon, 21 Jun 2021 22:52:22 -0700 MIME-Version: 1.0 In-Reply-To: <20210622054423.31851-1-ryan@arctype.co> Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="jHI4JFPlg48tvUdQaXjaLvUQQ0TlUZDhf" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 49167 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --jHI4JFPlg48tvUdQaXjaLvUQQ0TlUZDhf Content-Type: multipart/mixed; boundary="G00xzA8OnFMMLN5hSAtyPbOVvCzrXVXJ9"; protected-headers="v1" From: Ryan Sundberg To: 49167@debbugs.gnu.org Message-ID: Subject: Re: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls References: <20210622054423.31851-1-ryan@arctype.co> In-Reply-To: <20210622054423.31851-1-ryan@arctype.co> --G00xzA8OnFMMLN5hSAtyPbOVvCzrXVXJ9 Content-Type: multipart/mixed; boundary="------------6F6DEA760CE529E5D554DA41" Content-Language: en-US This is a multi-part message in MIME format. --------------6F6DEA760CE529E5D554DA41 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Sorry, I missed a spot rebasing this last patch. Please use the attached patch which builds. -- Sincerely, Ryan Sundberg On 6/21/21 10:44 PM, Ryan Sundberg wrote: > Disable the thread local storage model in jemalloc 5 to prevent > shared libraries linked to libjemalloc from crashing on dlopen(). > https://github.com/jemalloc/jemalloc/issues/937 >=20 > This bug affects both Java JNI and python libraries which link to > jemalloc 5, such as RocksDB, which will crash the program when loaded. >=20 > * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initia= l-exec-tls > configure flag. > --- > gnu/packages/jemalloc.scm | 26 +++++++++++++++++--------- > 1 file changed, 17 insertions(+), 9 deletions(-) >=20 > diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm > index c4b87b540d..67a1ca8e14 100644 > --- a/gnu/packages/jemalloc.scm > +++ b/gnu/packages/jemalloc.scm > @@ -2,6 +2,7 @@ > ;;; Copyright =C2=A9 2015 Sou Bunnbu > ;;; Copyright =C2=A9 2017 Efraim Flashner > ;;; Copyright =C2=A9 2017 Eric Bavier > +;;; Copyright =C2=A9 2021 Ryan Sundberg > ;;; > ;;; This file is part of GNU Guix. > ;;; > @@ -29,10 +30,10 @@ > #:use-module (gnu packages perl) > #:use-module (guix build-system gnu)) > =20 > -(define-public jemalloc > +(define jemalloc-4.5.0 > (package > (name "jemalloc") > - (version "5.2.1") > + (version "4.5.0") > (source (origin > (method url-fetch) > (uri (string-append > @@ -40,7 +41,7 @@ > version "/jemalloc-" version ".tar.bz2")) > (sha256 > (base32 > - "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"= )))) > + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"= )))) > (build-system gnu-build-system) > (arguments > `(#:phases > @@ -58,7 +59,7 @@ > ;; Transparent huge pages are only enabled by default on In= tel processors > '() > '(#:configure-flags (list "--disable-thp"))))) > - (inputs `(("perl" ,perl))) > + (inputs '()) > ;; Install the scripts to a separate output to avoid referencing P= erl and > ;; Bash in the default output, saving ~75 MiB on the closure. > (outputs '("out" "bin")) > @@ -69,10 +70,10 @@ > fragmentation avoidance and scalable concurrency support.") > (license bsd-2))) > =20 > -(define-public jemalloc-4.5.0 > +(define-public jemalloc > (package > - (inherit jemalloc) > - (version "4.5.0") > + (inherit jemalloc-4.5.0) > + (version "5.2.1") > (source (origin > (method url-fetch) > (uri (string-append > @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency sup= port.") > version "/jemalloc-" version ".tar.bz2")) > (sha256 > (base32 > - "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"= )))) > - (inputs '()))) > + "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"= )))) > + (arguments > + (substitute-keyword-arguments (package-arguments jemalloc-base) > + ;; Disable the thread local storage model in jemalloc 5 to pre= vent > + ;; shared libraries linked to libjemalloc from crashing on dlo= pen() > + ;; https://github.com/jemalloc/jemalloc/issues/937 > + ((#:configure-flags base-configure-flags '()) > + `(cons "--disable-initial-exec-tls" ,base-configure-flags))))= > + (inputs `(("perl" ,perl))))) >=20 --------------6F6DEA760CE529E5D554DA41 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-jemalloc-disable-initial-exec-tls.patch" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="0001-gnu-jemalloc-disable-initial-exec-tls.patch" =46rom a0f9f8206613efa659922f5164414832119a4d33 Mon Sep 17 00:00:00 2001 From: Ryan Sundberg Date: Fri, 29 Jan 2021 21:18:56 -0800 Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls Disable the thread local storage model in jemalloc 5 to prevent shared libraries linked to libjemalloc from crashing on dlopen(). https://github.com/jemalloc/jemalloc/issues/937 This bug affects both Java JNI and python libraries which link to jemalloc 5, such as RocksDB, which will crash the program when loaded. * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-= exec-tls configure flag. --- gnu/packages/jemalloc.scm | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index c4b87b540d..67a1ca8e14 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -2,6 +2,7 @@ ;;; Copyright =C2=A9 2015 Sou Bunnbu ;;; Copyright =C2=A9 2017 Efraim Flashner ;;; Copyright =C2=A9 2017 Eric Bavier +;;; Copyright =C2=A9 2021 Ryan Sundberg ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,10 +30,10 @@ #:use-module (gnu packages perl) #:use-module (guix build-system gnu)) =20 -(define-public jemalloc +(define jemalloc-4.5.0 (package (name "jemalloc") - (version "5.2.1") + (version "4.5.0") (source (origin (method url-fetch) (uri (string-append @@ -40,7 +41,7 @@ version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))= )) + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))= )) (build-system gnu-build-system) (arguments `(#:phases @@ -58,7 +59,7 @@ ;; Transparent huge pages are only enabled by default on Inte= l processors '() '(#:configure-flags (list "--disable-thp"))))) - (inputs `(("perl" ,perl))) + (inputs '()) ;; Install the scripts to a separate output to avoid referencing Per= l and ;; Bash in the default output, saving ~75 MiB on the closure. (outputs '("out" "bin")) @@ -69,10 +70,10 @@ fragmentation avoidance and scalable concurrency support.") (license bsd-2))) =20 -(define-public jemalloc-4.5.0 +(define-public jemalloc (package - (inherit jemalloc) - (version "4.5.0") + (inherit jemalloc-4.5.0) + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency suppo= rt.") version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))= )) - (inputs '()))) + "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))= )) + (arguments + (substitute-keyword-arguments (package-arguments jemalloc-base) + ;; Disable the thread local storage model in jemalloc 5 to preve= nt + ;; shared libraries linked to libjemalloc from crashing on dlope= n() + ;; https://github.com/jemalloc/jemalloc/issues/937 + ((#:configure-flags base-configure-flags '()) + `(cons "--disable-initial-exec-tls" ,base-configure-flags)))) + (inputs `(("perl" ,perl))))) --=20 2.31.1 --------------6F6DEA760CE529E5D554DA41-- --G00xzA8OnFMMLN5hSAtyPbOVvCzrXVXJ9-- --jHI4JFPlg48tvUdQaXjaLvUQQ0TlUZDhf Content-Type: application/pgp-signature; name="OpenPGP_signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="OpenPGP_signature" -----BEGIN PGP SIGNATURE----- wsB5BAABCAAjFiEEyVG5Gm1pvFAzyXC2aiMi+MCr96sFAmDRepYFAwAAAAAACgkQaiMi+MCr96vc qQf/VBzCo4Bb6PkC3/igNicU5TmPvtHx4tkJR4gCoyhfI78wEiMQ9RKc75f4jlE2kEoVWqSD2R4B msHD1y+TL4beQP3SlpWDteCT+7gcym0Lp5dtKCxV/cGywMTjDkoj6Kj3ZRzFDV7ya2TQm4Z7Voxl P/Emr5G7ZcCG2SfLt6KunCwn+q4/MrtwAODja20dsEmIsm2vt6eK6WyCarNZYDIGU7TY2JUoWL8g ix5IvQvZ/UnPKcWbK8aQEFfo2evxYsxRC6dz4d+qFBggXC67Owaz/5cLq8pFgL08CcnuVHwT0GSi tfbluh0I/TZyLppcOTcXFZfjgAzM9z0vaIhP/MA+Vg== =1Xrh -----END PGP SIGNATURE----- --jHI4JFPlg48tvUdQaXjaLvUQQ0TlUZDhf-- From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 22 01:58:33 2021 Received: (at 49167) by debbugs.gnu.org; 22 Jun 2021 05:58:33 +0000 Received: from localhost ([127.0.0.1]:37583 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZQe-0000tx-Gx for submit@debbugs.gnu.org; Tue, 22 Jun 2021 01:58:33 -0400 Received: from mail.arctype.co ([138.68.9.245]:58661) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lvZQc-0000te-6N for 49167@debbugs.gnu.org; Tue, 22 Jun 2021 01:58:30 -0400 Received: from authenticated-user (mail.arctype.co [138.68.9.245]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by mail.arctype.co (Postfix) with ESMTPSA id 5A0EC11F07F for <49167@debbugs.gnu.org>; Mon, 21 Jun 2021 22:58:24 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=arctype.co; s=mail; t=1624341504; bh=DhikskEDcqnqeC6ZyroKhYTdhc3b14KcDJoNp2Dxww8=; h=Subject:References:To:From:Date:In-Reply-To:From; b=tTyt4Sql9HwGrlI+2ouF4jejXI3IDPtJx4XggLw20F/r9bD7uuIILv9EHppeJnoVS zxTDAUfvqDLiLPPgH/GIByO8cIGc3inyxHTNxMGjFyOyzYJBQJNUPvaF25jFc9M/PB ku/KzhHmRRxdIOAfI01e1L3ELNFi1ach6C1RMXnEDbAZLqFaaT+7bBEmRxz3bJ8pvB HB1CEnf2cyqf+dH3hSyh4I0CsKE62jRsk04hbMmGWnp3iWXIA0x987tsLSiCeL2FMZ O96wyWpsEljEnd9JsUD9vMHwlpGceKl++w0kRkHFfdgt2UD8JFCIV7TcCt6mZhKq8f j6hI8PLtsUjpw== Subject: Re: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls References: <20210622054423.31851-1-ryan@arctype.co> To: 49167@debbugs.gnu.org From: Ryan Sundberg Message-ID: Date: Mon, 21 Jun 2021 22:58:24 -0700 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="cMJ5tCfuUucHRuj8BgDBo7xQaFUYkwqlY" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 49167 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --cMJ5tCfuUucHRuj8BgDBo7xQaFUYkwqlY Content-Type: multipart/mixed; boundary="ArpsudfU5HQ6mkgbJPoS9adq7UdM8is3X"; protected-headers="v1" From: Ryan Sundberg To: 49167@debbugs.gnu.org Message-ID: Subject: Re: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls References: <20210622054423.31851-1-ryan@arctype.co> In-Reply-To: --ArpsudfU5HQ6mkgbJPoS9adq7UdM8is3X Content-Type: multipart/mixed; boundary="------------12B7447D52040EDC1F65D045" Content-Language: en-US This is a multi-part message in MIME format. --------------12B7447D52040EDC1F65D045 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Please excuse my clumsiness, THIS is the fixed patch file. (I accidentally re-sent the original patch.) -- Sincerely, Ryan Sundberg On 6/21/21 10:52 PM, Ryan Sundberg via Guix-patches via wrote: > Sorry, I missed a spot rebasing this last patch. Please use the attache= d > patch which builds. >=20 >=20 > -- > Sincerely, > Ryan Sundberg >=20 > On 6/21/21 10:44 PM, Ryan Sundberg wrote: >> Disable the thread local storage model in jemalloc 5 to prevent >> shared libraries linked to libjemalloc from crashing on dlopen(). >> https://github.com/jemalloc/jemalloc/issues/937 >> >> This bug affects both Java JNI and python libraries which link to >> jemalloc 5, such as RocksDB, which will crash the program when loaded.= >> >> * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initi= al-exec-tls >> configure flag. >> --- >> gnu/packages/jemalloc.scm | 26 +++++++++++++++++--------- >> 1 file changed, 17 insertions(+), 9 deletions(-) >> >> diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm >> index c4b87b540d..67a1ca8e14 100644 >> --- a/gnu/packages/jemalloc.scm >> +++ b/gnu/packages/jemalloc.scm >> @@ -2,6 +2,7 @@ >> ;;; Copyright =C2=A9 2015 Sou Bunnbu >> ;;; Copyright =C2=A9 2017 Efraim Flashner >> ;;; Copyright =C2=A9 2017 Eric Bavier >> +;;; Copyright =C2=A9 2021 Ryan Sundberg >> ;;; >> ;;; This file is part of GNU Guix. >> ;;; >> @@ -29,10 +30,10 @@ >> #:use-module (gnu packages perl) >> #:use-module (guix build-system gnu)) >> =20 >> -(define-public jemalloc >> +(define jemalloc-4.5.0 >> (package >> (name "jemalloc") >> - (version "5.2.1") >> + (version "4.5.0") >> (source (origin >> (method url-fetch) >> (uri (string-append >> @@ -40,7 +41,7 @@ >> version "/jemalloc-" version ".tar.bz2")) >> (sha256 >> (base32 >> - "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl= ")))) >> + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl= ")))) >> (build-system gnu-build-system) >> (arguments >> `(#:phases >> @@ -58,7 +59,7 @@ >> ;; Transparent huge pages are only enabled by default on I= ntel processors >> '() >> '(#:configure-flags (list "--disable-thp"))))) >> - (inputs `(("perl" ,perl))) >> + (inputs '()) >> ;; Install the scripts to a separate output to avoid referencing = Perl and >> ;; Bash in the default output, saving ~75 MiB on the closure. >> (outputs '("out" "bin")) >> @@ -69,10 +70,10 @@ >> fragmentation avoidance and scalable concurrency support.") >> (license bsd-2))) >> =20 >> -(define-public jemalloc-4.5.0 >> +(define-public jemalloc >> (package >> - (inherit jemalloc) >> - (version "4.5.0") >> + (inherit jemalloc-4.5.0) >> + (version "5.2.1") >> (source (origin >> (method url-fetch) >> (uri (string-append >> @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency su= pport.") >> version "/jemalloc-" version ".tar.bz2")) >> (sha256 >> (base32 >> - "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl= ")))) >> - (inputs '()))) >> + "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl= ")))) >> + (arguments >> + (substitute-keyword-arguments (package-arguments jemalloc-base)= >> + ;; Disable the thread local storage model in jemalloc 5 to pr= event >> + ;; shared libraries linked to libjemalloc from crashing on dl= open() >> + ;; https://github.com/jemalloc/jemalloc/issues/937 >> + ((#:configure-flags base-configure-flags '()) >> + `(cons "--disable-initial-exec-tls" ,base-configure-flags)))= ) >> + (inputs `(("perl" ,perl))))) >> --------------12B7447D52040EDC1F65D045 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-jemalloc-disable-initial-exec-tls.patch" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="0001-gnu-jemalloc-disable-initial-exec-tls.patch" =46rom 8b97b60ab78ba1e616efaf477e629cfa2457b1a9 Mon Sep 17 00:00:00 2001 From: Ryan Sundberg Date: Fri, 29 Jan 2021 21:18:56 -0800 Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls Disable the thread local storage model in jemalloc 5 to prevent shared libraries linked to libjemalloc from crashing on dlopen(). https://github.com/jemalloc/jemalloc/issues/937 This bug affects both Java JNI and python libraries which link to jemalloc 5, such as RocksDB, which will crash the program when loaded. * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-= exec-tls configure flag. --- gnu/packages/jemalloc.scm | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index c4b87b540d..d93cf41081 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -2,6 +2,7 @@ ;;; Copyright =C2=A9 2015 Sou Bunnbu ;;; Copyright =C2=A9 2017 Efraim Flashner ;;; Copyright =C2=A9 2017 Eric Bavier +;;; Copyright =C2=A9 2021 Ryan Sundberg ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,10 +30,10 @@ #:use-module (gnu packages perl) #:use-module (guix build-system gnu)) =20 -(define-public jemalloc +(define jemalloc-4.5.0 (package (name "jemalloc") - (version "5.2.1") + (version "4.5.0") (source (origin (method url-fetch) (uri (string-append @@ -40,7 +41,7 @@ version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))= )) + "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))= )) (build-system gnu-build-system) (arguments `(#:phases @@ -58,7 +59,7 @@ ;; Transparent huge pages are only enabled by default on Inte= l processors '() '(#:configure-flags (list "--disable-thp"))))) - (inputs `(("perl" ,perl))) + (inputs '()) ;; Install the scripts to a separate output to avoid referencing Per= l and ;; Bash in the default output, saving ~75 MiB on the closure. (outputs '("out" "bin")) @@ -69,10 +70,10 @@ fragmentation avoidance and scalable concurrency support.") (license bsd-2))) =20 -(define-public jemalloc-4.5.0 +(define-public jemalloc (package - (inherit jemalloc) - (version "4.5.0") + (inherit jemalloc-4.5.0) + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append @@ -80,5 +81,12 @@ fragmentation avoidance and scalable concurrency suppo= rt.") version "/jemalloc-" version ".tar.bz2")) (sha256 (base32 - "10373xhpc10pgmai9fkc1z0rs029qlcb3c0qfnvkbwdlcibdh2cl"))= )) - (inputs '()))) + "1xl7z0vwbn5iycg7amka9jd6hxd8nmfk7nahi4p9w2bnw9f0wcrl"))= )) + (arguments + (substitute-keyword-arguments (package-arguments jemalloc-4.5.0) + ;; Disable the thread local storage model in jemalloc 5 to preve= nt + ;; shared libraries linked to libjemalloc from crashing on dlope= n() + ;; https://github.com/jemalloc/jemalloc/issues/937 + ((#:configure-flags base-configure-flags '()) + `(cons "--disable-initial-exec-tls" ,base-configure-flags)))) + (inputs `(("perl" ,perl))))) --=20 2.31.1 --------------12B7447D52040EDC1F65D045-- --ArpsudfU5HQ6mkgbJPoS9adq7UdM8is3X-- --cMJ5tCfuUucHRuj8BgDBo7xQaFUYkwqlY Content-Type: application/pgp-signature; name="OpenPGP_signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="OpenPGP_signature" -----BEGIN PGP SIGNATURE----- wsB5BAABCAAjFiEEyVG5Gm1pvFAzyXC2aiMi+MCr96sFAmDRfAAFAwAAAAAACgkQaiMi+MCr96ua /AgA10MU1NPv9LjY6egN2rN4PtKd/PUI4GSXtoiTHQ6Auqpmstq+VDg+nAffuVJIH0fb+ymFP4wP +a+D63ioJpPuw9Cbz5fy+6TUVPuI4DAwpHkSCc4R41bG4u40yftWKK1uHa2F20DgtIFRXg7cpugF QA6WRhfXnCC4NevjRDfUq2WvXZqKh7uMD6kvl0+4H02lxgtQRjp/h06Lki/ReL68Vg8cwok6D7Hf DPjaT2IC+6BkRI31MIbFtHemklx8PWu107zn+xrG+MGjgikfMKThJ07F5xOZp/7vBOGZV9l25Yse ZDZ4MGbKzZAHCgCe5PTtVHOtuRsaqwj9iSJFB6wWUg== =2evo -----END PGP SIGNATURE----- --cMJ5tCfuUucHRuj8BgDBo7xQaFUYkwqlY-- From debbugs-submit-bounces@debbugs.gnu.org Fri Sep 03 06:06:44 2021 Received: (at 49167-done) by debbugs.gnu.org; 3 Sep 2021 10:06:44 +0000 Received: from localhost ([127.0.0.1]:43009 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mM65r-0000Pq-DC for submit@debbugs.gnu.org; Fri, 03 Sep 2021 06:06:43 -0400 Received: from eggs.gnu.org ([209.51.188.92]:39772) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mM65h-0000PT-64 for 49167-done@debbugs.gnu.org; Fri, 03 Sep 2021 06:06:42 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:46012) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mM65b-0007wZ-DJ; Fri, 03 Sep 2021 06:06:27 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=48838 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mM65b-0005oo-53; Fri, 03 Sep 2021 06:06:27 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Ryan Sundberg Subject: Re: bug#49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls References: <20210622054423.31851-1-ryan@arctype.co> Date: Fri, 03 Sep 2021 12:06:25 +0200 In-Reply-To: (Ryan Sundberg's message of "Mon, 21 Jun 2021 22:58:24 -0700") Message-ID: <87k0jy2cta.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 49167-done Cc: 49167-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi Ryan, Ryan Sundberg skribis: > From 8b97b60ab78ba1e616efaf477e629cfa2457b1a9 Mon Sep 17 00:00:00 2001 > From: Ryan Sundberg > Date: Fri, 29 Jan 2021 21:18:56 -0800 > Subject: [PATCH] gnu: jemalloc: --disable-initial-exec-tls > > Disable the thread local storage model in jemalloc 5 to prevent > shared libraries linked to libjemalloc from crashing on dlopen(). > https://github.com/jemalloc/jemalloc/issues/937 > > This bug affects both Java JNI and python libraries which link to > jemalloc 5, such as RocksDB, which will crash the program when loaded. > > * gnu/packages/jemalloc.scm (jemalloc)[arguments]: Add --disable-initial-= exec-tls > configure flag. It took a long while, but it=E2=80=99s now in =E2=80=98core-updates-frozen= =E2=80=99 as 68dd6d809398297dc2ebef522186c9b9f2566739 (with minor tweaks so it would apply and so that =E2=80=98jemalloc-4.5.0=E2=80=99 remains public.) Thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Sat Sep 04 19:40:58 2021 Received: (at 49167) by debbugs.gnu.org; 4 Sep 2021 23:40:58 +0000 Received: from localhost ([127.0.0.1]:48863 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mMfHO-0007V7-Ht for submit@debbugs.gnu.org; Sat, 04 Sep 2021 19:40:58 -0400 Received: from mail.arctype.co ([138.68.9.245]:52293) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mMfHM-0007Uu-8L for 49167@debbugs.gnu.org; Sat, 04 Sep 2021 19:40:57 -0400 Received: from authenticated-user (mail.arctype.co [138.68.9.245]) (using TLSv1.3 with cipher TLS_AES_128_GCM_SHA256 (128/128 bits)) (No client certificate requested) by mail.arctype.co (Postfix) with ESMTPSA id 62C4313B22B for <49167@debbugs.gnu.org>; Sat, 4 Sep 2021 23:40:50 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=arctype.co; s=mail; t=1630798850; bh=BdFhRDPMpvPcCDedLu5VPCrOTcWyMqLHAdsBxu6dLRk=; h=Subject:To:References:From:Date:In-Reply-To:From; b=EKBcr0UZCLjpOPrx7ytRYd16Y57ITyWucIuyd+4RyKYUHMqRwTfaPXyyaXaewMOnB iDN4pn5Tr2mXzKZKRbxY35FBZdhYR3zWQM3bh+GX6MJX7qqllPfrVLezMJD7AJp+oM fBd/WiZDVQfHEyAW3CCK7I1LCf1x9lrawkfh3Op6yR9pSbXHqNQLZbaJZuloHuUswR BbpaLoJRAmHbwIGQyA25Jsq83sO+F3ozqyestmlKSCVqCXsKd4XlDR9jUVgNIniYE6 XTQvz6PeTQncMwnFWQguRJCgU7U1s2ldycnqMLsdMewU97z3RJnk+A8z67DAOKN7rK 2OHvUr1rPE+5g== Subject: Re: bug#49167: closed (Re: bug#49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls) To: 49167@debbugs.gnu.org References: <87k0jy2cta.fsf_-_@gnu.org> <20210622054423.31851-1-ryan@arctype.co> From: Ryan Sundberg Message-ID: Date: Sat, 4 Sep 2021 16:40:48 -0700 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="uAhj7Tsra3o3T1I230lLeX1G7LzEwS2lJ" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 49167 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --uAhj7Tsra3o3T1I230lLeX1G7LzEwS2lJ Content-Type: multipart/mixed; boundary="6kcvprmfpvFXgjelz0Rs2zazn3QPkAqIl"; protected-headers="v1" From: Ryan Sundberg To: 49167@debbugs.gnu.org Message-ID: Subject: Re: bug#49167: closed (Re: bug#49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls) References: <87k0jy2cta.fsf_-_@gnu.org> <20210622054423.31851-1-ryan@arctype.co> In-Reply-To: --6kcvprmfpvFXgjelz0Rs2zazn3QPkAqIl Content-Type: text/plain; charset=utf-8 Content-Language: en-US Content-Transfer-Encoding: quoted-printable Awesome. Thanks Ludo. This will unblock the rocksdb-java package I've been sitting on. -- Sincerely, Ryan Sundberg On 9/3/21 3:07 AM, GNU bug Tracking System wrote: > Your bug report >=20 > #49167: [PATCH core-updates] gnu: jemalloc: --disable-initial-exec-tls >=20 > which was filed against the guix-patches package, has been closed. >=20 > The explanation is attached below, along with your original report. > If you require more details, please reply to 49167@debbugs.gnu.org. >=20 --6kcvprmfpvFXgjelz0Rs2zazn3QPkAqIl-- --uAhj7Tsra3o3T1I230lLeX1G7LzEwS2lJ Content-Type: application/pgp-signature; name="OpenPGP_signature.asc" Content-Description: OpenPGP digital signature Content-Disposition: attachment; filename="OpenPGP_signature" -----BEGIN PGP SIGNATURE----- wsB5BAABCAAjFiEEyVG5Gm1pvFAzyXC2aiMi+MCr96sFAmE0BAAFAwAAAAAACgkQaiMi+MCr96vk tAgAvRaeQhKNEHAAF2PtjJepu7efAOkyBlmnV3hCDE2qbk3SKB6D7/248H/OIK5JapWT/Ot2tF7S KNSdfZWmOrP+L3zAf4d+xVL+dLsnacpOPaYecV3+yFdp5u0nt5lsXKju/9EsoLCHSctF75qZnFJW s/hTtN2P9go9UvaC+FWoYeuUhKBE8+066F2r4ohJ6KmZFUJyD0QLXWGNVQ/a2qvwNAgalYeMs30i 4tnDkmJUOw9WF4bBn5wkCoxoHm9yDFZAWbteQ7jOGztAOL/PjTxS9p6ZUVV1D/4jsJC3vtF3Tb++ owkwsLunpvbgK3mq98k3huFJSSkeEP71NAXAffS9cg== =qj5Z -----END PGP SIGNATURE----- --uAhj7Tsra3o3T1I230lLeX1G7LzEwS2lJ-- From unknown Sun Jul 27 00:55:57 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sun, 03 Oct 2021 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator