From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id WBZpAHiYAGHwVwEAgWs5BA (envelope-from ) for ; Wed, 28 Jul 2021 01:36:24 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id slqzN3eYAGEcRgAA1q6Kng (envelope-from ) for ; Tue, 27 Jul 2021 23:36:23 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 20DAD1AA23 for ; Wed, 28 Jul 2021 01:36:23 +0200 (CEST) Received: from localhost ([::1]:54478 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m8WcX-0004NK-C0 for larch@yhetil.org; Tue, 27 Jul 2021 19:36:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:49834) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m8WcI-0004M5-Hi for bug-guix@gnu.org; Tue, 27 Jul 2021 19:36:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42708) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m8WcE-00073H-Rg for bug-guix@gnu.org; Tue, 27 Jul 2021 19:36:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m8WcE-0001j2-Pp for bug-guix@gnu.org; Tue, 27 Jul 2021 19:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#49439: grafts cause =?UTF-8?Q?=E2=80=9Cguix_?= =?UTF-8?Q?environment=E2=80=9D?= to get killed with OOM Resent-From: Sarah Morgensen Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Tue, 27 Jul 2021 23:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49439 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Received: via spool by 49439-submit@debbugs.gnu.org id=B49439.16274289186557 (code B ref 49439); Tue, 27 Jul 2021 23:36:02 +0000 Received: (at 49439) by debbugs.gnu.org; 27 Jul 2021 23:35:18 +0000 Received: from localhost ([127.0.0.1]:54252 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m8WbV-0001hg-Gk for submit@debbugs.gnu.org; Tue, 27 Jul 2021 19:35:17 -0400 Received: from out1.migadu.com ([91.121.223.63]:10843) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m8WbQ-0001hF-83 for 49439@debbugs.gnu.org; Tue, 27 Jul 2021 19:35:16 -0400 X-Report-Abuse: Please report any abuse attempt to abuse@migadu.com and include these headers. DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mgsn.dev; s=key1; t=1627428910; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references; bh=kGd7hX7wigiuvw94qOTEBN/yRYCSqxEBsgMYay/ebV8=; b=a8Ssmggr3M3qtB79hrXtVM8rBVvWo/qe5a1hrNPxnUDvR+JU4wavWiBkAoUSh38CjNwQll ht3iXZfsLHtZ6xxaqUIn0wnrEO+Qz3+30QBMQNnJQmaiHeXSxm9GdAYTrC9DKPb4GWJhfr I5wDCETERyNSLU2u4KvSlowJwlUkDck= From: Sarah Morgensen References: <87sg0rse1n.fsf@elephly.net> <86tuklr5g6.fsf@mgsn.dev> <87y29r3enb.fsf@gnu.org> Date: Tue, 27 Jul 2021 16:35:06 -0700 In-Reply-To: <87y29r3enb.fsf@gnu.org> ("Ludovic =?UTF-8?Q?Court=C3=A8s?="'s message of "Tue, 27 Jul 2021 18:28:08 +0200") Message-ID: <867dhbpbyt.fsf@mgsn.dev> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Migadu-Auth-User: iskarian@mgsn.dev X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: Ricardo Wurmus , 49439@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1627428983; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=kGd7hX7wigiuvw94qOTEBN/yRYCSqxEBsgMYay/ebV8=; b=g0svphWzAtiAnj2bV9vp4PKS2rIIPg/iD8px9q28C3Je67XV8ivzLxwim0wsPpdBppRJmm JIdzFptWIyFDtUkZqCg420Rbgc5/zLobo3OV3g2BoA3MfLoi/7+wyS24ZQTJv/gGAzQtUu CwU4zWauj11n6YCrB6/LrYBHMyfmveSpGmscVulVWqEitEn2O+vBXKtRxjZBL0ACkIJvRy ldDybub65RJYCPSFV0kOJXWyJtHVLTHDX6eJbqf2Fg5F1OGCL9HCWMCcASMUvHtKBNHMel TTZ2lx9bzLDykjKEIVwvWOco+xJJAmNGfF+tm/kM9LvoXt9JY9yF5A4RmGRVDg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1627428983; a=rsa-sha256; cv=none; b=RISNjhB/tNCgCJXXAv5hqI1jUVve8qMO2Z/8YFCgO0wIJByT7540W6fm6rcp2Ewhi1l9/+ BMfySJOLvaMPx6X8cea5AnER1n6axHp1vvdngc/USz9gh8F6kjirmWr1Qj9Q0wkQOWx6nz PWM6gSrdFLHgw/5q0y9N0c7l8lm4d8PeeD3vR67hapMgLflHJLcihWSTxefRVXGb746FdB +LTEZ9LNM8ksEBxXhnBuqwstIOHoAuOuvtlgvKSvdTZ9Tz3ozKC0H6RuQIQfAzTSLNIbSI BbiROVfsIERulE9T/z435hvyKisHeHvV2v/XdioQZZVp6J/Wf/pAyPlmmopCVA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=a8Ssmggr; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Spam-Score: -1.32 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=a8Ssmggr; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mgsn.dev (policy=none); spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Queue-Id: 20DAD1AA23 X-Spam-Score: -1.32 X-Migadu-Scanner: scn0.migadu.com X-TUID: z/R2znHrcKup Hi, Ludovic Court=C3=A8s writes: [...] >> I can reproduce this with pigx-scrnaseq as well a number of other >> packages (listed below). >> >> $ ./pre-inst-env guix describe -f channels >> (list (channel >> (name 'guix) >> (url "/home/sarah/guix") >> (commit >> "3217a04b0352c2dd13323257b369604eeabfccc3"))) >> >> Does not complete within 5 minutes: Okay, so all of a sudden I can't reproduce this; even with the same commit as above, it completes in ~20s. guix time-machine --commit=3D3217a04 -- environment pigx-scrnaseq --searc= h-paths >/dev/null > What hardware are you using? Virtualbox VM with VT-x etc. on a host i7-6700. The VM has 6GB of memory. > > Here=E2=80=99s what I observe (with everything already in store and on a = hot > cache, with an i7 CPU): > > $ guix describe > Generacio 188 Jul 25 2021 12:47:29 (nuna) > guix a92dfbc > repository URL: https://git.savannah.gnu.org/git/guix.git > branch: master > commit: a92dfbce30777de6ca05031e275410cf9f56c84c > $ time GUIX_PROFILING=3Dgc guix environment pigx-scrnaseq --search-paths = --no-grafts >/dev/null > Garbage collection statistics: > heap size: 160.31 MiB > allocated: 1440.70 MiB > GC times: 39 > time spent in GC: 4.51 seconds (46% of user time) > > real 0m7.534s > user 0m9.747s > sys 0m0.167s > $ time GUIX_PROFILING=3Dgc guix environment pigx-scrnaseq --search-paths = >/dev/null > Garbage collection statistics: > heap size: 168.31 MiB > allocated: 2111.71 MiB > GC times: 53 > time spent in GC: 6.92 seconds (45% of user time) > > real 0m12.100s > user 0m15.517s > sys 0m0.198s > > > Commit 78daf9e02e5bc51f91488d8237cab2050cc060cf optimizes > =E2=80=98coalesce-duplicate-inputs=E2=80=99, which was quadratic in the n= umber of inputs (!). > After that change, I get: > > $ time GUIX_PROFILING=3Dgc ./pre-inst-env guix environment pigx-scrnaseq = --search-paths --no-grafts >/dev/null > Garbage collection statistics: > heap size: 168.31 MiB > allocated: 716.58 MiB > GC times: 24 > time spent in GC: 2.65 seconds (40% of user time) > > real 0m5.720s > user 0m6.708s > sys 0m0.149s > $ time GUIX_PROFILING=3Dgc ./pre-inst-env guix environment pigx-scrnaseq = --search-paths >/dev/null > Garbage collection statistics: > heap size: 160.31 MiB > allocated: 1387.96 MiB > GC times: 42 > time spent in GC: 5.87 seconds (43% of user time) > > real 0m10.821s > user 0m13.513s > sys 0m0.198s > > Could you tell me if it improves the situation for you? *Now* my experience is like yours: --8<---------------cut here---------------start------------->8--- $ guix describe Generation 9 Jul 27 2021 12:35:05 (current) guix d0ec739 repository URL: https://git.savannah.gnu.org/git/guix.git branch: master commit: d0ec73907c2995034a34339f4a7c2c72c2e21fea time GUIX_PROFILING=3Dgc guix time-machine --commit=3D3217a04 -- environmen= t pigx-scrnaseq --search-paths >/dev/null Garbage collection statistics: heap size: 176.31 MiB allocated: 2107.82 MiB GC times: 52 time spent in GC: 5.26 seconds (23% of user time) real 0m20.471s user 0m22.605s sys 0m0.372s $ time GUIX_PROFILING=3Dgc guix environment pigx-scrnaseq --search-paths >/= dev/null Garbage collection statistics: heap size: 152.31 MiB allocated: 1367.16 MiB GC times: 40 time spent in GC: 3.25 seconds (21% of user time) real 0m14.701s user 0m15.698s sys 0m0.361s --8<---------------cut here---------------end--------------->8--- But why was it occurring before? The only I thing I can think of is that I didn't have everything in the store first. Is there a way I can prune just the relevant items from the store to test this? > > It=E2=80=99s not the end of the road, but it should be an improvement. > > Thanks, > Ludo=E2=80=99. -- Sarah