From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id VEd5Dd9M+mD9fAAAgWs5BA (envelope-from ) for ; Fri, 23 Jul 2021 07:00:15 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id IFCgCN9M+mCDHgAAB5/wlQ (envelope-from ) for ; Fri, 23 Jul 2021 05:00:15 +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 10B733D74 for ; Fri, 23 Jul 2021 07:00:14 +0200 (CEST) Received: from localhost ([::1]:47502 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m6nIB-0005Wc-Q7 for larch@yhetil.org; Fri, 23 Jul 2021 01:00:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34120) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m6nI3-0005WB-0H for bug-guix@gnu.org; Fri, 23 Jul 2021 01:00:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:58769) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m6nI2-0002Mk-OB for bug-guix@gnu.org; Fri, 23 Jul 2021 01:00:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m6nI2-0000OD-M9 for bug-guix@gnu.org; Fri, 23 Jul 2021 01:00:02 -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: Fri, 23 Jul 2021 05:00:02 +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: Ricardo Wurmus Received: via spool by 49439-submit@debbugs.gnu.org id=B49439.16270163721430 (code B ref 49439); Fri, 23 Jul 2021 05:00:02 +0000 Received: (at 49439) by debbugs.gnu.org; 23 Jul 2021 04:59:32 +0000 Received: from localhost ([127.0.0.1]:42082 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m6nHY-0000N0-HW for submit@debbugs.gnu.org; Fri, 23 Jul 2021 00:59:32 -0400 Received: from out2.migadu.com ([188.165.223.204]:33794) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m6nHT-0000Mn-BO for 49439@debbugs.gnu.org; Fri, 23 Jul 2021 00:59:30 -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=1627016365; 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=24SdvVd059qkU2e4OdaujT405WmyvmPX/eQEIq1IJpQ=; b=Bt5Sh3DUnql78ZMy5VhIIdRHvQmfLJcBo5aGv1QJgt0g2vYOJ9uXGUhei5EMFeo5da84Um 56xCopehKnAyJZhGE1Jdn8FRZt1YDiDwUYWY7s2CX8MbNVpamvSBLoczFkutS72fCnxPhB hSDvhig3mAisSA4PmVuYYFihFznTWek= From: Sarah Morgensen References: <87sg0rse1n.fsf@elephly.net> Date: Thu, 22 Jul 2021 21:59:21 -0700 In-Reply-To: <87sg0rse1n.fsf@elephly.net> (Ricardo Wurmus's message of "Tue, 06 Jul 2021 16:38:28 +0200") Message-ID: <86tuklr5g6.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: 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=1627016415; 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=24SdvVd059qkU2e4OdaujT405WmyvmPX/eQEIq1IJpQ=; b=JhO9sVXSIrNmI5+0XZmtpFy9qfT37d6k3jFlwT+ibEzW8Rdz71my2RHJUZCsQAHVYoxkCz gCgDqoaype1+f1LX/0MZpSamZd9rA5f/2zl/7Ho35LpSys3buSS6f12AQy0IOke6N0fO98 d0usVzkx31M6Hhp9BAuE3vdo89RBoZFxlBaVS169BfpuGjYECCXqeBch5ptoIMZc9I9Iuk N9jH1CPY7STn0r7vekE6TkQGfqg8hGSnZGmJSq5DSLgtSMEOD8epn6iZByYXVGkYf/uhMO kLSsQts0Hvc6/A1BZmJlZbcsQCy/FeONBbwkDlFwNXeYBP86F75LViMM9ruz1g== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1627016415; a=rsa-sha256; cv=none; b=MRjVKH9b0P5xsnOQo+skGJkKYblkvMbKGrVpnOzWe1vmULq2XLEntF/EMm+7O5qzXiXRmZ hTRzkza30CumTm8paL7CX30AOX8yKKmiiGE3UuusijllNIJpgLu0hEsxgUmHbPSOX3dZHV 6ofPN8U09u/XmkmUtAiATfjD0Wd+kJzofz4TEPT/glEqt8w//0EakPFsq6177ZT7MD6Lkq 7pHYGuAN2v8lauPGOcYZYO4qmloT4gqdYbsOkZ7SNS5KXc00Z/aDf0AtiEYC3gOJTMPtQI 50UmtpSpEB3ijw2i8r5bDv5/fXXlPHNpMqr47Pd+xKacSpHaKWOYKME2nYl/SA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=Bt5Sh3DU; 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-Spam-Score: -1.32 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mgsn.dev header.s=key1 header.b=Bt5Sh3DU; 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: 10B733D74 X-Spam-Score: -1.32 X-Migadu-Scanner: scn0.migadu.com X-TUID: aOYnFISwIaqm Hello, Ricardo Wurmus writes: > With a recent version of Guix, =E2=80=9Cguix environment=E2=80=9D will no= t=20 > terminate on its own, keeps the CPU busy, and gets killed when the=20 > system eventually runs out of memory. > > $ guix describe -f channels > > (list (channel > (name 'guix) > (url "/home/rekado/dev/gx/branches/master") > (commit > "685cfdec94e5e48c4ad28de53466a28dfc258edb"))) > > > $ guix environment pigx-scrnaseq > [wait until it gets killed] 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: package # inputs # transitive inputs (from package-transitive-inputs) pigx-chipseq 48 338 pigx-scrnaseq 41 321 r-cellchat 34 110 pigx-rnaseq 34 343 pigx-bsseq 32 358 pigx-sars-cov2-ww 25 261 r-circus 16 134 Does complete: r-chipseq 6 37 completes in >2m r-shortread 17 36 completes in >1m python-scanpy 25 113 completes in <15s I suspect it has something to do with the number of transitive inputs, because it is so prevalent with these R packages, which all use propagated inputs. However... python-scanpy succeeds in under 15 seconds, and it has more transitive inputs than r-chipseq. Can we reproduce this with a large number of low-transitivity packages directly on the command line? > > The problem disappears when grafts are disabled: > > $ guix environment --no-grafts pigx-scrnaseq > $ [env] yay! -- Sarah