From debbugs-submit-bounces@debbugs.gnu.org Fri Jul 23 00:59:32 2021 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 To: Ricardo Wurmus Subject: Re: bug#49439: grafts cause =?utf-8?Q?=E2=80=9Cguix_environment?= =?utf-8?Q?=E2=80=9D?= to get killed with OOM 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-Flow: FLOW_OUT X-Migadu-Auth-User: iskarian@mgsn.dev X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 49439 Cc: 49439@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: -1.0 (-) 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