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 ms11 with LMTPS id MIiaDGr0o19aUgAA0tVLHw (envelope-from ) for ; Thu, 05 Nov 2020 12:47:38 +0000 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 iL5vCGr0o1+pTQAAB5/wlQ (envelope-from ) for ; Thu, 05 Nov 2020 12:47:38 +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 8503D940105 for ; Thu, 5 Nov 2020 12:47:37 +0000 (UTC) Received: from localhost ([::1]:44814 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kaefw-000701-AE for larch@yhetil.org; Thu, 05 Nov 2020 07:47:36 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:46294) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kaeXf-00068A-09 for guix-devel@gnu.org; Thu, 05 Nov 2020 07:39:03 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56008) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kaeXe-0007d4-JJ; Thu, 05 Nov 2020 07:39:02 -0500 Received: from 2001-1c02-0b2a-aa00-93bf-7c8c-0fae-b738.cable.dynamic.v6.ziggo.nl ([2001:1c02:b2a:aa00:93bf:7c8c:fae:b738]:60188) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1kaeXd-0000c9-3L; Thu, 05 Nov 2020 07:39:02 -0500 Message-ID: Subject: Re: =?UTF-8?Q?=E2=80=9Cguix?= pack -RR =?UTF-8?Q?r=E2=80=9C?= fails? From: Roel Janssen To: zimoun , guix-devel@gnu.org Date: Thu, 05 Nov 2020 13:38:57 +0100 In-Reply-To: <87v9eldm7p.fsf@gmail.com> References: <87v9eldm7p.fsf@gmail.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.38.1 (3.38.1-1.fc33) MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+larch=yhetil.org@gnu.org Sender: "Guix-devel" X-Scanner: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-devel-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-devel-bounces@gnu.org X-Spam-Score: -0.51 X-TUID: BpzjBqBa8jmC Hi Simon, On Wed, 2020-11-04 at 19:13 +0100, zimoun wrote: > Dear, > > Using Guix fd0ef0e, I run: > > --8<---------------cut here---------------start------------->8--- > rsync -av --progress                            \ >       $(guix pack -RR --save-provenance         \ >                   -S /bin=bin                   \ >                   -S /etc=etc                   \ >                   -S /include=include           \ >                   -S /lib=lib                   \ >                   -S /share=share               \ >                   -S /site-library=site-library \ >                   r)                            \ >       cluster:/path/to/my/stuff > --8<---------------cut here---------------end--------------->8--- > > then log via SSH to cluster and untar the pack. > > --8<---------------cut here---------------start------------->8--- > $ ls -ahl > total 422M > drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:05 . > drwxrwxrwx. 15 root   root   3.8K Nov  4 19:02 .. > -r--r--r--   1 sitour sitour 421M Jan  1  1970 > 5n55mgjcj33s700g91x0zzf3ngflnba7-tarball-pack.tar.gz > lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 bin -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/bin > lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 etc -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/etc > drwxrwxr-x   3 sitour sitour 3.8K Nov  4 19:03 gnu > lrwxrwxrwx   1 sitour sitour   58 Nov  4 19:05 include -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/include > lrwxrwxrwx   1 sitour sitour   54 Nov  4 19:05 lib -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/lib > lrwxrwxrwx   1 sitour sitour   56 Nov  4 19:05 share -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/share > lrwxrwxrwx   1 sitour sitour   63 Nov  4 19:05 site-library -> > gnu/store/fvvn6mc4s7p52frdlsfj502k4zbqb9j7-profile/site-library > --8<---------------cut here---------------end--------------->8--- > > The usual ‘./bin/R’ fails with: > > --8<---------------cut here---------------start------------->8--- > $ ./bin/R > : unsupported Guix execution engine; ignoring > ./bin/R > R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" > > [...] > >  *** caught segfault *** > address 0x7f44f4b11008, cause 'memory not mapped' > --8<---------------cut here---------------end--------------->8--- > > and then has to be killed.  Last, > > --8<---------------cut here---------------start------------->8--- > $ gdb ./bin/R > GNU gdb (GDB) Red Hat Enterprise Linux (7.2-92.el6) > Copyright (C) 2010 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later < > http://gnu.org/licenses/gpl.html> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law.  Type "show > copying" > and "show warranty" for details. > This GDB was configured as "x86_64-redhat-linux-gnu". > For bug reporting instructions, please see: > ... > Reading symbols from > /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal- > 4.0.3R/bin/R...(no debugging symbols found)...done. > (gdb) run > Starting program: > /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal- > 4.0.3R/bin/R > : unsupported Guix execution engine; ignoring > /data2/tmp/foo/gnu/store/yz0zww6i4pafvwh6ysmqxr5pm72ks7lv-r-minimal- > 4.0.3R/bin/Rprocess 36927 is executing new program: > /data2/tmp/foo/gnu/store/jwdvnklncaqw15376vbbr1vgpfr17j18-proot- > static-5.1.0/bin/proot > Detaching after fork from child process 36930. > > R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" > Copyright (C) 2020 The R Foundation for Statistical Computing > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Error: package or namespace load failed for 'grDevices' in > dyn.load(file, DLLpath = DLLpath, ...): >  unable to load shared object > '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so': >   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared > object file: Bad address > Error: package or namespace load failed for 'graphics' in > dyn.load(file, DLLpath = DLLpath, ...): >  unable to load shared object > '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so': >   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared > object file: Bad address > Error: package or namespace load failed for 'stats' in dyn.load(file, > DLLpath = DLLpath, ...): >  unable to load shared object > '/gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so': >   /gnu/store/nqqhaz59gdr5q6mb6mw9dd8jk133rna2-r-minimal- > 4.0.3/lib/R/library/grDevices/libs/grDevices.so: cannot open shared > object file: Bad address > During startup - Warning messages: > 1: package 'grDevices' in options("defaultPackages") was not found > 2: package 'graphics' in options("defaultPackages") was not found > 3: package 'stats' in options("defaultPackages") was not found > 4: Setting LC_CTYPE failed, using "C" > 5: Setting LC_COLLATE failed, using "C" > 6: Setting LC_TIME failed, using "C" > 7: Setting LC_MESSAGES failed, using "C" > 8: Setting LC_MONETARY failed, using "C" > 9: Setting LC_PAPER failed, using "C" > 10: Setting LC_MEASUREMENT failed, using "C" > > > --8<---------------cut here---------------end--------------->8--- > > > The cluster machine is an old kernel: > > --8<---------------cut here---------------start------------->8--- > HEAD$ uname -a > Linux HEAD 2.6.32-573.8.1.el6.x86_64 #1 SMP Tue Nov 10 18:01:38 UTC > 2015 x86_64 x86_64 x86_64 GNU/Linux > --8<---------------cut here---------------end--------------->8--- > > > What do I miss? Perhaps completely misguided, but is this inside an SGE or SLURM job? I've seen similar errors when starting R on a cluster node with too little memory allocated to the compute job. In my experience you need at least 2G of memory available. Kind regards, Roel Janssen