From: Roel Janssen <roel@gnu.org>
To: zimoun <zimon.toutoune@gmail.com>, guix-devel@gnu.org
Subject: Re: “guix pack -RR r“ fails?
Date: Thu, 05 Nov 2020 13:38:57 +0100 [thread overview]
Message-ID: <f9ff8f9c65dcb42458f61d2685f865e81619fbc2.camel@gnu.org> (raw)
In-Reply-To: <87v9eldm7p.fsf@gmail.com>
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:
> <http://www.gnu.org/software/gdb/bugs/>...
> 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
next prev parent reply other threads:[~2020-11-05 12:47 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-11-04 18:13 “guix pack -RR r“ fails? zimoun
2020-11-05 12:38 ` Roel Janssen [this message]
2020-11-06 18:52 ` zimoun
2020-11-06 10:05 ` Ludovic Courtès
2020-11-06 18:48 ` zimoun
2020-11-08 17:34 ` Ludovic Courtès
2020-11-09 12:01 ` zimoun
2020-11-12 20:41 ` Ludovic Courtès
2020-11-12 23:21 ` zimoun
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