Re: “guix pack -RR r“ fails?

[Roel Janssen]

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)
> 
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> 
> 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