Dear,
Using Guix fd0ef0e, I run:
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rsync -av --progress \
$(guix pack -RR --save-provenance \
-S /bin=bin \
-S /etc=etc \
-S /include=include \
-S /lib=lib \
-S /share=share \
-S /site-library=site-library \
r) \
cluster:/path/to/my/stuff
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then log via SSH to cluster and untar the pack.
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$ 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
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The usual ‘./bin/R’ fails with:
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$ ./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'
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and then has to be killed. Last,
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$ 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"
>
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The cluster machine is an old kernel:
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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
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What do I miss?
All the best,
simon
