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
