Re: Introducing Guix to HPC at my institution

["Sébastien Lerique" <sl@eauchat.org>]

Hi Ludo, zimoun, all,

Thanks again for your answers, for the links to documentation, and 
for the support on IRC!

> Hmm could it be that nscd is not running, and that 
> /etc/nsswitch.conf
> specifies a “non-standard” NSS plugin, such as ‘sssd’?
>
>   https://guix.gnu.org/manual/en/html_node/Application-Setup.html#Name-Service-Switch-1
>
> Does ‘guix install hello --no-offload’ work around the issue?

Yes, that solves the issue!

>>  $ guix archive --authorize < \
>>    /gnu/store/xb4szjambyi52bpnkjv080g2mlfqqpp0-profile/share/guix/ci.guix.gnu.org.pub
>>  guix archive: error: mkdir: Permission denied
>
> I guess it’s trying to write to /etc/guix.  You probably need to 
> set
> GUIX_STATE_DIRECTORY=$HOME/.local/var/guix here.

Yes, that would be GUIX_CONFIGURATION_DIRECTORY. As discussed on 
IRC though, /etc in the tarball is a symlink to the profile, so 
neither `guix archive` nor I can create /etc/guix. So I resorted 
to creating a `/etc-guix` folder which I use for 
GUIX_CONFIGURATION_DIRECTORY.

>> 2. knowing that my environment has user namespaces (and knowing 
>> that
>> that may not be enough), would it be possible to set up 
>> guix-daemon as
>> non-root with the assistance of a sysadmin (so say with root 
>> access
>> during setup), with build users and all, and have it provide 
>> identical
>> guarantees to a guix-daemon running as root? If not, why not, 
>> and
>> could we work around that?
>
> Good question.  It should be possible to make the daemon run as
> non-root; that’s what the trick with the ‘guix pack -R’ wrapper 
> should
> achieve, but it could also be a built-in capability.

Yes, I'd be very happy to try and build that once things work!

So, to summarize the current status, here is what I do:

On my Guix System (`deigo` is my ssh config for the cluster):

  $ scp (guix pack -R -S /bin=bin -S /etc=etc guix bash) 
  deigo:guix-pack.tar.gz

Then on deigo:

  $ mkdir -p /a-working-directory/guix
  $ cd /a-working-directory/guix
  $ tar xzf ~/guix-pack.tar.gz
  $ mkdir etc-guix
  $ bin/bash
  $ . etc/profile
  $ export GUIX_STATE_DIRECTORY=$(pwd)/var/guix
  $ export GUIX_LOG_DIRECTORY=$(pwd)/var/log
  $ export GUIX_CONFIGURATION_DIRECTORY=$(pwd)/etc-guix

Then the fun starts. There are 4 different cases and problems, 
depending on whether I use substitutes or not, and on whether 
`/a-working-directory` is an NFS share or a local mount.


Case 1: with substitutes, on a local (non-NFS) folder
-----------------------------------------------------

  $ guix archive --authorize < 
  bin/../share/guix/ci.guix.gnu.org.pub
  $ guix-daemon --disable-chroot &
  $ guix install hello
  [... dowloading ...]
  unexpected substituter message 'defining `GUIX_LOCPATH', along 
  these lines:

       guix install glibc-utf8-locales
       export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"

  See the "Application Setup" section in the manual, for more 
  info.
  '

I think this is https://issues.guix.gnu.org/45166.

Using instead `guix pack -R -S /bin=bin -S /etc=etc -S /lib=lib 
guix bash glibc-utf8-locales`, and:

  $ export GUIX_LOCPATH=$(pwd)/lib/locale
  $ ls $GUIX_LOCPATH/
  2.31

seems to start working, but then `guix install hello` fails with 
the same error, and:

  $ ls $GUIX_LOCPATH/
  ls: cannot access '/tmp/sebastien-lerique/guix/lib/locale/': No 
  such file or directory

Is it possible that glibc-utf8-locales gets garbage-collected?


Case 2: from source (no substitutes), on a local (non-NFS) folder
-----------------------------------------------------------------

No need for the locale fix here (another bug appears before that):

  $ guix-daemon --disable-chroot &
  # --no-offload works around the missing nscd problem; up to now 
  this
  # doesn't seem necessary when using substitutes
  $ guix install hello --no-offload
  [... builds for a while ...]
  build of 
  /gnu/store/pkn1w1q3xkn273kpmggc4dnq6n6hr9jy-bzip2-mesboot-1.0.8.drv 
  failed

The build log for bzip2-mesboot ends with:

  tcc -ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o 
  compress.o decompress.o bzlib.o
  ranlib libbz2.a
  /gnu/store/prkqai3zwh3shlqpll6xyncmmqpj49dd-gash-boot-0.2.0/bin/sh: 
  ranlib: Command not found.
  make: *** [libbz2.a] Error 127
  command "make" "CC=tcc -I ." "AR=tcc -ar" "bzip2" 
  "PREFIX=/gnu/store/s94hyrv1vgllxir5niiyzfc9g80l5kcd-bzip2-mesboot-1.0.8" 
  failed with status 2

Is this new and should be reported as a bug? Should 
binutils-mesboot0 be part of bzip2-mesboot's inputs? (I haven't 
learned about the boostrapping mechanism yet.)


Case 3: with substitutes, on an NFS share
-----------------------------------------

Again no need for the locale fix (another bug appears before 
that):

  $ guix archive --authorize < 
  bin/../share/guix/ci.guix.gnu.org.pub
  $ guix-daemon --disable-chroot &
  $ guix install hello
  [... downloading ...]
  guix install: error: cannot unlink 
  `/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib': 
  Directory not empty

so checking:

  $ ls -lA 
  /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib
  total 3840
  -r-xr-xr-x 1 sebastien-lerique froeseuni   64832 Jan  1  1970 
  .nfs000000000172caa5000054bd
  [... more .nfs files ...]

  $ lsof -f -- 
  /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/.nfs000000000172caa5000054bd` 
  reports:
  [... some warnings ...]
  COMMAND     PID              USER  FD   TYPE DEVICE SIZE/OFF 
  NODE NAME
  bash      25616 sebastien-lerique mem    REG   0,52    64832 
  24300197 
  /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/.nfs000000000172caa5000054bd
  guix-daem 25934 sebastien-lerique mem    REG   0,52    64832 
  24300197 
  /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib/.nfs000000000172caa5000054bd

Not sure what's going wrong here. Maybe it's more 
garbage-collecting (as in case 1), failing because of an nfs 
nuance or bug?


Case 4: from source (no substitutes), on an NFS share
-----------------------------------------------------

Fails in the exact same way as Case 2.


I have no idea how to make progress in any of these cases (except 
the bzip2-mesboot one maybe), so any input on these different 
problems is very welcome :)

Thanks and happy hacking!
Sébastien