No luck with singularity (/var/singularity/mnt/container not found)

No luck with singularity (/var/singularity/mnt/container not found)

[Wiktor Żelazny]

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Hi all,

I’ve never worked with singularity before. Reading “Using Guix
Without Being root” on GuixHPC blog convinced me to give it a try.
With system-wide (/etc/config.scm) singularity installation (per-user
installation gave the same errors, and sudo does not help, either):

   $ singularity selftest
   + sh -c test -f /gnu/store/wh729j45fd68yxnrjc85072fxsna0c9g-singularity-2.6.1/etc/    (retval=0) OK
   + test -u /run/setuid-programs/singularity-action-helper                              (retval=1) ERROR
   Full output in: /tmp/tmp.mll6ICopmA

/tmp/tmp.mll6ICopmA was empty. Also:

   $ singularity shell pack.squashfs
   ERROR  : Failed to resolve path to /var/singularity/mnt/container: No such file or directory
   ABORT  : Retval = 255

I took a look into the GUIX Manual whether there is some related service that
needs to be appended, something extra to be configured (like a user group
membership). I also checked the singularity documentation, which suggests that
the software should work out of the box. No hints. Also nothing of value from
an on-line search using the error message as the query.

I’m on GuixSD.

What could I be doing wrong?

WŻ

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Re: No luck with singularity (/var/singularity/mnt/container not found)

[Eric Bavier]

Hello Wiktor,

----- On Nov 14, 2019, at 3:37 PM, Wiktor Żelazny wz@freeshell.de wrote:

> Hi all,
> 
> I’ve never worked with singularity before. Reading “Using Guix
> Without Being root” on GuixHPC blog convinced me to give it a try.
> With system-wide (/etc/config.scm) singularity installation (per-user
> installation gave the same errors, and sudo does not help, either):
> 
>   $ singularity selftest
...
>   + test -u /run/setuid-programs/singularity-action-helper  (retval=1) ERROR
>   Full output in: /tmp/tmp.mll6ICopmA

Did you add a singularity service to your config.scm?  That should handle declaring the helper programs as setuid, and creating the container mount directory in /var/singularity/mnt (see "Miscellaneous Services" in the manual).  You'll add the service via, e.g.:

  (operating-system
    ;; ...
    (services
      (cons (service singularity-service-type)
            %base-services)))

-- 
`~Eric

Re: No luck with singularity (/var/singularity/mnt/container not found)

[Wiktor Żelazny]

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On Thu, Nov 21, 2019 at 12:29:38AM -0500, Eric Bavier wrote:

>   (operating-system
>     ;; ...
>     (services
>       (cons (service singularity-service-type)
>             %base-services)))

Hi Eric,

Thanks a lot. It’s not in the on-line version of the manual, so I
missed it. Unfortunately, now I’m getting

   ERROR  : No valid /bin/sh in container
   ABORT  : Retval = 255

even while following the tutorial [1]:

   $ guix pack -f docker -S /bin=bin hwloc

   substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
   substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
   The following derivations will be built:
      /gnu/store/81bzccc2r3lm4zkk9n55z1r9mh10lg0p-docker-pack.tar.gz.drv
      /gnu/store/0v50h4xbaxmawpm1fngg8b7gmlf3vj1m-module-import.drv
      /gnu/store/1m60igyjnkq1xr91x61kh0k0r680jwhs-module-import-compiled.drv
      /gnu/store/wi9mikyalfq5bjn0b41w1k2vbrbxp8vq-profile.drv
   2.9 MB will be downloaded:
      /gnu/store/2zi4y374rvsp4xld4cdw8x6imjjczp26-hwloc-2.1.0-debug
      /gnu/store/cyd4qzrl2h7phpj0skv9xp6nybybvl2r-hwloc-2.1.0-lib
      /gnu/store/2jqmr45v6fqsvpad515v73nsvbb1l8rb-hwloc-2.1.0
   The following graft will be made:
      /gnu/store/5lfv9vrmmkrqj1qipgll5gqls2hnah6n-hwloc-2.1.0.drv
   The following profile hooks will be built:
      /gnu/store/3w23faaw1402xb23lff9kmnrah4qjdny-xdg-mime-database.drv
      /gnu/store/7k9sblz8z4d524s7cgbkfam1zifz7xsi-xdg-desktop-database.drv
      /gnu/store/7x6vc9qb6aap2515wak2kk3y2d55sq4y-glib-schemas.drv
      /gnu/store/aajx31a1sx28vxfh2wwkswammr22aym6-info-dir.drv
      /gnu/store/l9r0z6l7x52xdqwmvqwydmhh2yl899wz-fonts-dir.drv
      /gnu/store/w1079rvgnhqjghw770lbh45h1j661pi8-ca-certificate-bundle.drv
      /gnu/store/zvagzwgd1ac0zq4c435kq01mwbc4fda4-manual-database.drv
   building /gnu/store/0v50h4xbaxmawpm1fngg8b7gmlf3vj1m-module-import.drv...
   downloading from https://ci.guix.gnu.org/nar/lzip/cyd4qzrl2h7phpj0skv9xp6nybybvl2r-hwloc-2.1.0-lib...
   hwloc-2.1.0-lib  186KiB                                                                                                                                                                            164KiB/s 00:01 [##################] 100.0%

   building /gnu/store/1m60igyjnkq1xr91x61kh0k0r680jwhs-module-import-compiled.drv...
   downloading from https://ci.guix.gnu.org/nar/lzip/2jqmr45v6fqsvpad515v73nsvbb1l8rb-hwloc-2.1.0...
   hwloc-2.1.0  2.1MiB                                                                                                                                                                                 82KiB/s 00:26 [##################] 100.0%

   downloading from https://ci.guix.gnu.org/nar/lzip/2zi4y374rvsp4xld4cdw8x6imjjczp26-hwloc-2.1.0-debug...
   hwloc-2.1.0-debug  479KiB                                                                                                                                                                           47KiB/s 00:10 [##################] 100.0%

   applying 3 grafts for /gnu/store/5lfv9vrmmkrqj1qipgll5gqls2hnah6n-hwloc-2.1.0.drv...
   building CA certificate bundle...
   building fonts directory...
   generating GLib schema cache...
   building directory of Info manuals...
   building database for manual pages...
   building XDG desktop file cache...
   building XDG MIME database...
   building /gnu/store/wi9mikyalfq5bjn0b41w1k2vbrbxp8vq-profile.drv...
   building /gnu/store/81bzccc2r3lm4zkk9n55z1r9mh10lg0p-docker-pack.tar.gz.drv...
   /gnu/store/36x4jdzz7fm3gwkfy5cw7hh2bbz4mck0-docker-pack.tar.gz

   $ singularity exec /gnu/store/36x4jdzz7fm3gwkfy5cw7hh2bbz4mck0-docker-pack.tar.gz /bin/lstopo
   Opening tar archive, stand by...
   ERROR  : No valid /bin/sh in container
   ABORT  : Retval = 255

[1]: https://hpc.guix.info/blog/2017/10/using-guix-without-being-root/

WŻ

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