From: Sarah Morgensen <iskarian@mgsn.dev>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 49439@debbugs.gnu.org
Subject: bug#49439: grafts cause “guix environment” to get killed with OOM
Date: Thu, 22 Jul 2021 21:59:21 -0700 [thread overview]
Message-ID: <86tuklr5g6.fsf@mgsn.dev> (raw)
In-Reply-To: <87sg0rse1n.fsf@elephly.net> (Ricardo Wurmus's message of "Tue, 06 Jul 2021 16:38:28 +0200")
Hello,
Ricardo Wurmus <rekado@elephly.net> writes:
> With a recent version of Guix, “guix environment” will not
> terminate on its own, keeps the CPU busy, and gets killed when the
> system eventually runs out of memory.
>
> $ guix describe -f channels
>
> (list (channel
> (name 'guix)
> (url "/home/rekado/dev/gx/branches/master")
> (commit
> "685cfdec94e5e48c4ad28de53466a28dfc258edb")))
>
>
> $ guix environment pigx-scrnaseq
> [wait until it gets killed]
I can reproduce this with pigx-scrnaseq as well a number of other
packages (listed below).
$ ./pre-inst-env guix describe -f channels
(list (channel
(name 'guix)
(url "/home/sarah/guix")
(commit
"3217a04b0352c2dd13323257b369604eeabfccc3")))
Does not complete within 5 minutes:
package # inputs # transitive inputs
(from package-transitive-inputs)
pigx-chipseq 48 338
pigx-scrnaseq 41 321
r-cellchat 34 110
pigx-rnaseq 34 343
pigx-bsseq 32 358
pigx-sars-cov2-ww 25 261
r-circus 16 134
Does complete:
r-chipseq 6 37 completes in >2m
r-shortread 17 36 completes in >1m
python-scanpy 25 113 completes in <15s
I suspect it has something to do with the number of transitive inputs,
because it is so prevalent with these R packages, which all use
propagated inputs. However... python-scanpy succeeds in under 15
seconds, and it has more transitive inputs than r-chipseq.
Can we reproduce this with a large number of low-transitivity packages
directly on the command line?
>
> The problem disappears when grafts are disabled:
>
> $ guix environment --no-grafts pigx-scrnaseq
> $ [env] yay!
--
Sarah
next prev parent reply other threads:[~2021-07-23 5:00 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-07-06 14:38 bug#49439: grafts cause “guix environment” to get killed with OOM Ricardo Wurmus
2021-07-23 4:59 ` Sarah Morgensen [this message]
2021-07-27 14:52 ` Julien Lepiller
2021-07-27 16:28 ` Ludovic Courtès
2021-07-27 23:35 ` Sarah Morgensen
2021-07-28 10:00 ` Ludovic Courtès
2021-07-28 22:03 ` Ludovic Courtès
2021-07-29 3:20 ` Sarah Morgensen
2021-08-09 21:26 ` Ludovic Courtès
2021-08-10 15:36 ` Ludovic Courtès
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=86tuklr5g6.fsf@mgsn.dev \
--to=iskarian@mgsn.dev \
--cc=49439@debbugs.gnu.org \
--cc=rekado@elephly.net \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.