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bug#49439: grafts cause “guix environment” to get killed with OOM

From: Julien Lepiller
Subject: bug#49439: grafts cause “guix environment” to get killed with OOM
Date: Tue, 27 Jul 2021 10:52:44 -0400
User-agent: K-9 Mail for Android

I have a similar issue with an ocaml package I use at work. It's not free software, but all its dependencies are. The dependencies are not all yeet in guix, so to reproduce you might have to import them first with "guix import opam -r foo" for ocaml-foo.

The package depends on ocaml-ounit, ocaml-lp, ocaml-apronext, menhir, ocaml-async, ocaml-core, ocaml-graph, ocaml-libsvm, ocaml-minisat, ocaml-ppx-deriving-yojson, ocaml-yojson, ocaml-z3, ocaml-zarith and z3.

In total, that's 118 transitive inputs. Building the profile takes 30 minutes for me, on an SSD. The builder takes 1.5g resident.

Other than that, I measured time and memory for creating the environment when the profile was already built (no more derivation to build):

`which time` -v ~/guix/pre-inst-env guix environment ocaml-dummy-package -- echo done

User time: 121.43s
System time: 2.28s
Maximum resident: 1803028kB (1.8 GB)

With a warning from GC:

Repeated allocation of very large block (approx. size 35606528)

Note that I get the same numbers with --no-grafts, so it might be a different issue.

"guix build" terminates quickly.

Le 23 juillet 2021 00:59:21 GMT-04:00, Sarah Morgensen <iskarian@mgsn.dev> a écrit :

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")

$ 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")

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!


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