Ludovic Courtès <ludo@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.Ludovic Courtès <ludo@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.
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From: Ricardo Wurmus <rekado@HIDDEN>
To: bug-guix@HIDDEN
Subject: low performance when building profile of already built packages
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Here is a manifest that isn=E2=80=99t unusual for a bioinformatics=20
workflow:
--8<---------------cut here---------------start------------->8---
(define packages
(list "bash-minimal"
"fastqc"
"gzip"
"htseq"
"multiqc"
"r-corrplot"
"r-crosstalk"
"r-data-table"
"r-deseq2"
"r-dt"
"r-genomicalignments"
"r-genomicranges"
"r-ggplot2"
"r-ggrepel"
"r-gprofiler"
"r-knitr"
"r-pheatmap"
"r-plotly"
"r-reshape2"
"r-rmarkdown"
"r-rsamtools"
"r-rtracklayer"
"r-s4vectors"
"r-scales"
"r-summarizedexperiment"
"r-tximport"
"samtools"
"sed"
"trim-galore"))
(specifications->manifest packages)
--8<---------------cut here---------------end--------------->8---
When all these packages already exist and nothing is to be done=20
when Guix is asked to instantiate this manifest, more than 13=20
seconds pass.
--8<---------------cut here---------------start------------->8---
$ [env] export GUIX_PROFILING=3D"object-cache=20
add-data-to-store-cache rpc"
$ [env] time guix package -m manifest-test.scm -p /tmp/foo
The following packages will be installed:
bash-minimal 5.0.16
fastqc 0.11.5
gzip 1.10
htseq 0.9.1
multiqc 1.5
r-corrplot 0.84
r-crosstalk 1.1.1
r-data-table 1.14.0
r-deseq2 1.30.1
r-dt 0.17
r-genomicalignments 1.26.0
r-genomicranges 1.42.0
r-ggplot2 3.3.3
r-ggrepel 0.9.1
r-gprofiler 0.7.0
r-knitr 1.31
r-pheatmap 1.0.12
r-plotly 4.9.3
r-reshape2 1.4.4
r-rmarkdown 2.7
r-rsamtools 2.6.0
r-rtracklayer 1.50.0
r-s4vectors 0.28.1
r-scales 1.1.1
r-summarizedexperiment 1.20.0
r-tximport 1.18.0
samtools 1.11
sed 4.8
trim-galore 0.6.6
[[most of the time passes here]]
nothing to be done
Store object cache:
fresh caches: 2
lookups: 45493
hits: 43943 (96.6%)
cache size: 1549 entries
'add-data-to-store' cache:
lookups: 7755
hits: 3411 (44.0%)
.drv files: 4357 (56.2%)
Scheme files: 3343 (43.1%)
Remote procedure call summary: 5283 RPCs
built-in-builders ... 1
add-to-store/tree ... 27
add-to-store ... 213
query-references ... 698
add-text-to-store ... 4344
real 0m13.379s
user 0m16.414s
sys 0m0.253s
--8<---------------cut here---------------end--------------->8---
Some of these R packages have a lot of transitive inputs, such as=20
r-deseq2 with 81 transitive propagated inputs. So there=E2=80=99s a lot=20
of propagation here, which I suspect contributes to things being=20
so unexpectedly slow.
This report may be related to performance issues reported for=20
=E2=80=9Cguix environment=E2=80=9D in https://issues.guix.gnu.org/41702, wh=
ich=20
also involves R packages (such as r-learnr with 46 transitive=20
propagated inputs).
--=20
Ricardo
Ricardo Wurmus <rekado@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#48005; Package guix.
Full text available.
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