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BatchtoolsParam and bpiterate: registry not empty error

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#107 0 comentarios 1 reacción 0 asignados Ver en GitHub

Nadie ha tomado este issue todavía.

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Estancado
Stack tecnológico
r
Área
backend, distributed-systems

Línea de trabajo

Reproduce the commands using BatchtoolsParam, register(), bpstart(), and the repeated matrix operation shown in the report. Trace how the batchtools registry is managed across calls when the backend is started in advance. Done means repeated operations no longer fail with “Registry must be empty” without requiring bpstop() between calls.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Behold this innocuous series of commands:

library(BiocParallel)

bpp2 <- BatchtoolsParam(10, cluster = "slurm",
    resources = list(walltime = 3600, memory = 8000, ncpus = 1))

library(HCAData)
sce.bone <- HCAData('ica_bone_marrow')

register(bpp2)
bpstart(bpp2)
out <- counts(sce.bone) %*% runif(ncol(sce.bone)) # Okay
out <- counts(sce.bone) %*% runif(ncol(sce.bone))
## Error in batchtools::batchMap(fun = FUN, fl, more.args = list(...), reg = BPPARAM$registry) :
##   Registry must be empty

I assume some required clean-up after the first call is not taking place when I start the backend in advance. Stopping it and running it the second time works fine:

bpstop(bpp2)
out <- counts(sce.bone) %*% runif(ncol(sce.bone)) # okay again.
Session info 
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /gstore/apps/R/R_3.6.1_Bioc_3.10/R-3.6.1-Bioc-3.10-tst-20191103/lib64/R/lib/libRblas.so
LAPACK: /gstore/apps/R/R_3.6.1_Bioc_3.10/R-3.6.1-Bioc-3.10-tst-20191103/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] HCAData_1.2.0               SingleCellExperiment_1.8.0
 [3] SummarizedExperiment_1.16.0 DelayedArray_0.12.0
 [5] matrixStats_0.55.0          Biobase_2.46.0
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0
 [9] IRanges_2.20.1              S4Vectors_0.24.1
[11] BiocGenerics_0.32.0         BiocParallel_1.20.0

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5              HDF5Array_1.14.1
 [3] BiocVersion_3.10.1            purrr_0.3.3
 [5] rhdf5_2.30.1                  lattice_0.20-38
 [7] vctrs_0.2.0                   htmltools_0.4.0
 [9] BiocFileCache_1.10.2          yaml_2.2.0
[11] interactiveDisplayBase_1.24.0 blob_1.2.0
[13] rlang_0.4.2                   pillar_1.4.2
[15] later_1.0.0                   glue_1.3.1
[17] DBI_1.0.0                     rappdirs_0.3.1
[19] bit64_0.9-7                   dbplyr_1.4.2
[21] GenomeInfoDbData_1.2.2        zlibbioc_1.32.0
[23] ExperimentHub_1.12.0          memoise_1.1.0
[25] fastmap_1.0.1                 httpuv_1.5.2
[27] curl_4.3                      AnnotationDbi_1.48.0
[29] Rcpp_1.0.3                    xtable_1.8-4
[31] backports_1.1.5               promises_1.1.0
[33] BiocManager_1.30.10           XVector_0.26.0
[35] mime_0.7                      bit_1.1-14
[37] AnnotationHub_2.18.0          digest_0.6.23
[39] dplyr_0.8.3                   shiny_1.4.0
[41] grid_3.6.1                    tools_3.6.1
[43] bitops_1.0-6                  magrittr_1.5
[45] RCurl_1.95-4.12               tibble_2.1.3
[47] RSQLite_2.1.4                 crayon_1.3.4
[49] pkgconfig_2.0.3               zeallot_0.1.0
[51] Matrix_1.2-18                 assertthat_0.2.1
[53] httr_1.4.1                    Rhdf5lib_1.8.0
[55] R6_2.4.1                      compiler_3.6.1
Lenguaje dominante
R
Estrellas
69
Forks
32
Sin PR fusionados en 30 d

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