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BatchtoolsParam and bpiterate: registry not empty error #107

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LTLA opened this issue Dec 10, 2019 · 0 comments
Open

BatchtoolsParam and bpiterate: registry not empty error #107

LTLA opened this issue Dec 10, 2019 · 0 comments

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@LTLA
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LTLA commented Dec 10, 2019

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
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