How to make BiocParallel work in DiffBind when working under windows system
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Entering edit mode
@shangguandong1996-21805
Last seen 17 months ago
China

Hi, Dr Stark

I find it seems that Parallel execution do not work in DiffBind when working under Windows system

library(DiffBind)
library(BiocParallel)

> tamoxifen <- dba(sampleSheet="tamoxifen.csv")
BT4741 BT474 ER Resistant Full-Media 1 bed
BT4742 BT474 ER Resistant Full-Media 2 bed
MCF71 MCF7 ER Responsive Full-Media 1 bed
MCF72 MCF7 ER Responsive Full-Media 2 bed
MCF73 MCF7 ER Responsive Full-Media 3 bed
T47D1 T47D ER Responsive Full-Media 1 bed
T47D2 T47D ER Responsive Full-Media 2 bed
MCF7r1 MCF7 ER Resistant Full-Media 1 bed
MCF7r2 MCF7 ER Resistant Full-Media 2 bed
ZR751 ZR75 ER Responsive Full-Media 1 bed
ZR752 ZR75 ER Responsive Full-Media 2 bed
> tamoxifen <- dba.count(tamoxifen, summits=250)
Computing summits...
Sample: reads/Chr18_BT474_ER_1.bam125 
Sample: reads/Chr18_BT474_ER_2.bam125 
Sample: reads/Chr18_MCF7_ER_1.bam125 
Sample: reads/Chr18_MCF7_ER_2.bam125 
Sample: reads/Chr18_MCF7_ER_3.bam125 
Sample: reads/Chr18_T47D_ER_1.bam125 
Sample: reads/Chr18_T47D_ER_2.bam125 
Sample: reads/Chr18_TAMR_ER_1.bam125 
Sample: reads/Chr18_TAMR_ER_2.bam125 
Sample: reads/Chr18_ZR75_ER_1.bam125 
Sample: reads/Chr18_ZR75_ER_2.bam125 
Sample: reads/Chr18_BT474_input.bam125 
Sample: reads/Chr18_MCF7_input.bam125 
Sample: reads/Chr18_T47D_input.bam125 
Sample: reads/Chr18_TAMR_input.bam125 
Sample: reads/Chr18_ZR75_input.bam125 
Re-centering peaks...
Reads will be counted as Single-end.
Sample: reads/Chr18_BT474_ER_1.bam125 
Sample: reads/Chr18_BT474_ER_2.bam125 
Sample: reads/Chr18_MCF7_ER_1.bam125 
Sample: reads/Chr18_MCF7_ER_2.bam125 
Sample: reads/Chr18_MCF7_ER_3.bam125 
Sample: reads/Chr18_T47D_ER_1.bam125 
Sample: reads/Chr18_T47D_ER_2.bam125 
Sample: reads/Chr18_TAMR_ER_1.bam125 
Sample: reads/Chr18_TAMR_ER_2.bam125 
Sample: reads/Chr18_ZR75_ER_1.bam125 
Sample: reads/Chr18_ZR75_ER_2.bam125 
Sample: reads/Chr18_BT474_input.bam125 
Sample: reads/Chr18_MCF7_input.bam125 
Sample: reads/Chr18_T47D_input.bam125 
Sample: reads/Chr18_TAMR_input.bam125 
Sample: reads/Chr18_ZR75_input.bam125 
Warning messages:
1: Parallel execution unavailable: executing serially. 
2: UNKNOWN PARALLEL PACKAGE: 0
sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19041)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=Chinese (Simplified)_China.936 
#> [2] LC_CTYPE=Chinese (Simplified)_China.936   
#> [3] LC_MONETARY=Chinese (Simplified)_China.936
#> [4] LC_NUMERIC=C                              
#> [5] LC_TIME=Chinese (Simplified)_China.936    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.0.2  magrittr_2.0.1  tools_4.0.2     htmltools_0.5.0
#>  [5] yaml_2.2.1      stringi_1.5.3   rmarkdown_2.6   highr_0.8      
#>  [9] knitr_1.30      stringr_1.4.0   xfun_0.20       digest_0.6.27  
#> [13] rlang_0.4.10    evaluate_0.14
Created on 2021-01-28 by the reprex package (v0.3.0)

Best wishes

Guandong Shang

DiffBind • 761 views
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1
Entering edit mode
Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

This is correct. BiocParallel (and by extension DiffBind) does not support multiple parallel operations on Windows platforms.

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Entering edit mode

It is not correct that BiocParallel does not support parallel evaluation on Windows. Windows doesn't support forked (MulticoreParam()) evaluation, but it does support parallel evaluation in independent processes (SnowParam()). There are some complications, in particular because the workers are completely independent, implying that they must load DiffBind (and pay the time cost of loading it) each time a new bplapply() is evaluated. There are some hints in the vignette, but I'll try to improve that with some additional guidance.

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