Closed krademaker closed 5 years ago
It was developed on mac. Pretty sure I've run it on a Unix cluster as well. Check if there are known Ubuntu issues with the parallel package? If so, easiest way is probably to add a test for whether OS is Ubuntu and convert mclapply calls to lapply. Let me know how it goes.
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From: Koen Rademaker notifications@github.com Sent: Tuesday, May 28, 2019 9:42:58 PM To: NathanSkene/EWCE Cc: Subscribed Subject: [NathanSkene/EWCE] parallel computing issues during generate.celltype.data (#5)
Before calculating specificity data for my own dataset, I was following the example code on my sysyem (Ubuntu 18.04, R v3.6.0)
download.file("goo.gl/r5Y24y", destfile="expression_mRNA_17-Aug-2014.txt") path = "expression_mRNA_17-Aug-2014.txt" cortex_mrna = load.linnarsson.sct.data(path) exp_CortexOnly_DROPPED = drop.uninformative.genes(exp=cortex_mrna$exp,level2annot = cortex_mrna$annot$level2class) annotLevels = list(level1class=cortex_mrna$annot$level1class,level2class=cortex_mrna$annot$level2class) fNames_CortexOnly = generate.celltype.data(exp=exp_CortexOnly_DROPPED,annotLevels=annotLevels,groupName="kiCortexOnly")
Which returns the following error:
fNames_CortexOnly = generate.celltype.data(exp=exp_CortexOnly_DROPPED,annotLevels=annotLevels,groupName="kiCortexOnly") Loading required package: parallel Error in makePSOCKcluster(names = spec, ...) : numeric 'names' must be >= 1
Apparently, determining the n.o. cores (source codehttps://github.com/NathanSkene/EWCE/blob/a4e4e4595eb016321094b814a78fc01c1674103c/R/generate.celltype.data.r#L28) returns a NA, which in turn causes makeCluster() to fail. On what OS was the code developed / tested? Perhaps this is a Ubuntu specific issue?
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Hi,
so I repeated running the code a few times, and sporadically detectCores returns NA, while in other instances it returns 8 (matching the n.o. cores on my system), after which I can successfully run generate.celltype.data.
I am not sure why detecting the number of cores fails every now and then, but the original issue is resolved for me right now.
Before calculating specificity data for my own dataset, I was following the example code on my sysyem (Ubuntu 18.04, R v3.6.0)
Which returns the following error:
Apparently, determining the n.o. cores (source code) returns a NA, which in turn causes makeCluster() to fail. On what OS was the code developed / tested? Perhaps this is a Ubuntu specific issue?