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bug fix - parallel error handling #13

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bug fix - parallel error handling #13

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dc7f7b8
bug fix - parallel error handling
ned-procogia Jan 19, 2022
7006145
bug fix - parallel processing
ned-procogia Jan 19, 2022
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46 changes: 45 additions & 1 deletion R/NBthDE.R
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Original file line number Diff line number Diff line change
Expand Up @@ -350,6 +350,27 @@ fitNBthDE_funct = function(form, annot,
preci1, threshold_mean * probenum[features_high[start_index:end_index]], preci2,
startpara, sizescalebythreshold, (iter == iterations))
}, mc.cores = n_parallel)
bad = sapply(result,is.null)
to_retry = 1:n_parallel
to_retry = to_retry[bad]
if(sum(bad)>0){
print("need to retry")
print(to_retry)
more_results = mclapply(to_retry, function(i) {
my_len = length(features_all)
start_index = (round(((i-1)*my_len/n_parallel))+1)
end_index = round(i*my_len/n_parallel)
NBthDE_paraOptall(
t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
startpara, sizescalebythreshold, (iter == iterations))
}, mc.cores = sum(bad))
for(i in 1:length(to_retry)){
print("changed entry")
print(to_retry[i])
result[to_retry[i]] = more_results[i]
}
}
new_result= list('par'=matrix(,nrow=NROW(result[[1]]$par),ncol=0),
'hes',
'conv'=matrix(,nrow=0,ncol=1))
Expand Down Expand Up @@ -381,11 +402,32 @@ fitNBthDE_funct = function(form, annot,
my_len = length(features_all)
start_index = (round(((i-1)*my_len/n_parallel))+1)
end_index = round(i*my_len/n_parallel)
NBthDE_paraOptall(
GeoDiff:::NBthDE_paraOptall(
t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
startpara, sizescalebythreshold, (iter == iterations))
}, mc.cores = n_parallel)
bad = sapply(result,is.null)
to_retry = 1:n_parallel
to_retry = to_retry[bad]
if(sum(bad)>0){
print("need to retry")
print(to_retry)
more_results = mclapply(to_retry, function(i) {
my_len = length(features_all)
start_index = (round(((i-1)*my_len/n_parallel))+1)
end_index = round(i*my_len/n_parallel)
GeoDiff:::NBthDE_paraOptall(
t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
startpara, sizescalebythreshold, (iter == iterations))
}, mc.cores = sum(bad))
for(i in 1:length(to_retry)){
print("changed entry")
print(to_retry[i])
result[to_retry[i]] = more_results[i]
}
}
new_result= list('par'=matrix(,nrow=NROW(result[[1]]$par),ncol=0),
'hes',
'conv'=matrix(,nrow=0,ncol=1))
Expand All @@ -397,6 +439,8 @@ fitNBthDE_funct = function(form, annot,
result=new_result
}
para <- result$par
print(length(para))
print(length(features_all))
colnames(para) <- features_all
conv <- result$conv
names(conv) <- features_all
Expand Down