temporarily use static scheduler for multithreaded CV #53

OpenMendel · Jun 11, 2023 · c43c18e · c43c18e · biona001 · Jun 11, 2023
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commit c43c18e
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Showing 3 changed files with 2 additions and 5 deletions.
diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "MendelIHT"
 uuid = "921c7187-1484-5754-b919-5d3ed9ac03c4"
 keywords = ["GWAS", "Genome-wide association studies", "feature selection", "iterative hard thresholding"]
 authors = ["Benjamin Chu <benchu99@hotmail.com>", "Kevin Keys <kevin.keys@ucsf.edu>"]
-version = "1.4.10"
+version = "1.4.11"
 
 [deps]
 BGEN = "6db4b851-9beb-4b83-9d64-eb1cfb37721d"
@@ -20,7 +20,6 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-ThreadPools = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431"
 VCFTools = "a620830f-fdd7-5ebc-8d26-3621ab35fbfe"
 
 [compat]
@@ -36,7 +35,6 @@ Reexport = "1"
 SnpArrays = "0.3.15"
 SpecialFunctions = "1, 2"
 StatsBase = "0.33, 0.34"
-ThreadPools = "2"
 VCFTools = "0.2"
 julia = "1.5, 1.6"
 

diff --git a/src/MendelIHT.jl b/src/MendelIHT.jl
@@ -19,7 +19,6 @@ module MendelIHT
     using DelimitedFiles
     using ProgressMeter
     using Reexport
-    using ThreadPools
     using BGEN
 
     @reexport using Distributions

diff --git a/src/cross_validation.jl b/src/cross_validation.jl
@@ -97,7 +97,7 @@ function cv_iht(
     # cross validate. TODO: wrap pmap with batch_size keyword to enable distributed CV
     combinations = allocate_fold_and_k(q, path)
     mses = zeros(length(combinations))
-    ThreadPools.@qthreads for i in 1:length(combinations)
+    Threads.@threads :static for i in eachindex(combinations)
         fold, sparsity = combinations[i]
 
         # assign train/test indices