Hi,

when I run IHW on our server it uses lots of computational resources (at least 20 cores). I can't seem to find any way to modify this in the call to ihw(). Is there a way to reduce the number of cores used by IHW?

Thanks!

Example code (from the IHW package) and session info:

library(IHW)
X <- runif(20000, min=0, max=2.5)
H <- rbinom(20000,1,0.1)
Z <- rnorm(20000, H*X)
pvalue <- 1-pnorm(Z)
ihw_fdr <- ihw(pvalue, X, .1)

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/local/R/R-3.4.0/lib/libRblas.so
LAPACK: /usr/local/R/R-3.4.0/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] IHW_1.4.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0      parallel_3.4.0      slam_0.1-40
[4] fdrtool_1.2.15      BiocGenerics_0.22.0 lpsymphony_1.4.1

Hi Charlotte,

I assume this problem arises because of the lpsymphony package, on which IHW depends. On Linux machines SYMPHONY is built with '--enable-openmp' flag by default. 

I think it is possible to set the number of threads by export OMP_NUM_THREADS=2 (if you want only 2 threads).

Otherwise a quick fix would be to manually change line 62 of the configure script in the lpsymphony package from OMP_FLAG="--enable-openmp" to OMP_FLAG="--disable-openmp" and re-install the package from source. Then the OpenMP multithread functionality is disabled. Apologies for the inconvenience and let me know if this has worked.