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Question: OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
0
gravatar for davide.chicco
9 days ago by
davide.chicco0 wrote:

I've a problem with ComBat() function from the SVA package of Bioconductor in R.

On my laptop (Latitude 5590 running a Linux Ubuntu 18 operating system), it works well. But if I ran it on a TORQUE cluster, the call to the ComBat() function generates an infinite waiting loop:

> "ComBat()"   Found25batches
> 
> Note: one batch has only one sample, setting mean.only=TRUE
> 
> Adjusting for0covariate(s) or covariate level(s)
> 
> Standardizing Data across genes
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable
> 
> OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable
> 
> OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable
> 
> OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable
> 
> OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable
> 
> OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
> 
> OpenBLAS blas_thread_init: pthread_create: Resource temporarily
> unavailable

Do you know how I can fix it?

I checked online and some people already had that problem, which is related to Python. That sounds weird to me: if it's a Python problem, why does it show up in R? I also asked this question on StackOverflow.com, but nobody was able to help me so far.

Thanks

sva R openblas • 29 views
ADD COMMENTlink written 9 days ago by davide.chicco0
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