[英]OpenBLAS issue with ComBat() function of the R Bioconductor SVA package on Torque cluster
I've a problem with ComBat() function from the SVA package of Bioconductor in R. 我在R中的Bioconductor的SVA包中使用ComBat()函数时遇到问题。
On my laptop (Latitude 5590 running a Linux Ubuntu 18 operating system), it works well. 在我的笔记本电脑上(运行Linux Ubuntu 18操作系统的Latitude 5590),它运行良好。 But if I ran it on a TORQUE cluster, the call to the ComBat() function generates an infinite waiting loop:
但是如果我在TORQUE集群上运行它,对ComBat()函数的调用会产生一个无限的等待循环:
"ComBat()" Found25batches
“ComBat()”Found25batches
Note: one batch has only one sample, setting mean.only=TRUE
注意:一个批次只有一个样本,设置mean.only = TRUE
Adjusting for0covariate(s) or covariate level(s)
调整0变量或协变量水平
Standardizing Data across genes
跨基因标准化数据
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
OpenBLAS blas_thread_init:RLIMIT_NPROC 903725当前,最大值903725
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
OpenBLAS blas_thread_init:RLIMIT_NPROC 903725当前,最大值903725
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
OpenBLAS blas_thread_init:RLIMIT_NPROC 903725当前,最大值903725
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
OpenBLAS blas_thread_init:RLIMIT_NPROC 903725当前,最大值903725
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
OpenBLAS blas_thread_init: RLIMIT_NPROC 903725 current, 903725 max
OpenBLAS blas_thread_init:RLIMIT_NPROC 903725当前,最大值903725
OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable
OpenBLAS blas_thread_init:pthread_create:资源暂时不可用
Do you know how I can fix it? 你知道我怎么解决它吗?
I checked online and some people already had that problem , which is related to Python. 我在网上查了一下,有些人已经遇到了这个与Python有关的问题 。 That sounds weird to me: if it's a Python problem, why does it show up in R?
这对我来说听起来很奇怪:如果它是一个Python问题,它为什么会出现在R?
Thanks 谢谢
A colleague of mine (outside StackOverflow) helped me and found the solution. 我的一位同事(在StackOverflow之外)帮助我并找到了解决方案。
I needed to insert this command in my R script: 我需要在我的R脚本中插入此命令:
Sys.setenv(OPENBLAS_NUM_THREADS="1")
That was it. 就是这样。
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