Open LnLogN opened 5 years ago
Found the problem, I only have 1 gpu on the node, and the gpu_cores is hard coded to 1, but rgtsvm uses this number as gpu id. change this to gpu_cores=gpu_id worked, not sure if it'll work for multi-GPUs.
run.time <- system.time(r <- peak_calling( asvm, gdm, ps_plus_path, ps_minus_path, cpu_cores=cpu_cores, use_rgtsvm=use_rgtsvm, gpu_cores=1));
Thank you for your feedback. I tried to fix this question. Can you try the new codes again?
Or you can use the online gateway to run your data. http://dreg.dnasequence.org
Best, Zhong Wang
I tried to run dReg without GPU option and received an error about rgtsvm library. When I check the code in run_dREG.R
closely, I noticed that there is a parameter initiation error.
use_rgtsvm <- FALSE;
gpu_id <- as.integer(args[6])
if (!is.na(gpu_id)) use_rgtsvm<-TRUE
If I provide 0 for gpu_id
, it is not NA
anymore and use_rgtsvm
is set to TRUE
. Then, this will cause an error in peak_calling
function.
If I don't provide any value for gpu_id
, use_rgtsvm
would be set to FALSE
, but then the next step would return an error:
if(gpu_id>0)
{
library(Rgtsvm);
ret <- selectGPUdevice(gpu_id);
}
I manually edited run_dREG.R
to bypass this error.
Thank you for your feedback. I will change it as you did. But I don't suggest running dREG without GPU. You can use our online computing resource: dREG Gateway ( https://dreg.dnasequence.org/ )
I'm getting "Error in device initialization" error when running peak calling with dREG, but the prediction function runs fines. .
I'm running on a node with:
OS: redhat 7.4 kernel 3.10.0-693 GPU: GTX1080 Cuda: cuda9.0 dreg version: latest version checked out from github rgtsvm version: latest version bedops: 2.4.14
All the data are test data downloaded from ftp server provided, below is the test run output:
What have I tried:
Please let me know of any insights to this problem.