Closed SanBast closed 8 months ago
@GregorKoehler @FabianIsensee
Hi again, in awaiting your response I run other experiments. The problem was still the liver database. I suppose there are some limitation concerning the nnUNetv2_plan_and_preprocess
(in particular batchgenerators) if there's a "limited" CPU memory. With other datasets this do not happen.
So I was wondering if you can run the same experiment I did, i.e. using the MSD Liver dataset and splitting a train,test,val set on the imagesTr set (so using even a lower number than the one experimented in your original paper) and monitor the memory usage of this preprocessing. My fear is that for certain datasets nnUNet and batchgenerators require a minimum amount of memory specs that must be declared for future usage...
I'm available for any discussion :)
Are you on the latest master? We do not use batchgenerators in inference. Also not during preprocessing.
But yes, CPU memory can be a problem. We recommend reducing the number of workers for that. In nnUNetv2_plan_and_preprocess
this would be -np
1 and for nnUNetv2_predict
this is -npp 1 -nps 1
.
We cannot go lower than a single worker, so at some point the RAM is just too small. Last effort to save things could be a swap partition located on an SSD
To be fair, I don't know. I just followed the instruction here with a basic pip install nnunet
.
But this branch doubt actually answers something that I noticed, so maybe I am not in the right nnUNetV2 branch: by using the library installed with pip, I got some modules being changed from the one on github (this module is an example).
Let me clone the repo directly, and I'll come back here to update :)
Thanks for the hint
any updates on your issue?
Hi @FabianIsensee Apparently that solved the issue. I thank you very much for you time!
Best, V
Glad it works now!
Hello, I was trying to predict liver segmentations on my own with nnUNetv2. With other datasets the following never happened (tried on prostate, spleen, hippocampus, heart, pancreas):
As I can see I think the problem is in batchgenerators. However, I don't know how to procede. I already read all the other threads concerning this issue (I even try to set the
OMP_NUM_THREADS=1
in the cmd line), but nothing solved it.Can you please help me with this? Thanks for your kind attention, V