Open cron-weasley opened 2 years ago
Hi,
We only tested tensorflow2.5. and python3.6 on A100 GPUs. IsoNet works fine with A100.
Could you run the command with parameter: "--log_level debug" and see what is the error message?
Hi,
We only tested tensorflow2.5. and python3.6 on A100 GPUs. IsoNet works fine with A100.
Could you run the command with parameter: "--log_level debug" and see what is the error message?
Dear procyontao, Thanks a lot! And could you tell me which cuda version and which NVIDIA A100 driver did you use?
I sloved the problem. Thanks procyontao! I use python 3.8 with miniconda and install: pip install imageio==2.10.5 numpy==1.19.2 then install pip install tensorflow-gpu==2.5.0 pip install -r requirements.txt And Isonet run successfully.
Hi all, I also required TensorFlow v2.6.0 to run IsoNet properly on A100 GPUs. I figured it would be nice to provide some GPU benchmarks for the tutorial dataset
I used TF2.6.0 Cuda11.6 IsoNet0.1 on the three tutorial tomograms
System Time/step speedup 2x 2070S 950ms 1 4x2080TI 700ms ~1.4 4x1080TI 900ms ~1 1xRTX8000 1000ms ~1 2xRTX8000 700ms ~1.3 4xA100 270ms ~3.5
Cheers
Hi proteincommandr,
Thank you for providing the GPU benchmarks. We do not even afford that many types of GPU for a speed test.
One question, did you consider the differences in batch_size (i.e. number of subtomograms processed in one step)? the default relation between number of GPUs and default batch_size is listed below: nGPUs batch_size 1 4 2 4 3 6 4 8 5 10 6 12 7 14 8 16
If you do not specify the batch size in your command, your list should be: System Time/step speedup batch_size speedup_persubtomo 2x 2070S 950ms 1 4 0.5 4x2080TI 700ms ~1.4 8 1.4 4x1080TI 900ms ~1 8 1 1xRTX8000 1000ms ~1 4 0.5 2xRTX8000 700ms ~1.3 4 0.65 4xA100 270ms ~3.5 8 3.5
Dear Author, First thanks a lot for this powerful software ! I have a question: Is IsoNet support CUDA 11.2 and NVIDIA A100 with tensorflow-gpu_2.7? I install isonet with conda python3.9 and tensorflow-gpu_2.7+cuda11.2+NVIDIA A100 get this error:
(py39) [root@Isonet]$ isonet.py refine subtomo.star --gpuID 0,1,2,3 --iterations 30 --noise_start_iter 10,15,20,25 --noise_level 0.05,0.1,0.15,0.2 04-16 22:14:09, INFO
Isonet starts refining
04-16 22:14:27, INFO Note: detected 128 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable. 04-16 22:14:27, INFO Note: NumExpr detected 128 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 04-16 22:14:27, INFO NumExpr defaulting to 8 threads. 04-16 22:14:30, WARNING The results folder already exists before the 1st iteration The old results folder will be renamed (to results~) 04-16 22:14:50, INFO Done preperation for the first iteration! 04-16 22:14:50, INFO Start Iteration1! /data1/apps/miniconda3/envs/py39/lib/python3.9/site-packages/keras/optimizer_v2/adam.py:105: UserWarning: The
lr
argument is deprecated, uselearning_rate
instead. super(Adam, self).init(name, **kwargs) /data1/apps/miniconda3/envs/py39/lib/python3.9/site-packages/keras/engine/functional.py:1410: CustomMaskWarning: Custom mask layers require a config and must override get_config. When loading, the custom mask layer must be passed to the custom_objects argument. layer_config = serialize_layer_fn(layer) 04-16 22:14:54, INFO Noise Level:0.0 2022-04-16 22:15:06.826516: F tensorflow/stream_executor/cuda/cuda_driver.cc:153] Failed setting context: CUDA_ERROR_NOT_INITIALIZED: initialization errorThanks a lot!