Urinx
commented
4 years ago Thanks for reporting this, now it's fixed and works fine on gpu.
Closed pentadotddot closed 4 years ago
Urinx
commented
4 years ago Thanks for reporting this, now it's fixed and works fine on gpu.
Hi!
I am trying using your great implementation of alphafold in pytorch. I am new to pytorch as I mostly used tensorflow and I ran into this problem:
python alphafold.py -i test_data/T0953s2/T0953s2.tfrec -o T0953s2_out -m tf_model_path/ Input file: test_data/T0953s2/T0953s2.tfrec Output dir: T0953s2_out/Distogram/0 Distogram model: tf_model_path/873731 Replica: 0 Device: cuda Model parameters: 21182345 Data: T0953s2-l128_s32 128 Traceback (most recent call last): File "alphafold.py", line 221, in
run_eval(TARGET_PATH, MODEL_PATH, REPLICA, OUT_DIR, DEVICE)
File "alphafold.py", line 68, in run_eval
out = model(x_2d, crop_x, crop_y)
File "/scratch/domeemod/anaconda3/envs/pytorch_env/lib/python3.8/site-packages/torch/nn/modules/module.py", line 532, in call
result = self.forward(*input, **kwargs)
File "/mnt/meganeura/domeemod/alphafold-pytroch/alphafold_pytorch/network.py", line 295, in forward
biases = self.build_crops_biases(config.position_specific_bias_size, self.position_specific_bias, crop_x, crop_y)
File "/mnt/meganeura/domeemod/alphafold-pytroch/alphafold_pytorch/network.py", line 269, in build_crops_biases
row_offsets = start_diag + increment
RuntimeError: expected device cuda:0 but got device cpu
I found during some search on the net that this bug is related to how I am specifying the parts of the code to the cpu and the gpu. I have installed everything properly and I am using your provided scripts as it was written in your readme file.
We are doing research related to phylogenetics here in Hungary and your implementation can provide us some really good insights.
Thank you for uploading this project to github, and hope you can help us move forward.
Best wishes!
Kind regard, Demeter Márton