Merge pull request #97 from CyrusBiotechnology/small-bugfixes

fixing CUDA versions in dockerfile and a small bug in run_pretrained_openfold.py

Dockerfile

-FROM nvidia/cuda:11.0-cudnn8-runtime-ubuntu18.04
+FROM nvidia/cuda:10.2-cudnn8-runtime-ubuntu18.04
 
-RUN apt-get update && apt-get install -y wget cuda-minimal-build-11-0 git
+RUN apt-get update && apt-get install -y wget cuda-minimal-build-10-2 git
 RUN wget -P /tmp \
     "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \

environment.yml

@@ -23,6 +23,7 @@ dependencies:
   - conda-forge::pip
   - conda-forge::openmm=7.5.1
   - conda-forge::pdbfixer
+  - conda-forge::cudatoolkit==10.2.*
   - bioconda::hmmer==3.3.2
   - bioconda::hhsuite==3.3.0
   - bioconda::kalign2==2.04

run_pretrained_openfold.py

@@ -167,7 +167,7 @@ def main(args):
         
         # Relax the prediction.
         t = time.perf_counter()
-        visible_devices = os.getenv("CUDA_VISIBLE_DEVICES")
+        visible_devices = os.getenv("CUDA_VISIBLE_DEVICES", default="")
         if("cuda" in args.model_device):
             device_no = args.model_device.split(":")[-1]
             os.environ["CUDA_VISIBLE_DEVICES"] = device_no