Merge branch 'main' of github.com:aqlaboratory/openfold

scripts/prep_mmseqs_dbs.sh

@@ -23,7 +23,7 @@ DOWNLOAD_DIR="$1"
 ROOT_DIR="${DOWNLOAD_DIR}/mmseqs_dbs"
 mkdir -p $ROOT_DIR
 
-for f in $(ls ${DOWNLOAD_DIR}/*.tar.gz)
+for f in $(ls ${DOWNLOAD_DIR}/*.tar*)
 do
   tar --extract --verbose --file="${f}" \
       --directory=$ROOT_DIR

setup.py

@@ -16,7 +16,7 @@ import os
 from setuptools import setup, Extension, find_packages
 import subprocess
 
-from torch.utils.cpp_extension import BuildExtension, CUDAExtension, CUDA_HOME
+from torch.utils.cpp_extension import BuildExtension, CppExtension, CUDAExtension, CUDA_HOME
 
 from scripts.utils import get_nvidia_cc
 
@@ -37,6 +37,10 @@ extra_cuda_flags = [
 ]
 
 def get_cuda_bare_metal_version(cuda_dir):
+    if cuda_dir==None:
+        print("CUDA is not found, cpu version is installed")
+        return None, -1, 0
+    else:
         raw_output = subprocess.check_output([cuda_dir + "/bin/nvcc", "-V"], universal_newlines=True)
         output = raw_output.split()
         release_idx = output.index("release") + 1
@@ -70,22 +74,8 @@ for major, minor in list(compute_capabilities):
 
 extra_cuda_flags += cc_flag
 
-
-setup(
-    name='openfold',
-    version='1.0.0',
-    description='A PyTorch reimplementation of DeepMind\'s AlphaFold 2',
-    author='Gustaf Ahdritz & DeepMind',
-    author_email='gahdritz@gmail.com',
-    license='Apache License, Version 2.0',
-    url='https://github.com/aqlaboratory/openfold',
-    packages=find_packages(exclude=["tests", "scripts"]),
-    include_package_data=True,
-    package_data={
-        "openfold": ['utils/kernel/csrc/*'],
-        "": ["resources/stereo_chemical_props.txt"]
-    },
-    ext_modules=[CUDAExtension(
+if bare_metal_major != -1:
+    modules = [CUDAExtension(
         name="attn_core_inplace_cuda",
         sources=[
             "openfold/utils/kernel/csrc/softmax_cuda.cpp",
@@ -105,7 +95,34 @@ setup(
                 extra_cuda_flags
             ),
         }
-    )],
+    )]
+else:
+    modules = [CppExtension(
+        name="attn_core_inplace_cuda",
+        sources=[
+            "openfold/utils/kernel/csrc/softmax_cuda.cpp",
+            "openfold/utils/kernel/csrc/softmax_cuda_stub.cpp",
+        ],
+        extra_compile_args={
+            'cxx': ['-O3'],
+        }
+    )]
+
+setup(
+    name='openfold',
+    version='1.0.1',
+    description='A PyTorch reimplementation of DeepMind\'s AlphaFold 2',
+    author='Gustaf Ahdritz & DeepMind',
+    author_email='gahdritz@gmail.com',
+    license='Apache License, Version 2.0',
+    url='https://github.com/aqlaboratory/openfold',
+    packages=find_packages(exclude=["tests", "scripts"]),
+    include_package_data=True,
+    package_data={
+        "openfold": ['utils/kernel/csrc/*'],
+        "": ["resources/stereo_chemical_props.txt"]
+    },
+    ext_modules=modules,
     cmdclass={'build_ext': BuildExtension},
     classifiers=[
         'License :: OSI Approved :: Apache Software License',
@@ -114,6 +131,3 @@ setup(
         'Topic :: Scientific/Engineering :: Artificial Intelligence',
     ],
 )
-
-
-

train_openfold.py

@@ -567,6 +567,9 @@ if __name__ == "__main__":
          (args.num_nodes is not None and args.num_nodes > 1))):
         raise ValueError("For distributed training, --seed must be specified")
 
+    if(str(args.precision) == "16" and args.deepspeed_config_path is not None):
+        raise ValueError("DeepSpeed and FP16 training are not compatible")
+
     # This re-applies the training-time filters at the beginning of every epoch
     args.reload_dataloaders_every_n_epochs = 1