utils.py

import argparse
import ctypes
from datetime import date
import os
import sys
from pathlib import Path


CONDA_ENV_BINARY_PATH= Path(os.environ['CONDA_PREFIX']) / 'bin'

def add_data_args(parser: argparse.ArgumentParser):
    parser.add_argument(
        '--uniref90_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--mgnify_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--pdb70_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--pdb_seqres_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--uniref30_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--uniclust30_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--uniprot_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--bfd_database_path', type=str, default=None,
    )
    parser.add_argument(
        '--jackhmmer_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'jackhmmer'),
    )
    parser.add_argument(
        '--hhblits_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'hhblits'),
    )
    parser.add_argument(
        '--hhsearch_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'hhsearch'),
    )
    parser.add_argument(
        '--hmmsearch_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'hmmsearch'),
    )
    parser.add_argument(
        '--hmmbuild_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'hmmbuild'),
    )
    parser.add_argument(
        '--kalign_binary_path', type=str, default=str(CONDA_ENV_BINARY_PATH / 'kalign'),
    )
    parser.add_argument(
        '--max_template_date', type=str,
        default=date.today().strftime("%Y-%m-%d"),
    )
    parser.add_argument(
        '--obsolete_pdbs_path', type=str, default=None
    )
    parser.add_argument(
        '--release_dates_path', type=str, default=None
    )


def get_nvidia_cc():
    """
    Returns a tuple containing the Compute Capability of the first GPU
    installed in the system (formatted as a tuple of strings) and an error
    message. When the former is provided, the latter is None, and vice versa.

    Adapted from script by Jan Schlüte t
    https://gist.github.com/f0k/63a664160d016a491b2cbea15913d549
    """
    CUDA_SUCCESS = 0

    libnames = [
        'libcuda.so', 
        'libcuda.dylib', 
        'cuda.dll',
        '/usr/local/cuda/compat/libcuda.so', # For Docker
    ]
    for libname in libnames:
        try:
            cuda = ctypes.CDLL(libname)
        except OSError:
            continue
        else:
            break
    else:
        return None, "Could not load any of: " + ' '.join(libnames)

    nGpus = ctypes.c_int()
    cc_major = ctypes.c_int()
    cc_minor = ctypes.c_int()

    result = ctypes.c_int()
    device = ctypes.c_int()
    error_str = ctypes.c_char_p()

    result = cuda.cuInit(0)
    if result != CUDA_SUCCESS:
        cuda.cuGetErrorString(result, ctypes.byref(error_str))
        if error_str.value:
            return None, error_str.value.decode()
        else:
            return None, "Unknown error: cuInit returned %d" % result
    result = cuda.cuDeviceGetCount(ctypes.byref(nGpus))
    if result != CUDA_SUCCESS:
        cuda.cuGetErrorString(result, ctypes.byref(error_str))
        return None, error_str.value.decode()

    if nGpus.value < 1:
        return None, "No GPUs detected"

    result = cuda.cuDeviceGet(ctypes.byref(device), 0)
    if result != CUDA_SUCCESS:
        cuda.cuGetErrorString(result, ctypes.byref(error_str))
        return None, error_str.value.decode()

    if cuda.cuDeviceComputeCapability(ctypes.byref(cc_major), ctypes.byref(cc_minor), device) != CUDA_SUCCESS:
        return None, "Compute Capability not found"

    major = cc_major.value
    minor = cc_minor.value

    return (major, minor), None