# Starting MD simulation on all GPUs using OpenMM
jobs = job_list()
for gpu_id in GPU_ids:
job = omm_job(job_id=int(time.time()), gpu_id=gpu_id, top_file=top_file, pdb_file=pdb_file)
job.start()
jobs.append(job)
print(' Started OpenMM jobs on GPU', gpu_id)
time.sleep(2)
print('\nWaiting 2 mins for omm to write valid contact map .h5 files ')
time.sleep(120)
# Read all the contact map .h5 file in local dir
cm_files = sorted(glob('omm*/*_cm.h5'))
cm_data_lists = [read_h5py_file(cm_file) for cm_file in cm_files]
print('Waiting for the OpenMM to complete the first 100,000 frames as CVAE training data')
frame_number = lambda lists: sum([cm.shape[1] for cm in lists])
frame_marker = 0
# number of training frames for cvae, change to 1e5 later, HM
while frame_number(cm_data_lists) < 100000:
for cm in cm_data_lists:
cm.refresh()
if frame_number(cm_data_lists) >= frame_marker:
print('Current number of frames from OpenMM:', frame_number(cm_data_lists))
frame_marker = int((10000 + frame_marker) / 10000) * 10000
print(' Next report at frame', frame_marker)
print('Ready for CAVE with total number of frames:', frame_number(cm_data_lists))
for gpu_id in GPU_ids:
job = omm_job(job_id=int(time.time()),
gpu_id=gpu_id,
top_file=top_file,
pdb_file=pdb_file)
job.start()
jobs.append(job)
print('Started OpenMM jobs on GPU', gpu_id)
time.sleep(2)
print('Waiting 10 mins for omm to write valid contact map .h5 files ')
time.sleep(600)
# Read all the contact map .h5 file in local dir
cm_files = sorted(glob('./omm*/*_cm.h5'))
cm_data_lists = [read_h5py_file(cm_file) for cm_file in cm_files]
print(
'Waiting for the OpenMM to complete the first 100,000 frames as CVAE training data'
)
frame_number = lambda lists: sum([cm.shape[1] for cm in lists])
frame_marker = 0
# number of training frames for cvae, change to 1e5 later, HM
while frame_number(cm_data_lists) < 20000:
for cm in cm_data_lists:
cm.refresh()
if frame_number(cm_data_lists) >= frame_marker:
print('Current number of frames from OpenMM:',
frame_number(cm_data_lists))
frame_marker = int((10000 + frame_marker) / 10000) * 10000