-------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: c434-094 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c434-094 Local device: hfi1_0 -------------------------------------------------------------------------- /usr/local/lib/python3.8/dist-packages/ase/atoms.py:504: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. a = np.asarray(a) /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:677: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead e.append(np.asscalar(val)) /usr/local/lib/python3.8/dist-packages/ase/atoms.py:504: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. a = np.asarray(a) /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:677: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead e.append(np.asscalar(val)) /usr/local/lib/python3.8/dist-packages/ase/atoms.py:504: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. a = np.asarray(a) /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:596: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead nth[n], np.asscalar(val), yesno[is_continuous] /work2/08773/bwaters/stampede2/bwaters/job-83c20338-22a3-42ed-bf0d-d8cd49bb5e86-007-6c04748a-06f2-4630-887d-66cfd44ace55/VC_303890932454_004-and-SM_066295357485_000-1659393871/staged_job_files/repository/vc/DimerContinuityC1__VC_303890932454_004/runner:677: DeprecationWarning: np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead e.append(np.asscalar(val)) {"realtime":4135.10,"usertime":4792.59,"systime":2880.82,"memmax":142476,"memavg":0}