-------------------------------------------------------------------------- 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: pd-compute-3-35 Local adapter: qib0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: pd-compute-3-35 Local device: qib0 -------------------------------------------------------------------------- /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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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) /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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] /scratch.hyperion/kim-jobs/jobs/bwaters/job-93a51180-45a1-4c96-b210-05d8a7d1080f-007-42fdbf55-96ce-4110-9737-67426ba7ece5/VC_303890932454_004-and-SM_887684855692_000-1659395093/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":2305.20,"usertime":1929.75,"systime":1277.69,"memmax":107516,"memavg":0}