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maoxinxina银虫 (小有名气)
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[求助]
GPAW计算过程中报错 已有1人参与
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gpaw计算过程中出现如下错误： ImportError: numpy.core.multiarray failed to import -------------------------------------------------------------------------- mpirun has exited due to process rank 9 with PID 25960 on node a530 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). 想问下应该如何解决呢？ |
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charleslian
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2楼2017-03-16 11:06:45
maoxinxina
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安装了你说的这个，但是还是报错，变成这样了。An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: a264 (PID 28715) MPI_COMM_WORLD rank: 4 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- [a264:28710] 23 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork [a264:28710] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages rank=20 L00: Traceback (most recent call last): rank=20 L01: File "C6N7-C3N3.py", line 64, in <module> rank=20 L02: atom.get_potential_energy() rank=20 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=20 L04: energy = self._calc.get_potential_energy(self) rank=20 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=20 L06: self.calculate(atoms, converge=True) rank=20 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 251, in calculate rank=20 L08: self.set_positions(atoms) rank=20 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 329, in set_positions rank=20 L10: self.wfs.initialize(self.density, self.hamiltonian, spos_ac) rank=20 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py", line 71, in initialize rank=20 L12: basis_functions, density, hamiltonian, spos_ac) rank=20 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py", line 108, in initialize_wave_functions_from_basis_functions rank=20 L14: lcaobd.mynbands) rank=20 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/wavefunctions/fd.py", line 250, in initialize_from_lcao_coefficients rank=20 L16: kpt.psit_nG = self.gd.zeros(self.bd.mynbands, self.dtype) rank=20 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 199, in zeros rank=20 L18: return self._new_array(n, dtype, True, global_array, pad) rank=20 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 224, in _new_array rank=20 L20: return np.zeros(shape, dtype) rank=20 L21: MemoryError GPAW CLEANUP (node 20): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 20 in communicator MPI_COMM_WORLD with errorcode 42. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- gpaw-python: c/extensions.h:36: gpaw_malloc: Assertion `p != ((void *)0)' failed. gpaw-python: c/extensions.h:36: gpaw_malloc: Assertion `p != ((void *)0)' failed. gpaw-python: c/extensions.h:36: gpaw_malloc: Assertion `p != ((void *)0)' failed. gpaw-python: c/extensions.h:36: gpaw_malloc: Assertion `p != ((void *)0)' failed. -------------------------------------------------------------------------- mpirun has exited due to process rank 20 with PID 28731 on node a264 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). |
3楼2017-03-20 16:20:48
4楼2017-03-22 04:04:54
maoxinxina
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增加了核变成这样子了。 An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: a244 (PID 28444) MPI_COMM_WORLD rank: 2 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- [a244:28399] 71 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork [a244:28399] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages rank=56 L00: Traceback (most recent call last): rank=56 L01: File "C6N7-C3N3.py", line 64, in <module> rank=56 L02: atom.get_potential_energy() rank=56 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=56 L04: energy = self._calc.get_potential_energy(self) rank=56 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=56 L06: self.calculate(atoms, converge=True) rank=56 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=56 L08: self.occupations, self.forces): rank=56 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=56 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=56 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=56 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=56 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=56 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=56 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=56 L16: self.allocate_arrays() rank=56 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=56 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=56 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=56 L20: return self._new_array(n, dtype, False, global_array, pad) rank=56 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=56 L22: return np.empty(shape, dtype) rank=56 L23: MemoryError rank=49 L00: Traceback (most recent call last): rank=49 L01: File "C6N7-C3N3.py", line 64, in <module> rank=49 L02: atom.get_potential_energy() rank=49 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=49 L04: energy = self._calc.get_potential_energy(self) rank=49 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=49 L06: self.calculate(atoms, converge=True) rank=49 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=49 L08: self.occupations, self.forces): rank=49 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=49 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=49 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=49 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=49 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=49 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=49 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=49 L16: self.allocate_arrays() rank=49 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=49 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=49 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=49 L20: return self._new_array(n, dtype, False, global_array, pad) rank=49 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=49 L22: return np.empty(shape, dtype) rank=49 L23: MemoryError rank=57 L00: Traceback (most recent call last): rank=57 L01: File "C6N7-C3N3.py", line 64, in <module> rank=57 L02: atom.get_potential_energy() rank=57 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=57 L04: energy = self._calc.get_potential_energy(self) rank=57 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=57 L06: self.calculate(atoms, converge=True) rank=57 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=57 L08: self.occupations, self.forces): rank=57 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=57 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=57 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=57 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=57 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=57 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=57 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=57 L16: self.allocate_arrays() rank=57 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=57 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=57 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=57 L20: return self._new_array(n, dtype, False, global_array, pad) rank=57 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=57 L22: return np.empty(shape, dtype) rank=57 L23: MemoryError rank=65 L00: Traceback (most recent call last): rank=65 L01: File "C6N7-C3N3.py", line 64, in <module> rank=65 L02: atom.get_potential_energy() rank=65 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=65 L04: energy = self._calc.get_potential_energy(self) rank=65 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=65 L06: self.calculate(atoms, converge=True) rank=65 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=65 L08: self.occupations, self.forces): rank=65 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=65 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=65 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=65 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=65 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=65 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=65 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=65 L16: self.allocate_arrays() rank=65 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=65 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=65 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=65 L20: return self._new_array(n, dtype, False, global_array, pad) rank=65 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=65 L22: return np.empty(shape, dtype) rank=65 L23: MemoryError rank=66 L00: Traceback (most recent call last): rank=66 L01: File "C6N7-C3N3.py", line 64, in <module> rank=66 L02: atom.get_potential_energy() rank=66 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=66 L04: energy = self._calc.get_potential_energy(self) rank=66 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=66 L06: self.calculate(atoms, converge=True) rank=66 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=66 L08: self.occupations, self.forces): rank=66 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=66 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=66 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=66 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=66 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=66 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=66 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=66 L16: self.allocate_arrays() rank=66 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=66 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=66 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=66 L20: return self._new_array(n, dtype, False, global_array, pad) rank=66 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=66 L22: return np.empty(shape, dtype) rank=66 L23: MemoryError rank=69 L00: Traceback (most recent call last): rank=69 L01: File "C6N7-C3N3.py", line 64, in <module> rank=69 L02: atom.get_potential_energy() rank=69 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=69 L04: energy = self._calc.get_potential_energy(self) rank=69 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=69 L06: self.calculate(atoms, converge=True) rank=69 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=69 L08: self.occupations, self.forces): rank=69 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=69 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=69 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=69 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=69 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=69 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=69 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=69 L16: self.allocate_arrays() rank=69 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=69 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=69 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=69 L20: return self._new_array(n, dtype, False, global_array, pad) rank=69 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=69 L22: return np.empty(shape, dtype) rank=69 L23: MemoryError rank=70 L00: Traceback (most recent call last): rank=70 L01: File "C6N7-C3N3.py", line 64, in <module> rank=70 L02: atom.get_potential_energy() rank=70 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=70 L04: energy = self._calc.get_potential_energy(self) rank=70 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=70 L06: self.calculate(atoms, converge=True) rank=70 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=70 L08: self.occupations, self.forces): rank=70 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=70 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=70 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 58, in iterate rank=70 L12: self.initialize(wfs) rank=70 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/davidson.py", line 45, in initialize rank=70 L14: Eigensolver.initialize(self, wfs) rank=70 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 35, in initialize rank=70 L16: self.Htpsit_nG = wfs.empty(self.nbands) rank=70 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/wavefunctions/fd.py", line 44, in empty rank=70 L18: return self.gd.empty(n, self.dtype, global_array) rank=70 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=70 L20: return self._new_array(n, dtype, False, global_array, pad) rank=70 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=70 L22: return np.empty(shape, dtype) rank=70 L23: MemoryError rank=67 L00: Traceback (most recent call last): rank=67 L01: File "C6N7-C3N3.py", line 64, in <module> rank=67 L02: atom.get_potential_energy() rank=67 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=67 L04: energy = self._calc.get_potential_energy(self) rank=67 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=67 L06: self.calculate(atoms, converge=True) rank=67 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=67 L08: self.occupations, self.forces): rank=67 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=67 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=67 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=67 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=67 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=67 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=67 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=67 L16: self.allocate_arrays() rank=67 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=67 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=67 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=67 L20: return self._new_array(n, dtype, False, global_array, pad) rank=67 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=67 L22: return np.empty(shape, dtype) rank=67 L23: MemoryError rank=64 L00: Traceback (most recent call last): rank=64 L01: File "C6N7-C3N3.py", line 64, in <module> rank=64 L02: atom.get_potential_energy() rank=64 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=64 L04: energy = self._calc.get_potential_energy(self) rank=64 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=64 L06: self.calculate(atoms, converge=True) rank=64 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=64 L08: self.occupations, self.forces): rank=64 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=64 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=64 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=64 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=64 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=64 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=64 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=64 L16: self.allocate_arrays() rank=64 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=64 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=64 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=64 L20: return self._new_array(n, dtype, False, global_array, pad) rank=64 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=64 L22: return np.empty(shape, dtype) rank=64 L23: MemoryError GPAW CLEANUP (node 65): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 49): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 57): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 56): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 69): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 67): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 66): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 70): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! rank=53 L00: Traceback (most recent call last): rank=53 L01: File "C6N7-C3N3.py", line 64, in <module> rank=53 L02: atom.get_potential_energy() rank=53 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=53 L04: energy = self._calc.get_potential_energy(self) rank=53 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=53 L06: self.calculate(atoms, converge=True) rank=53 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=53 L08: self.occupations, self.forces): rank=53 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=53 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=53 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=53 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=53 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=53 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=53 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=53 L16: self.allocate_arrays() rank=53 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=53 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=53 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=53 L20: return self._new_array(n, dtype, False, global_array, pad) rank=53 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=53 L22: return np.empty(shape, dtype) rank=53 L23: MemoryError rank=52 L00: Traceback (most recent call last): rank=52 L01: File "C6N7-C3N3.py", line 64, in <module> rank=52 L02: atom.get_potential_energy() rank=52 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=52 L04: energy = self._calc.get_potential_energy(self) rank=52 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=52 L06: self.calculate(atoms, converge=True) rank=52 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=52 L08: self.occupations, self.forces): rank=52 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=52 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=52 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=52 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=52 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=52 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=52 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=52 L16: self.allocate_arrays() rank=52 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=52 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=52 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=52 L20: return self._new_array(n, dtype, False, global_array, pad) rank=52 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=52 L22: return np.empty(shape, dtype) rank=52 L23: MemoryError rank=68 L00: Traceback (most recent call last): rank=68 L01: File "C6N7-C3N3.py", line 64, in <module> rank=68 L02: atom.get_potential_energy() rank=68 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=68 L04: energy = self._calc.get_potential_energy(self) rank=68 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=68 L06: self.calculate(atoms, converge=True) rank=68 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=68 L08: self.occupations, self.forces): rank=68 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=68 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=68 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=68 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=68 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=68 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=68 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=68 L16: self.allocate_arrays() rank=68 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=68 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=68 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=68 L20: return self._new_array(n, dtype, False, global_array, pad) rank=68 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=68 L22: return np.empty(shape, dtype) rank=68 L23: MemoryError GPAW CLEANUP (node 64): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 52): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 53): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 68): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! rank=50 L00: Traceback (most recent call last): rank=50 L01: File "C6N7-C3N3.py", line 64, in <module> rank=50 L02: atom.get_potential_energy() rank=50 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=50 L04: energy = self._calc.get_potential_energy(self) rank=50 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=50 L06: self.calculate(atoms, converge=True) rank=50 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=50 L08: self.occupations, self.forces): rank=50 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=50 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=50 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=50 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=50 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=50 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=50 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=50 L16: self.allocate_arrays() rank=50 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=50 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=50 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=50 L20: return self._new_array(n, dtype, False, global_array, pad) rank=50 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=50 L22: return np.empty(shape, dtype) rank=50 L23: MemoryError rank=51 L00: Traceback (most recent call last): rank=51 L01: File "C6N7-C3N3.py", line 64, in <module> rank=51 L02: atom.get_potential_energy() rank=51 L03: File "/public/home/users/zkchu/program/python-tools/ase-3.9.1/lib/python2.7/site-packages/ase/atoms.py", line 640, in get_potential_energy rank=51 L04: energy = self._calc.get_potential_energy(self) rank=51 L05: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/aseinterface.py", line 50, in get_potential_energy rank=51 L06: self.calculate(atoms, converge=True) rank=51 L07: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/paw.py", line 290, in calculate rank=51 L08: self.occupations, self.forces): rank=51 L09: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/scf.py", line 47, in run rank=51 L10: wfs.eigensolver.iterate(hamiltonian, wfs) rank=51 L11: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py", line 63, in iterate rank=51 L12: wfs.overlap.orthonormalize(wfs, kpt) rank=51 L13: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/overlap.py", line 76, in orthonormalize rank=51 L14: S_nn = operator.calculate_matrix_elements(psit_nG, P_ani, S, dS) rank=51 L15: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 301, in calculate_matrix_elements rank=51 L16: self.allocate_arrays() rank=51 L17: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/hs_operators.py", line 145, in allocate_arrays rank=51 L18: self.work1_xG = self.gd.empty(self.bd.mynbands, self.dtype) rank=51 L19: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 209, in empty rank=51 L20: return self._new_array(n, dtype, False, global_array, pad) rank=51 L21: File "/public/home/users/dicp004/gpaw/lib/python2.7/site-packages/gpaw/grid_descriptor.py", line 226, in _new_array rank=51 L22: return np.empty(shape, dtype) rank=51 L23: MemoryError GPAW CLEANUP (node 50): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! GPAW CLEANUP (node 51): <type 'exceptions.MemoryError'> occurred. Calling MPI_Abort! -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 65 in communicator MPI_COMM_WORLD with errorcode 42. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- [a244:28399] 12 more processes have sent help message help-mpi-api.txt / mpi-abort [a244:28399] 1 more process has sent help message help-mpi-api.txt / mpi-abort -------------------------------------------------------------------------- mpirun has exited due to process rank 52 with PID 17181 on node a122 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). |
5楼2017-03-22 09:20:28
maoxinxina
银虫 (小有名气)
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6楼2017-03-23 11:20:41
7楼2018-07-27 12:18:28
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