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maoxinxina

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[求助] GPAW计算过程中报错已有1人参与

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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1楼2017-03-16 09:20:05

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

charleslian

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安装numpy即可

发自小木虫IOS客户端

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2楼2017-03-16 11:06:45

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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).

赞一下

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3楼2017-03-20 16:20:48

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

adormer

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【答案】应助回帖

Memory不够了吧，多加点核数试试

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4楼2017-03-22 04:04:54

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maoxinxina

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引用回帖:

4楼: Originally posted by adormer at 2017-03-22 04:04:54
Memory不够了吧，多加点核数试试

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).

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5楼2017-03-22 09:20:28

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

maoxinxina

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引用回帖:

5楼: Originally posted by maoxinxina at 2017-03-22 09:20:28
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 t ...

已经解决了，就是在用GPAW计算的时候，当体系比较大，这时候K点得取得比较小，才能正常计算。

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6楼2017-03-23 11:20:41

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6楼: Originally posted by maoxinxina at 2017-03-23 11:20:41
已经解决了，就是在用GPAW计算的时候，当体系比较大，这时候K点得取得比较小，才能正常计算。...

我计算气体分子的能量的时候，也出现这个问题，那体系很小啊，K点也是取得gamma点，不知道怎么设置参数

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7楼2018-07-27 12:18:28

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