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simetenn / uncertainpy

Uncertainpy: a Python toolbox for uncertainty quantification and sensitivity analysis, tailored towards computational neuroscience.
http://uncertainpy.readthedocs.io
GNU General Public License v3.0
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Conflict with firedrake import #62

Open handraqui opened 11 months ago

handraqui commented 11 months ago

I've been trying to use uncertainpy for uncertainty quantification over FEM methods with firedrake. I ran into a 'PETSC ERROR" thatI could isolate in the coffee_cup example. After running the model, at UQ.quantify, this appears:

`[0]PETSC ERROR: [0]PETSC ERROR: [...] [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [...] [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [0]PETSC ERROR: [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [...] [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end[...] [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: [0]PETSC ERROR: [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [...] [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: [0]PETSC ERROR: [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ Try option -start_in_debugger or -on_error_attach_debugger [...] or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: [0]PETSC ERROR: [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. to get more information on the crash. [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run to get more information on the crash. [0]PETSC ERROR: [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: [0]PETSC ERROR: to get more information on the crash. to get more information on the crash. configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: [0]PETSC ERROR: to get more information on the crash. to get more information on the crash. to get more information on the crash. [0]PETSC ERROR: to get more information on the crash. [...] application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: [unset]: [unset]: [unset]: [unset]: [unset]: [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : [...] system msg for write_line failure : Bad file descriptor PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : [...] system msg for write_line failure : Bad file descriptor [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : system msg for write_line failure : Bad file descriptor [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : system msg for write_line failure : Bad file descriptor [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 : system msg for write_line failure : Bad file descriptor Calculating PC for each feature: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 108.52it/s] Calculating statistics from PCE: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:01<00:00, 1.25s/it] Saving data as: data/coffee_cup.h5 --- Logging error --- Traceback (most recent call last): File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/multiprocess/managers.py", line 827, in _callmethod conn = self._tls.connection AttributeError: 'ForkAwareLocal' object has no attribute 'connection'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/utils/logger.py", line 128, in emit self.send(s) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/utils/logger.py", line 108, in send self.queue.put_nowait(s) File "", line 2, in put_nowait File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/multiprocess/managers.py", line 831, in _callmethod self._connect() File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/multiprocess/managers.py", line 818, in _connect conn = self._Client(self._token.address, authkey=self._authkey) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/multiprocess/connection.py", line 505, in Client c = SocketClient(address) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/multiprocess/connection.py", line 633, in SocketClient s.connect(address) ConnectionRefusedError: [Errno 111] Connection refused Call stack: File "Scripts/IsolatePETSCError/isolate_copy.py", line 197, in data = UQ.quantify(seed = 10) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/uncertainty.py", line 415, in quantify data = self.polynomial_chaos(uncertain_parameters=uncertain_parameters, File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/uncertainty.py", line 721, in polynomial_chaos self.save(filename, folder=data_folder) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/uncertainty.py", line 1230, in save logger.info("Saving data as: {}".format(save_path)) File "/usr/lib/python3.8/logging/init.py", line 1446, in info self._log(INFO, msg, args, **kwargs) File "/usr/lib/python3.8/logging/init.py", line 1589, in _log self.handle(record) File "/usr/lib/python3.8/logging/init.py", line 1599, in handle self.callHandlers(record) File "/usr/lib/python3.8/logging/init.py", line 1661, in callHandlers hdlr.handle(record) File "/usr/lib/python3.8/logging/init.py", line 954, in handle self.emit(record) File "/home/users/henrique.aquino/firedrake/lib/python3.8/site-packages/uncertainpy/utils/logger.py", line 132, in emit self.handleError(record)`

I cut some repeated parts. It turned out that this error happens only by importing firedrake. So, if, in the beginning of the coffee_cup file, I add import firedrake as fd, this error happens. Even importing like this, even if I don't use any fd.method at all. And my intention is to use firedrake if the main routine of my model.

I couldn't figure out if