Update damask to 3.0.0a8

[jan-janssen]

No description provided.

[jan-janssen]

Exception encountered at "In [8]":
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:636, in execute_job_with_external_executable(job)
    635 try:
--> 636     out = subprocess.run(
    637         executable,
    638         cwd=job.project_hdf5.working_directory,
    639         shell=shell,
    640         stdout=subprocess.PIPE,
    641         stderr=subprocess.STDOUT,
    642         universal_newlines=True,
    643         check=True,
    644     ).stdout
    645 except subprocess.CalledProcessError as e:

File /usr/share/miniconda3/envs/test/lib/python3.11/subprocess.py:571, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    570     if check and retcode:
--> 571         raise CalledProcessError(retcode, process.args,
    572                                  output=stdout, stderr=stderr)
    573 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '/usr/share/miniconda3/envs/test/share/pyiron/damask/bin/run_damask_3.0.0.sh' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
Cell In[8], line 1
----> 1 job.run() # running your job, if you want the parallelization you can modify your 'pyiron/damask/bin/run_damask_3.0.0.sh file'

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    161     if kw in self.arguments:
    162         warnings.warn(
    163             message_format.format(
    164                 "{}.{}({}={})".format(
   (...)
    169             stacklevel=2,
    170         )
--> 171 return function(*args, **kwargs)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:727, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    725     self._run_if_repair()
    726 elif status == "initialized":
--> 727     self._run_if_new(debug=debug)
    728 elif status == "created":
    729     self._run_if_created()

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1228, in GenericJob._run_if_new(self, debug)
   1220 def _run_if_new(self, debug=False):
   1221     """
   1222     Internal helper function the run if new function is called when the job status is 'initialized'. It prepares
   1223     the hdf5 file and the corresponding directory structure.
   (...)
   1226         debug (bool): Debug Mode
   1227     """
-> 1228     run_job_with_status_initialized(job=self, debug=debug)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:91, in run_job_with_status_initialized(job, debug)
     89 else:
     90     job.save()
---> 91     job.run()

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
    161     if kw in self.arguments:
    162         warnings.warn(
    163             message_format.format(
    164                 "{}.{}({}={})".format(
   (...)
    169             stacklevel=2,
    170         )
--> 171 return function(*args, **kwargs)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:729, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
    727     self._run_if_new(debug=debug)
    728 elif status == "created":
--> 729     self._run_if_created()
    730 elif status == "submitted":
    731     run_job_with_status_submitted(job=self)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:1239, in GenericJob._run_if_created(self)
   1230 def _run_if_created(self):
   1231     """
   1232     Internal helper function the run if created function is called when the job status is 'created'. It executes
   1233     the simulation, either in modal mode, meaning waiting for the simulation to finish, manually, or submits the
   (...)
   1237         int: Queue ID - if the job was send to the queue
   1238     """
-> 1239     return run_job_with_status_created(job=self)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:114, in run_job_with_status_created(job)
    112     run_job_with_runmode_manually(job=job, _manually_print=True)
    113 elif job.server.run_mode.modal:
--> 114     job.run_static()
    115 elif job.server.run_mode.srun:
    116     run_job_with_runmode_srun(job=job)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py:763, in GenericJob.run_static(self)
    759 def run_static(self):
    760     """
    761     The run static function is called by run to execute the simulation.
    762     """
--> 763     execute_job_with_external_executable(job=self)

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:608, in run_time_decorator.<locals>.wrapper(job)
    606 if not state.database.database_is_disabled and job.job_id is not None:
    607     job.project.db.item_update({"timestart": datetime.now()}, job.job_id)
--> 608     func(job)
    609     job.project.db.item_update(job._runtime(), job.job_id)
    610 else:

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:646, in execute_job_with_external_executable(job)
    636     out = subprocess.run(
    637         executable,
    638         cwd=job.project_hdf5.working_directory,
   (...)
    643         check=True,
    644     ).stdout
    645 except subprocess.CalledProcessError as e:
--> 646     out, job_crashed = handle_failed_job(job=job, error=e)
    648 job._logger.info(
    649     "{}, status: {}, output: {}".format(job.job_info_str, job.status, out)
    650 )
    651 with open(
    652     posixpath.join(job.project_hdf5.working_directory, "error.out"), mode="w"
    653 ) as f_err:

File /usr/share/miniconda3/envs/test/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py:700, in handle_failed_job(job, error)
    698     if job.server.run_mode.non_modal:
    699         state.database.close_connection()
--> 700     raise RuntimeError("Job aborted")
    701 else:
    702     return True, out

RuntimeError: Job aborted

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[yangbai90]

Hi @jan-janssen , the following error is still there (comes from job.run()):

2023-12-01 11:19:24,459 - pyiron_log - WARNING - Job aborted
2023-12-01 11:19:24,460 - pyiron_log - WARNING - 
 <<<+-  parallelization init  -+>>>

 Open MPI v4.1.5, package: Open MPI ybai@MAPC162L Distribution, ident: 4.1.5, repo rev: v4.1.5, Feb 23, 2023
 MPI standard: 3.1
 OpenMP version: 201511

 MPI processes: 1
 OMP_NUM_THREADS: 4

 <<<+-  CLI init  -+>>>

     _/_/_/      _/_/    _/      _/    _/_/      _/_/_/  _/    _/    _/_/_/
    _/    _/  _/    _/  _/_/  _/_/  _/    _/  _/        _/  _/            _/
   _/    _/  _/_/_/_/  _/  _/  _/  _/_/_/_/    _/_/    _/_/          _/_/
  _/    _/  _/    _/  _/      _/  _/    _/        _/  _/  _/            _/
 _/_/_/    _/    _/  _/      _/  _/    _/  _/_/_/    _/    _/    _/_/_/
 Grid solver

 F. Roters et al., Computational Materials Science 158:420–478, 2019
 https://doi.org/10.1016/j.commatsci.2018.04.030

 Version: v3.0.0-alpha8

 Compiled with: GCC version 11.4.0
 Compiled on: Linux-5.15.0-89-generic
 Compiler options: -cpp -I /home/ybai/Programs/toolkits/gcc11/petsc/3.15.5/include -I /home/ybai/Programs/toolkits/gcc11/openmpi/4.1.5/include -I /home/ybai/Programs/toolkits/gcc11/openmpi/4.1.5/include -I /home/ybai/Programs/toolkits/gcc11/openmpi/4.1.5/lib -imultiarch x86_64-linux-gnu -D_REENTRANT -D CMAKE_SYSTEM="Linux-5.15.0-89-generic" -D DAMASKVERSION="v3.0.0-alpha8" -D GRID -D PETSC --param=l1-cache-size=32 --param=l1-cache-line-size=64 --param=l2-cache-size=8192 -mtune=skylake -march=x86-64 -O2 -pedantic-errors -Wall -Wextra -Wcharacter-truncation -Wunderflow -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wconversion-extra -Wimplicit-procedure -Wunused-parameter -std=f2018 -fopenmp -fPIE -ffree-line-length-none -fimplicit-none -ffpe-summary=all -fpre-include=/usr/include/finclude/math-vector-fortran.h

 Compiled on: Dec  1 2023 at 10:03:24

 PETSc version: 3.15.5

 Date: 01/12/2023
 Time: 11:19:24

 ┌─────────────────────────────────────────────────────────────────────┐
 │                        error 612                                    │
 ├─────────────────────────────────────────────────────────────────────┤
 │ missing option                                                      │
 │ --material                                                          │
 │                                                                     │
 └─────────────────────────────────────────────────────────────────────┘

 DAMASK terminated on:
 Date:               01/12/2023
 Time:               11:19:24
Note: The following floating-point exceptions are signalling: IEEE_INEXACT_FLAG
STOP 1

I checked the pyrion folder created by the conda package, it seems the run_damask_3.0.0.sh and run_damask_3.0.0_mpi.sh are not there (I reinstalled the pyrion package from conda). Maybe it is the problem.

Meanwhile, I implement a job.testrun() function, which will execute DAMASK_grid -m material.yaml -l loading.yaml -g damask.vti from the terminal instead of using the sh file(just a temporary solution, I will revise it back later), and the notebook works fine. You can find the details here: add testrun for damask-alpha8 test.

Once the run_damask_3.0.0.sh and run_damask_3.0.0_mpi.sh are back, I'll update the notebook.

[jan-janssen]

@yangbai90 Perfect, thanks a lot. I renamed damask_loading.hdf5 to damask_loading_material.hdf5 in #235 and with these changes everything is working again. So I am going to close this pull request.