Saint's Log

Crystal Growth Simulation Failure

After completing the mesh generation in Crystal Growth Simulation – Part 1, I decided to investigate how to run the actual crystal growth simulation using Elmer. On Windows, Elmer needs to either be installed into “Program Files“ or be present in the path to avoid this error:

$ python run.py
crucible
melt
crystal
inductor
...
using material steel-1.4541 from self.materials_dict
using material vacuum from self.materials_dict
Wrote sif-file.
Starting simulation  ./simdata/2022-07-25_13-17_ss_test-cz-induction_vacuum  ...
Traceback (most recent call last):
  File "D:\dev\repos\fem\research\test-cz-induction\run.py", line 32, in <module>
    sim.execute()
  File "d:\dev\repos\fem\research\opencgs\opencgs\sim.py", line 182, in execute
    run_elmer_grid(self.sim_dir, "case.msh")
  File "C:\Python310\lib\site-packages\pyelmer\execute.py", line 28, in run_elmer_grid
    subprocess.run(args, cwd=sim_dir, stdout=f, stderr=f)
  File "C:\Python310\lib\subprocess.py", line 501, in run
    with Popen(*popenargs, **kwargs) as process:
  File "C:\Python310\lib\subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Python310\lib\subprocess.py", line 1435, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified

I tried installing a locally built Elmer – see How to Build Elmer on Windows. Unfortunately, the layout created by setup defaulted to “C:\Program Files\Elmer 9.0-1b8e4f7ec” (ending with the hash of the commit I built, instead of “Release”). Worse still, it didn’t launch because of missing DLLs. I need to take a closer look at how NSIS is creating the setup executable, and also figure out how to set up the publisher so that a certificate is displayed with the UAC prompt. I ended up installing the publicly downloadable Elmer then retrying the python script.

using material steel-1.4541 from self.materials_dict
using material vacuum from self.materials_dict
Wrote sif-file.
Starting simulation  ./simdata/2022-07-25_17-23_ss_test-cz-induction_vacuum_1  ...
['ERROR:: systemc: Command exit status was 1'] [] {}
Finished simulation  ./simdata/2022-07-25_17-23_ss_test-cz-induction_vacuum_1  .
Post processing...
Traceback (most recent call last):
  File "D:\dev\repos\fem\research\test-cz-induction\run.py", line 32, in <module>
    sim.execute()
  File "d:\dev\repos\fem\research\opencgs\opencgs\sim.py", line 189, in execute
    self._postprocessing_probes()
  File "d:\dev\repos\fem\research\opencgs\opencgs\sim.py", line 139, in _postprocessing_probes
    names_data = self._read_names_file(self.sim_dir + "/results/probes.dat.names")
  File "d:\dev\repos\fem\research\opencgs\opencgs\sim.py", line 129, in _read_names_file
    with open(names_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: './simdata/2022-07-25_17-23_ss_test-cz-induction_vacuum_1/02_simulation/results/probes.dat.names'

A dialog popped up asking whether I wanted to grant some elmer process access to the domain network or private, etc, and I’m not sure if I took too long to answer it but the script continued with the above failure. This looks like a bug in opencgs – why continue post processing when the simulation has failed – I filed this issue to let the author know: Do not start post-processing when simulation fails · Issue #2 · nemocrys/opencgs (github.com).

I had no idea why the simulation is failing so I used Process Explorer to see which command line was being used to invoke ElmerGrid and ElmerSolver. I was able to then manually invoke ElmerSolver and notice a segmentation fault!

ELMER SOLVER (v 9.0) STARTED AT: 2022/07/25 17:23:13
ParCommInit:  Initialize #PEs:            1
MAIN: 
MAIN: =============================================================
MAIN: ElmerSolver finite element software, Welcome!
...
MAIN: Reading Model: case.sif
 Caught LUA error:[string "loadfile("C:/Program Files (x86)/Elmer/shar..."]:1: attempt to call a nil value
 Caught LUA error:[string "loadstring(readsif("case.sif"))()"]:1: attempt to call global 'readsif' (a nil value)
LoadInputFile: Scanning input file: case.sif
LoadInputFile: Scanning only size info
...
OptimizeBandwidth: Half bandwidth after optimization: 1447
OptimizeBandwidth: ---------------------------------------------------------
'ViewFactors' is not recognized as an internal or external command,
operable program or batch file.
ERROR:: systemc: Command exit status was 1
RadiationFactors: Message
RadiationFactors: All done time (s)                      4.9000E-02
...
      60 0.2041E-08
      61 0.3710E-09
ComputeChange: NS (ITER=11) (NRM,RELC): ( 0.17032920E-04 0.41334346E-05 ) :: statmagsolver
StatMagSolve: Convergence after 11 iterations
StatMagSolve: Joule Heating (W):      4.1375E+01
StatMagSolve: All done, exiting
StatMagSolve: ------------------------------------------------
ComputeChange: SS (ITER=1) (NRM,RELC): ( 0.17032920E-04  2.0000000     ) :: statmagsolver
HeatSolve:  Found Control Point at distance:   0.0000000000000000
HeatSolve:  Control Point Index:           0
HeatSolve: Using Steady-state Heater Control
HeatSolve: 
HeatSolve: 
HeatSolve: -------------------------------------
HeatSolve:  TEMPERATURE ITERATION           1
HeatSolve: -------------------------------------
HeatSolve: 
HeatSolve: Starting Assembly...

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0xffffffff
#1  0xffffffff
#2  0xffffffff
...
#19  0xffffffff
#20  0xffffffff

Looking at the simulation folders such as “simdata\2022-07-25_22-52_ss_test-cz-induction_vacuum_1\02_simulation” revealed that there are ElmerGrid and ElmerSolver log files present with this info, so I didn’t even need Process Explorer! At this point, I have to save the SIGSEGV investigation for another day.