[CIG-SEISMO] specfem3d : simple_model with CPML

[houssen]

OK, I believed the right branch to be on was master ! As far as I 
understand, you fast-forwarded master up to devel. Anyway, I on devel 
now.
At IPGP, we have the SEM code you may know ! :D For a start, I'd like 
to compare SEM and specfem3d on a simple case (with and without PML - 
then I'd like to play on NGLL).

To be back on the initial problem :
1. As far as I understand, changes between the old master and devel are 
mainly cosmetic (comments: #).
2. The problem (crash) persists on devel.
3. I started with what I believe to be the most simple case 
(xmeshfem3d, simple_model) :
3.1. Without PML, specfem3D runs fine (mesh OK, database OK, run OK).
3.2. With PML, the code crashes (mesh OK, database KO).

To focus on 3.2: basically, from the case without PML which works I 
just turned ON the PML_CONDITIONS keyword in Par_file.
1. I have now files from devel.
2. The only differences (PML - no PML) between Par_files are:
~> diff valid-run-specfem3d-nopml/meshfem3D/simple_model/DATA/Par_file 
valid-run-specfem3d-pml/meshfem3D/simple_model/DATA/Par_file
90c90
< PML_CONDITIONS = .false.
---
> PML_CONDITIONS = .true.
105c105
< STACEY_ABSORBING_CONDITIONS     = .true.
---
> STACEY_ABSORBING_CONDITIONS = .false.
I turned OFF STACEY_ABSORBING_CONDITIONS as I had an error message on 
the old master when I turned on PML_CONDITIONS.
3. No difference between Mesh_Par_files:
~> diff 
valid-run-specfem3d-nopml/meshfem3D/simple_model/DATA/meshfem3D_files/Mesh_Par_file 
valid-run-specfem3d-pml/meshfem3D/simple_model/DATA/meshfem3D_files/Mesh_Par_file

When I turn ON PML_CONDITIONS in Par_file, I get this:
  creating PML region
  Created a total of            0  unique CPML elements
     (i.e.,    0.00000000     % of the mesh)
In xmeshfem3D logs, and, I get this:
    ...creating C-PML damping profiles
Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.
Backtrace for this error:
#0  0x7fa98f0d7d17 in ???
#1  0x7fa98f0d6f7d in ???
#2  0x7fa98e3da03f in ???
#3  0x442aef in pml_set_local_dampingcoeff_
   at src/generate_databases/pml_set_local_dampingcoeff.f90:95
#4  0x418f0d in create_regions_mesh_
   at src/generate_databases/create_regions_mesh.f90:238
#5  0x45fe08 in setup_mesh_
   at src/generate_databases/setup_mesh.f90:66
#6  0x41c511 in generate_databases_
   at src/generate_databases/generate_databases.f90:254
#7  0x40269f in xgenerate_databases
   at src/generate_databases/program_generate_databases.f90:34
#8  0x40269f in main
   at src/generate_databases/program_generate_databases.f90:39
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node yoda exited on 
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
In xgenerate_database logs.

I tried to debug a bit, but, I didn't get what's wrong in Mesh_Par_file 
and / or Par_file : I understand the PML region has no element but I 
can't understand why and can't neither fix the issue.

Franck

Le 2016-10-25 19:53, Dimitri Komatitsch a écrit :
> Dear Franck,
>
> Could you try with the "devel" version and let us know?
>
> Let me replace "master" with a copy of "devel" because it is old.
>
> You can also check EXAMPLES/CPML_examples.

I do not have CUBIT. My understanding is that EXAMPLES/CPML_examples 
are all meshed with CUBIT.
~/specfem3d> find . -name Mesh_Par_file
./EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/meshfem3D_examples/cavity/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/meshfem3D_examples/simple_model/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/meshfem3D_examples/sep_bathymetry/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/meshfem3D_examples/many_interfaces/DATA/meshfem3D_files/Mesh_Par_file
./EXAMPLES/meshfem3D_examples/socal1D/DATA/meshfem3D_files/Mesh_Par_file

>
> Please keep us informed,
> Thanks,
>
> Dimitri.
>
> On 25/10/2016 16:28, houssen wrote:
>> Hello,
>>
>> I am new to specfem3d. Is it possible to run the test
>> EXAMPLES/meshfem3D_examples/simple_model from specfem (git clone) 
>> with
>> CPML ? If yes how ?
>> I tried to play over different parameters in Mesh_Par_file and 
>> Par_file
>> without success (in particular adding CPML_CONDITIONS keyword in
>> Mesh_Par_file - this didn't work).
>>
>> I git-cloned https://github.com/geodynamics/specfem3d.git (master). 
>> I am
>> running debian with gnu compilers on a laptop.
>>
>> Thanks
>>
>> Franck
>>
>>
>> _______________________________________________
>> CIG-SEISMO mailing list
>> CIG-SEISMO at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo
>>