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July 12, 2022, 02:39 |
Usage of flexi's posti_swapmesh tool
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#1 | |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear all,
I am using flexi (https://www.flexi-project.org/) for a supersonic flow simulation. I have read about the tool posti_swapmesh in flexi userguide. The brief description given there is as follows. Quote:
Code:
posti_swapmesh --help Code:
meshFileOld = ../grid1/grid1_mesh.h5 meshFileNew = grid2_mesh.h5 NNew = 2 NSuper = 6 NInter = 6 Code:
posti_swapmesh parameter_swapmesh.ini ../grid1/result_State_0000000.008400000.h5 Code:
| Extract parameter file from "../grid1/result_06Jul2022_State_0000000.008400000.h5" to ".parameter.ini" EVALUATING SOLUTION ON NEW MESH ... INTERPOLATE STATE TO NEW MESH...DONE [.037s] WRITING NEW SOLUTION ... WRITE STATE TO HDF5 FILE...HDF5-DIAG: Error detected in HDF5 (1.12.0) MPI-process 0: #000: /home/vachan/Documents/Work/flexi-framework/flexi/share/GNU-MPI/HDF5/build/src/HDF5/src/H5A.c line 312 in H5Acreate2(): unable to create attribute major: Attribute minor: Unable to initialize object #001: /home/vachan/Documents/Work/flexi-framework/flexi/share/GNU-MPI/HDF5/build/src/HDF5/src/H5VLcallback.c line 1023 in H5VL_attr_create(): attribute create failed major: Virtual Object Layer minor: Unable to create file #002: /home/vachan/Documents/Work/flexi-framework/flexi/share/GNU-MPI/HDF5/build/src/HDF5/src/H5VLcallback.c line 989 in H5VL__attr_create(): attribute create failed major: Virtual Object Layer minor: Unable to create file #003: /home/vachan/Documents/Work/flexi-framework/flexi/share/GNU-MPI/HDF5/build/src/HDF5/src/H5VLnative_attr.c line 66 in H5VL__native_attr_create(): not a datatype major: Invalid arguments to routine minor: Inappropriate type STOP Could not open or create attribute! Thanking in anticipation, Vachan |
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July 12, 2022, 04:42 |
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#2 |
New Member
Join Date: Jul 2022
Posts: 4
Rep Power: 4 |
Hi Vachan,
as far as I can tell it seems that the swap operation itself works fine, but writing the newly swapped state to the HDF5 fails for some reason. To narrow down the issue, could you compile FLEXI again using the "CMAKE_BUILD_TYPE=Debug" setting instead of "Release"?. This build configuration performs additional checks and gives more extensive output, which probably helps for debugging. Then, please, run your case again and provide the (hopefully more extensive) error output. If you have any problems in performing these steps, just let me know, then I can provide further assistance. Best, Marius |
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July 13, 2022, 00:51 |
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#3 |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear Marius,
Thank you very much for responding. Unfortunately, even the debug build gives the same error log, without any additional information. Do you suggest HDF5 also be compiled with debug flags for a detailed error log? If yes, then can you please guide me for this process? Thanks again! |
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July 13, 2022, 06:02 |
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#4 |
New Member
Join Date: Jul 2022
Posts: 4
Rep Power: 4 |
Hi Vachan,
that's unfortunate.Could you provide me with the "CMakeCache.txt" file in your build folder? Then I can check if there might be a problem with the build configuration or some external dependencies. Could you further provide me your:
Could you as last resort provide me with the two meshes and the state file? Then I might be able to find the issue, since debugging this remotely seems hard. Best, Marius |
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July 13, 2022, 06:34 |
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#5 |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear Marius,
While following your instructions to setup a new build, I just realised that posti_swapmesh works fine (without any error) if the build uses FLEXI_FV=OFF. I also checked the new State file and it looks correct. Is this the expected behaviour? If yes then I guess I will have to maintain two separate builds (one for simulations and one for swapmesh). Anyway, the issue has been sorted. Thank you very much for the prompt responses! Vachan |
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July 13, 2022, 07:42 |
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#6 |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear Marius,
Sorry for overloading you with questions. Can you please also look at Wall friction and heat transfer in flexi with FLEXI_FV=ON Thank you very much, Vachan |
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July 13, 2022, 11:19 |
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#7 | |
New Member
Join Date: Jul 2022
Posts: 4
Rep Power: 4 |
Quote:
this was indeed a bug when using the Swapmesh tool with FV enabled, for which we now have added a fix that should be available by tomorrow on Github, so you can just run a "git pull" by then. Please be aware that swapping to another mesh is only a provisional way of changing the grid and is only thought of as getting a fast initial guess to initialize the simulation on another grid. The swapping might introduce osciallations and/or artifacts into the solution and is by itself not an optimal solution to run analysis or visualization on, especially with FV subcells enabled. Best, Marius |
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July 14, 2022, 00:47 |
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#8 |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear Marius,
Thank you very much! Indeed I was using this tool to set the initial condition on a finer grid simulation. However, I am afraid the bug is not fully fixed. It now crashes with the following error, even with FLEXI_FV=OFF. Code:
INIT OLD MESH ... RUNNING A 2D SIMULATION! done in 1.2696579999999999E-003 INIT NEW MESH ... RUNNING A 2D SIMULATION! done in 2.0098820000000002E-003 EVALUATING PARAMETRIC COORDINATES ... 0 equal elements, 2000 remaining. 1000 elements of 2000 processed. Time= 0.79219174000000003 2000 elements of 2000 processed. Time= 0.67314885699999993 IP with ID: 0 0 0 1 is a troublemaker! Coords: -1.1549063565764680E-002 4.1572813613320832E-002 0.0000000000000000 Xi: 375521776384.16803 -259545482419.84808 _____________________________________________________________________________ Program abort caused on Proc 0 in File : posti/swapmesh/parametriccoords.f90 Line 287 This file was compiled at Jul 14 2022 09:28:41 Message: IP not found. I can send you the files over mail if you need them. Their size is large to be attached here. Vachan Last edited by vachan; July 14, 2022 at 02:26. |
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July 14, 2022, 09:36 |
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#9 |
New Member
Join Date: Jul 2022
Posts: 4
Rep Power: 4 |
Hi Vachan,
there was a bug for the swapmesh tool in 2D mode. We introduced the 2D-mode for the swapmesh quite recently (for 2D solutions way faster than swapping in 3D). The old POSTI version worked always in 3D and thus works fine for your example. The bugfix should be available the next days on Github, once it passes our release pipeline. Best, Marius |
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July 15, 2022, 01:40 |
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#10 |
New Member
Vachan Potluri
Join Date: Jul 2017
Posts: 29
Rep Power: 9 |
Dear Marius,
Thanks for the info. I will get back with an update once this fix becomes available on github. Vachan |
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Tags |
compressible flow, discontinuous galerkin, flexi |
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