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Bump extern/amrex from 74127d6 to 6d9c25b #761

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@dependabot dependabot bot commented on behalf of github Oct 1, 2024

Bumps extern/amrex from 74127d6 to 6d9c25b.

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Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `74127d6` to `6d9c25b`.
- [Release notes](https://github.com/AMReX-Codes/amrex/releases)
- [Commits](AMReX-Codes/amrex@74127d6...6d9c25b)

---
updated-dependencies:
- dependency-name: extern/amrex
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file submodules Pull requests that update Submodules code labels Oct 1, 2024
@dosubot dosubot bot added the size:XS This PR changes 0-9 lines, ignoring generated files. label Oct 1, 2024
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sonarcloud bot commented Oct 1, 2024

@BenWibking
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/azp run

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Azure Pipelines successfully started running 2 pipeline(s).

markkrumholz
markkrumholz previously approved these changes Oct 3, 2024
@dosubot dosubot bot added the lgtm This PR has been approved by a maintainer label Oct 3, 2024
@BenWibking
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/azp run

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Azure Pipelines successfully started running 2 pipeline(s).

@BenWibking
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We have an extremely weird test failure I've never seen before:

Total GPU global memory (MB) spread across MPI: [32494 ... 32494]
Free  GPU global memory (MB) spread across MPI: [6508 ... 6508]
[The         Arena] space (MB) allocated spread across MPI: [24370 ... 24370]
[The         Arena] space (MB) used      spread across MPI: [0 ... 0]
[The Managed Arena] space (MB) allocated spread across MPI: [8 ... 8]
[The Managed Arena] space (MB) used      spread across MPI: [0 ... 0]
[The  Pinned Arena] space (MB) allocated spread across MPI: [8 ... 8]
[The  Pinned Arena] space (MB) used      spread across MPI: [0 ... 0]
[The   Comms Arena] space (MB) allocated spread across MPI: [8 ... 8]
[The   Comms Arena] space (MB) used      spread across MPI: [0 ... 0]
pure virtual method called
terminate called without an active exception
[avatargpu:3904435] *** Process received signal ***
[avatargpu:3904435] Signal: Aborted (6)
[avatargpu:3904435] Signal code:  (362118880)
[avatargpu:3904435] [ 0] /lib64/libc.so.6(+0x3e6f0)[0x7f6290a3e6f0]
[avatargpu:3904435] [ 1] /lib64/libc.so.6(+0x8b94c)[0x7f6290a8b94c]
[avatargpu:3904435] [ 2] /lib64/libc.so.6(raise+0x16)[0x7f6290a3e646]
[avatargpu:3904435] [ 3] /lib64/libc.so.6(abort+0xd3)[0x7f6290a287f3]
[avatargpu:3904435] [ 4] /lib64/libstdc++.so.6(+0xa1b21)[0x7f6290ea1b21]
[avatargpu:3904435] [ 5] /lib64/libstdc++.so.6(+0xad52c)[0x7f6290ead52c]
[avatargpu:3904435] [ 6] /lib64/libstdc++.so.6(+0xad597)[0x7f6290ead597]
[avatargpu:3904435] [ 7] /lib64/libstdc++.so.6(+0xae2c5)[0x7f6290eae2c5]
[avatargpu:3904435] [ 8] /tmp/bwibking/_work/1/s/build/src/problems/RadTube/test_radiation_tube[0x458c5b]
[avatargpu:3904435] [ 9] /lib64/libc.so.6(+0x40ded)[0x7f6290a40ded]
[avatargpu:3904435] [10] /lib64/libc.so.6(on_exit+0x0)[0x7f6290a40f30]
[avatargpu:3904435] [11] /lib64/libc.so.6(+0x29597)[0x7f6290a29597]
[avatargpu:3904435] [12] /lib64/libc.so.6(__libc_start_main+0x80)[0x7f6290a29640]
[avatargpu:3904435] [13] /tmp/bwibking/_work/1/s/build/src/problems/RadTube/test_radiation_tube[0x435c25]
[avatargpu:3904435] *** End of error message ***

@markkrumholz
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Definitely something strange with the radtube test here -- there's a pure virtual function called exception in the log, and I have no idea what could be causing that. @chongchonghe, can you take a look and see if you can reproduce this problem?

@BenWibking
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I found this blog post: https://www.artima.com/articles/pure-virtual-function-called-an-explanation

It seems odd it happens at the very end, when the program would exit anyway. Hopefully something that should be obvious when run inside a debugger.

@chongchonghe
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I'll take a look.

@chongchonghe
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I was able to reproduce this error on gadi. It seems like the code that causes this error is sim.setInitialConditions();, so I suspect it has to do with preCalculateInitialConditions() and amrex::Gpu::HostVector<double>, amrex::Gpu::DeviceVector<double>. The same error appears when I remove everything after sim.setInitialConditions(); in problem_main(). However, I'm not able to fix it. I also wonder why this problem only occurs in this PR.

@markkrumholz
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Maybe we can sit down with the debugger together and have a look at this next week. I'll message you on slack to set a time.

@chongchonghe
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Both Release and Debug runs are successful on CPU. On gadi GPU, both Release and Debug runs give the same error message. The simulation finishes successfully (L1 norm is within tolerance), but as long as it executes sim.setInitialConditions();, the test fails.

@chongchonghe
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Maybe we can sit down with the debugger together and have a look at this next week. I'll message you on slack to set a time.

Yes, we can sit down together and try to debug it. Just let me know what time works for you.

github-merge-queue bot pushed a commit that referenced this pull request Oct 14, 2024
### Description
Move `DeviceVector` inside `setInitialConditionsOnGrid` to avoid the
`pure virtual method called` error, first seen in #761 .

This branch is based on dependabot/submodules/extern/amrex-6d9c25b . 

### Related issues
Fix issues in PR #761 

### Checklist
_Before this pull request can be reviewed, all of these tasks should be
completed. Denote completed tasks with an `x` inside the square brackets
`[ ]` in the Markdown source below:_
- [ ] I have added a description (see above).
- [ ] I have added a link to any related issues see (see above).
- [ ] I have read the [Contributing
Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
- [ ] I have added tests for any new physics that this PR adds to the
code.
- [ ] I have tested this PR on my local computer and all tests pass.
- [ ] I have manually triggered the GPU tests with the magic comment
`/azp run`.
- [ ] I have requested a reviewer for this PR.

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@chongchonghe
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Close after #774

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dependabot bot commented on behalf of github Oct 14, 2024

OK, I won't notify you again about this release, but will get in touch when a new version is available. You can also ignore all major, minor, or patch releases for a dependency by adding an ignore condition with the desired update_types to your config file.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.

@dependabot dependabot bot deleted the dependabot/submodules/extern/amrex-6d9c25b branch October 14, 2024 08:57
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