Fix mpiio with stdlibc++ range checking #3234
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## python #3234 +/- ##
======================================
- Coverage 85% 85% -1%
======================================
Files 528 528
Lines 25805 25805
======================================
- Hits 22150 22149 -1
- Misses 3655 3656 +1
Continue to review full report at Codecov.
|
jngrad
approved these changes
Oct 5, 2019
fweik
suggested changes
Oct 5, 2019
|
I tend to think that the C++ implementation used in #3230 is broken in this case. The standard states for copy_n: If an implementation for copy_n asserts: Nonetheless, this PR looks good because it is an easy workaround for the problem. |
hirschsn
reviewed
Oct 7, 2019
|
@hirschsn, the assertion is not inside |
fweik
approved these changes
Oct 7, 2019
|
@mkuron I see. That makes sense. :) Wouldn't NVM, I see that's what you've done. |
|
Build is failing because of #3235, which is fixed by espressomd/docker#139. |
|
bors r=fweik |
bors bot
added a commit
that referenced
this pull request
Oct 11, 2019
3234: Fix mpiio with stdlibc++ range checking r=fweik a=mkuron Fixes #3230. Reported by @junghans. When mpiio was used but no bonds were present, we would still try to copy zero bonds from a zero-length vector. This triggered an assertion when stdlibc++ range checking was enabled. Please tag for cherry-picking into 4.1.1. 3236: ESS2019 installation guide updates r=KaiSzuttor a=mkuron Lessons learned today: - We require MPI 3 because we depend on const-correctness in a few places. That means that OpenMPI 1.6.5 and lower are not supported anymore. - Installing the ROCm driver breaks access to /dev/kfd, causing hwloc initialization during `mpiexec` to hang. Rebooting helps. - Add matplotlib, ipython and jupyter to the Mac install guide. - Homebrew now defaults to Python 3, requires manually enabling cython, and it's unclear whether the hdf5 package still supports MPI (Homebrew/homebrew-core#26974) - Anaconda (~/anaconda[23]) and python.org packages (/Library/Python and /usr/local/bin) are also sources of conflict Please tag for the 4.1.1 release 3238: maintainer: Escape module python in wrapper script r=jngrad a=fweik Fixes #3237. Description of changes: - Added quotes around the module path in python wrapper script. Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Kai Szuttor <[email protected]> Co-authored-by: Florian Weik <[email protected]>
Canceled (will resume) |
|
bors r- |
Canceled |
|
bors r=fweik |
bors bot
added a commit
that referenced
this pull request
Oct 11, 2019
3234: Fix mpiio with stdlibc++ range checking r=fweik a=mkuron Fixes #3230. Reported by @junghans. When mpiio was used but no bonds were present, we would still try to copy zero bonds from a zero-length vector. This triggered an assertion when stdlibc++ range checking was enabled. Please tag for cherry-picking into 4.1.1. 3236: ESS2019 installation guide updates r=KaiSzuttor a=mkuron Lessons learned today: - We require MPI 3 because we depend on const-correctness in a few places. That means that OpenMPI 1.6.5 and lower are not supported anymore. - Installing the ROCm driver breaks access to /dev/kfd, causing hwloc initialization during `mpiexec` to hang. Rebooting helps. - Add matplotlib, ipython and jupyter to the Mac install guide. - Homebrew now defaults to Python 3, requires manually enabling cython, and it's unclear whether the hdf5 package still supports MPI (Homebrew/homebrew-core#26974) - Anaconda (~/anaconda[23]) and python.org packages (/Library/Python and /usr/local/bin) are also sources of conflict Please tag for the 4.1.1 release 3238: maintainer: Escape module python in wrapper script r=jngrad a=fweik Fixes #3237. Description of changes: - Added quotes around the module path in python wrapper script. Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Michael Kuron <[email protected]> Co-authored-by: Kai Szuttor <[email protected]> Co-authored-by: Florian Weik <[email protected]>
Build succeeded |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #3230. Reported by @junghans.
When mpiio was used but no bonds were present, we would still try to copy zero bonds from a zero-length vector. This triggered an assertion when stdlibc++ range checking was enabled.
Please tag for cherry-picking into 4.1.1.