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MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. #12503
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I found this thread and checked my PATH and LD_LIBRARY_PATH The LD_LIBRARY_PATH does not exist, but I am not an admin on the server and I do not think that's all there is to the problem because I was able to run a different job a few days ago! |
The error message is telling you that your application decided to abort for some reason (i.e., it called the MPI_ABORT API function). I'm unfamiliar with CP2K, so I don't know why it would have done that. You might want to look through the output and see if there's other warning/error messages before the abort message. Also, Open MPI v3.1.1 is fairly ancient. At a bare minimum, I would suggest upgrading to the latest 3.1.x version (v3.1.6), because it contains bunches of bug fixes beyond 3.1.1. That being said, 3.1.6 is from March of 2020, and is still pretty ancient. We are unlikely to ever make any more releases in the v3.1.x series. The most recent version of Open MPI is v5.0.3 -- I'd suggest upgrading to that. |
Hello @jsquyres Jeff, Thank you for your response! I also tried running a different simulation and I got another MPI error, albeit a different one:
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With Open MPI v4.1.4, it looks like you got an additional warning but the same underlying error (i.e., the application invoked I'm afraid we can't help you with whatever environment NEU has setup to run CP2K, nor can we help with CP2K itself -- we're not involved in either of those organizations. |
Hello Jeff, I was able to run a few CP2K jobs from a tutorial website - the Shell still outputs MPI errors, but no aborts. I am assuming, like you suggested, that it is a problem with my input files, and not the MPI package. thank you! |
Background information
Hello! I am running CP2K (a molecular dynamics simulation software) on a shell connected remotely to a supercomputer. I tried submitting a job today, and it did not quite work.
What version of Open MPI are you using? (e.g., v4.1.6, v5.0.1, git branch name and hash, etc.)
3.1.1
Describe how Open MPI was installed (e.g., from a source/distribution tarball, from a git clone, from an operating system distribution package, etc.)
This line is part of the sbatch file that I use to run jobs:
module load openmpi/3.1.1
The module is loaded from Discovery on Open On Demand (Northeastern U's supercomputer)
If you are building/installing from a git clone, please copy-n-paste the output from
git submodule status
./
Please describe the system on which you are running
Details of the problem
Please describe, in detail, the problem that you are having, including the behavior you expect to see, the actual behavior that you are seeing, steps to reproduce the problem, etc. It is most helpful if you can attach a small program that a developer can use to reproduce your problem.
Note: If you include verbatim output (or a code block), please use a GitHub Markdown code block like below:
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