Installation issue (PETSC ?) on Ubuntu 20.04.6 VM #596
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guillaume-florent
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Installation
Replies: 6 comments 11 replies
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Can you post the complete log file? Where did this happen? |
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1 reply
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Following https://dafoam.github.io/mydoc_installation_source.html, it happened when running Allrun in tests. |
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We never test the installation on Ubuntu Virtual Machines. So it is possible that it will break... Can you run the regression tests for other repos, like IDWarp, and see if it works? |
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4 replies
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Hi @guillaume-florent, did you try this? What's the update? I don't know how to run regression tests for other repos otherwise I would try. |
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Hi @friedenhe We have tested installation of dafoam versions 3.0.1, 3.0.3 and 3.1.0 on ubuntu virtual machines. We have used Ubuntu 20.04 and openfoam v1812 and everything works perfectly well |
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@uttamcadambi07 I tried DAFoam 3.1.1, Ubuntu 20.04.6 VirtualBox 7.0.14 with Windows 10 as host, but could not run it. Could you please try DAFoam 3.1.1? Also, did you use VirtualBox, if yes what version? |
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Apologies for the later response. We use Oracle Virtualbox 6.1. I think i tried upgrading the virtual box to v7 and then i could not launch mu Ubuntu. So perhaps try to install vBox v6 and see if it works. Yes I will be installing DAFoam v3.1.1 soon. Will keep you posted. |
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Same issue. Ubuntu 20.04.6 VirtualBox 7.0.14 with Windows 10 as host. |
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3 replies
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I got this error while compiling pyOptSparse: |
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Tried on Win 10 WSL-Ubuntu20.04.6 but still the same error. Update 2: Fixed pyOptSparse compilation issue as in update 1. On Win 10 WSL-Ubuntu20.04.6, I am now getting this error (while running test runs for dafoam): Update 3: I solved the problem by installing the latest version of pyOptSparse. (WSL) After this, I ran all DAFoam tests successfully. |
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This is very strange because we do have |
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Running the IDWarp tests (in short, module parameterized is not found by test scripts) guillaume@vm-u20:~/dafoam$ ./loadDAFoam.sh guillaume@vm-u20:~/dafoam/repos/idwarp-2.6.0/tests$ $HOME/dafoam/packages/miniconda3/bin/python test_USMesh.py [[36869,1],0]: A high-performance Open MPI point-to-point messaging module Module: OpenFabrics (openib) Another transport will be used instead, although this may result in NOTE: You can disable this warning by setting the MCA parameter Traceback (most recent call last): [[37927,1],0]: A high-performance Open MPI point-to-point messaging module Module: OpenFabrics (openib) Another transport will be used instead, although this may result in NOTE: You can disable this warning by setting the MCA parameter Traceback (most recent call last): |
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0 replies
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@guillaume-florent I'm not sure what happened, but it seems your IDWarp installation was incorrect. I suspect you were not following the exact steps, or something was not correctly installed, before you installed the MDOLab repos. |
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1 reply
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I went through the whole procedure again, double checking everything, which lead to the same issue. Here is the result of testing IDWarp(python -m unittest discover tests 2> idwarp_tests.log). I hope it helps to identify where the issue is coming from: |
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Also, we followed the instructions on the installation webpage of dafoam as it is and faced no problems. |
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2 replies
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Can you elaborate? Did you install on a plain Ubuntu or in a VM? Did you run the repos/packages tests? |
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Sure. We installed Ubuntu on a virtual box (Oracle Virtual Box v 6.1) and then installed dafoam v3.1.0 on it. Openfoam v1812 and Ubuntu v18.04. So I did not run the package tests because our group is interested only in a few specific capabilities of dafoam which we tested to check if it works and it did. Particularly we are not interested in the aerostructural aspects so we ignored it but i recall there was an issue using dafoam v3.0.3 with the aerostructural tests. |
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After religiously following the installation steps, I get the following PETSC error when attempting to run the tests. Looking for help!
I checked with glances and I do not seem to be running out of memory...
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption
...
[1]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 50176059.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
[3]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
...
Integration: Failed!
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