Cannot install moose on hpc, #inlcude <Eigen/Core> issue #27601
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Issue or question about MOOSEI am currently following this tutorial: https://mooseframework.inl.gov/getting_started/installation/inl_hpc_install_moose.html Specifically I do not think my libmesh.sh is working properly. I found this link: opencv/opencv#14868 I also tried cleaning it and the other trouble shooting steps from: #27046 here is my error message: In file included from /apps/herd/moose/moose-2024-04-27/libmesh/include/libmesh/point.h:25, Diagnostics for MOOSE installation issues################################################################################################## CC=mpicc ################################################################################################## CC=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpicc CXX=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpicxx FC=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif90 F77=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif77 F90=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif90 OK ################################################################################################## Verify OK ################################################################################################## OK [eggejohn@sawtooth4 scripts]$ |
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Replies: 2 comments 15 replies
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Hello I think we are still avoiding mvapich on sawtooth with moose. There is a bug on sparse communications mvapich folks are not fixing. Guillaume |
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Thank you for your help, I used that and started a new installation of MOOSE and now I am getting this error. Is there anyway I could reset my account and start from scratch? I must have missed something in the directions because this shouldn't be this hard. These are the directions I am using: https://mooseframework.inl.gov/getting_started/installation/inl_hpc_install_moose.html (base) [eggejohn@sawtooth3 scripts]$ module purge
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Don't use Sawtooth3. That is a visualization headnode. Use either At the time of when these instructions were created, only Sawtooth1 and 2 were available. I will create a PR to modify the instruction to make this more apparent.
This should not be necessary, as you have full control over your home directory (which is shared between all INL HPC clusters). Starting over is as simple as deleting the things you have created. In the case of MOOSE, you probably should start over before building on cd ~/projects/moose
git clean -xfd
git submodule foreach --recursive git clean -xfdShould do the trick! |
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Awesome thank you so much, this may be a dumb question but how would I get to sawtooth 1 or 2? |
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Sorry for the delayed response, You should be able to reach 
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From the console if you are already logged in with ssh, you can switch to another sawtooth node with ssh sawtooth1 |
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Thank you. I cleaned the folders and switched to sawtooth1 and sawtooth2 Using both the SSH command and through the GUI. However, I am still having the same issue. I believe something is wrong with my petsc but I don't know how I would go about updating it. ((base) [eggejohn@sawtooth2 ~]$ module load use.moose moose-dev remote: Enumerating objects: 756069, done. The version of PETSc you are using is out-of-date, we recommend updating to the new release Found environment variable: CC=mpicc. Ignoring it! Use "./configure CC=$CC" if you really Found environment variable: CXX=mpicxx. Ignoring it! Use "./configure CXX=$CXX" if you Found environment variable: FC=mpif90. Ignoring it! Use "./configure FC=$FC" if you Found environment variable: F77=mpif77. Ignoring it! Use "./configure F77=$F77" if you Found environment variable: F90=mpif90. Ignoring it! Use "./configure F90=$F90" if you Using default C optimization flags "-g -O". You might consider manually setting optimal Using default Cxx optimization flags "-g -O". You might consider manually setting optimal Using default FC optimization flags "-g -O". You might consider manually setting optimal TESTING: configureLibrary from config.packages.hdf5(config/BuildSystem/config/packages/hdf --with-hdf5-dir=/home/eggejohn/.local/share/Trash/files/Sawtooth/projects/moose/petsc/arch-moose/externalpackages/hdf5-1.12.2 There was an error. Exiting...) ... |
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Yes thank you so much, I ran that, and here is what was spat out: ################################################################################################## CC=mpicc ################################################################################################## CC=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpicc CXX=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpicxx FC=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif90 F77=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif77 F90=/apps/local/mvapich2/2.3.7-gcc-12.3.0/bin/mpif90 OK ################################################################################################## Verify /usr/bin/env python3 --version (reporting as: Python 3.10.12), OK ################################################################################################## OK ################################################################################################## WARNING: Not using Conda MOOSE packages, or conda activate moose not (base) [eggejohn@sawtooth2 scripts]$ I believe my issues are coming from me trying to install the demo version of moose on the HPC, then realized I needed the developer version and I don't think I cleaned/uninstalled everything properly. Thank you so much for your help |
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I believe you are right about wanting to "start over". I've caught our cd /home/eggejohn/sawtooth2/projects/moose
rm -rf petsc
git submodule update petscand then attempt to rebuild PETSc: cd /home/eggejohn/sawtooth2/projects/moose/scripts
./update_and_rebuild_petsc.sh |
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Thank you again for your time and expertise; I followed the steps twice and got the same result as last time :(. Is there a way I can fully wipe my HPC drive? Seems like it would be quicker to start from scratch at this point. Here is the error again, even though I believe its the same: |
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Lets try deleting this ".local" directory, and then run the update and rebuild script again: module purge
module load use.moose moose-dev
rm -rf /home/eggejohn/.local
cd /home/eggejohn/sawtooth2/projects/moose
git clean -xfd
git submodule foreach --recursive git clean -xfd
export MOOSE_JOBS=6
scripts/diagnostics.sh
scripts/update_and_rebuild_petsc.shPlease remember to encapsulate the above results using three tick marks:
Deleting your entire |
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That fixed it thank you so much! |
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I have no idea why or how HDF5 was being discovered in ~/.local. Glad deleting it was the answer! |
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Lets try deleting this ".local" directory, and then run the update and rebuild script again:
Please remember to encapsulate the above results using three tick marks:
```
results go here
```
Deleting your entire
~/is really going to be a headache, far worse than you might think. The oddness here is how we seem to be picking up HDF5 in this~/.localdirectory somehow.