WIP: Add internal wrappers #36
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version 0.1.3 of simphony-lammps-md now requires the lammps python module. The module uses the python wrapper to the LAMMPS library which needs to load the liblammps.so; we are currently adding the libraries location to LD_LIBRARY_PATH when testing the plugin
Updating the version of simphony-jyulb requires that (i) the master of jyulb was used as jyulb version 0.1.0 no longer works for simphony-version 0.1.2 and (ii) that we had to use "python setup.py develop" instead of "python setup.py install" due to problems when running the tests.
simphony-numerrin currently requires that the tests be run from a specific directory.
numerrin requires a license so the testing is optional and can be activated with setting the HAVE_NUMERRIN enviroment variable to "yes"
| @@ -84,6 +86,10 @@ various apt repositories, and require ``sudo`` access:: | |||
| please activate the related environment:: | |||
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| source /opt/openfoam222/etc/bashrc | |||
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| The ``apt-numerrin`` target will install nummerin library. To use this solver, please | |||
| ensure that environment variable PYNUMERRIN_LICENSE points to Numerrin license file. | |||
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to a valid Numerrin license file
commit a42d039 set simphony-lammps-md to version 0.1.3 but the README was not updated
Add note stating how we only test the numerrin plugin when a environment variable is set.
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We have solved some simphony-common version issues. |
@jmarcelogimenez, @ahashibon , the branch (simphony/simphony-openfoam#23) has not been merged to master (as the CI is still failing) |
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| sudo make base apt-openfoam apt-simphony apt-lammps apt-mayavi fix-pip | |||
| make apt-kratos apt-numerrin | |||
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The apt tasks usually need sudo correct?
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I am going to switch them from apt-kratos and apt-numerrin to kratos and numerrin. They both copy the libs (downloaded from a website from kratos and stored in the repository from numerrin) to $(SIMPHONYENV)/lib/.
I have also altered to the LD_LIBRARY_PATH in $(SIMPHONYENV)/bin/active to include $(SIMPHONYENV)/lib/.
I am still running the tests but will push after things are working locally.
Alter the constructed virtualenv's activate script so that the LD_LIBRARY_PATH contains the virtualenv's lib directory. Makefile was updated so that the library built for lammps and the libraries downloaded for Kratos and Numerrin are installed to this directory.
| wget https://web.cimne.upc.edu/users/croig/data/kratos-simphony.tgz -O src/kratos/kratos.tgz | ||
| (tar -xzf src/kratos/kratos.tgz -C src/kratos; rm -Rf src/kratos/kratos.tgz) | ||
| rm -rf $(SIMPHONYENV)/lib/python2.7/site-packages/KratosMultiphysics | ||
| (ln -s $(PWD)/src/kratos/KratosMultiphysics $(SIMPHONYENV)/lib/python2.7/site-packages/KratosMultiphysics) |
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I originally wanted to just copy KratosMultiphysics to site_packages, but for some reason I would get an error when testing.
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I guess I should open an issue to track this.
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yup, opening an issue and posting the error would be good
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@itziakos . can you take a look at this again. I added LD_LIBRARY_PATH to the activate sript..but did not add a means to "deactivate" the change to LD_LIBRARY_PATH |
ok let me have a look. |
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@nathanfranklin, It would be better if each engine is added on a separate PR. This will make it easier to sort out problems and debug the setup issues. (There are just to many moving parts) Is it ok if I split this PR to several smaller ones? |
i can split this into different PRS in the morning. If needed though, freel free to do it ahead of time. |
This PR adds the released INTERNAL wrappers to modeling engines.
workaround some of the issues in simphony/simphony-jyulb#21. See commit message of 0012609had to alter LD_LIBRARY_PATH when running tests to that lammps.py could find the lammps librarywaiting for simphony/simphony-kratos#9. blocking issues are simphony/simphony-kratos#11 and simphony/simphony-kratos#15. workaround for issue simphony/simphony-kratos#14