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exoplanet-dev / exoplanet

Fast & scalable MCMC for all your exoplanet needs!
https://docs.exoplanet.codes
MIT License
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system/environment issue on supercomputer #30

Closed Li-Yangyang closed 5 years ago

Li-Yangyang commented 5 years ago

Hi, I am doing unit-test of exoplanet on supercomputer cluster. However I met a problem of system or environment issue about it. It seems about the flag of theano module. Here is the test feedback. Do you have any insight how to configure those possible wrong flag value in the theano backend? Thanks, Yangyang bug_infos.log

dfm commented 5 years ago

The unit tests really only work when executed within the git repository (because of flags, as you say). Did you execute the tests as follows:

git clone https://github.com/dfm/exoplanet
cd exoplanet
py.test -v exoplanet

If so, can you tell me your Theano, PyMC3 and exoplanet versions?

Li-Yangyang commented 5 years ago

I just redid the test under git repository, still not passing. Theano: 1.0.4, PyMC3: 3.6, exoplanet: 0.1.5

dfm commented 5 years ago

Looking more closely, it looks like the error is coming from the fact that your system isn't exposing a c++ compiler. It looks like you'll need to set the cxx theano flag to point to your c++ compiler. All the ops in exoplanet are implemented in C so it won't work without this! Let me know how that goes.

Li-Yangyang commented 5 years ago

Many thanks. One more thing about the unit-test of exoplanet is that it seems that c++ compiler can not find Eigen3 and starry lib. After I added them to my system lib directory and point cxx to the c++ complier, unit-test worked. Therefore if possible, a brief guidance about that two lib configuration might be added to the testing part of exoplanet documentation.

Regards, Yangyang

dfm commented 5 years ago

This means that you didn't follow the docs and git clone --recursive :). I'm not sure that adding to the docs helps if it isn't followed... ;)

On Thu, Mar 21, 2019 at 5:26 PM Li-Yangyang notifications@github.com wrote:

Many thanks. One more thing about the unit-test of exoplanet is that it seems that c++ compiler can not find Eigen3 and starry lib. After I added them to my system lib directory and point cxx to the c++ complier, unit-test worked. Therefore if possible, a brief guidance about that two lib configuration might be added to the testing part of exoplanet documentation.

Regards, Yangyang

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Li-Yangyang commented 5 years ago

Oh, yeah! I just followed the "git clone" suggestions and didn't check the doc lol. Alright, that works if add --recursive. Still many thanks. It's perfect time to close this issue. :)

Regards, Yangyang