Installing with "make develop" using existing py2 environment

[dloney]

When I use an anaconda python 2 environment, I have the issue where the proteus build does not create the linux directory as its build destination, but rather overwrites the existing python 2 conda environment to create a python 3 environment. The issue appears to be that the build has an issue creating the correct folder structure. Here's what I see in my build process:

Linking stack/default.yaml for this arch
ln -s /home/dloney/Documents/repo/proteus-dev/stack/examples/proteus.linux.yaml /home/dloney/Documents/repo/proteus-dev/stack/default.yaml
ln: failed to create symbolic link '/home/dloney/Documents/repo/proteus-dev/stack/default.yaml': File exists
make: [Makefile:139: stack/default.yaml] Error 1 (ignored)
ln -sf /home/dloney/Documents/repo/proteus-dev/linux/lib64/* /home/dloney/Documents/repo/proteus-dev/linux/lib
ln: failed to create symbolic link '/home/dloney/Documents/repo/proteus-dev/linux/lib': No such file or directory
make: [Makefile:191: develop] Error 1 (ignored)
ln -sf /home/dloney/Documents/repo/proteus-dev/linux/lib64/cmake/* /home/dloney/Documents/repo/proteus-dev/linux/lib/cmake
ln: failed to create symbolic link '/home/dloney/Documents/repo/proteus-dev/linux/lib/cmake': No such file or directory
make: [Makefile:192: develop] Error 1 (ignored)

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Installing development version

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Please include this information in all bug reports.
+======================================================================================================+
PROTEUS : /home/dloney/Documents/repo/proteus-dev
PROTEUS_ARCH : linux
PROTEUS_PREFIX : /home/dloney/anaconda3/envs/proteus_dev
PROTEUS_VERSION:
+====================

[dloney]

I can replicate with a clean python 2 environment and newly downloaded copy of proteus.

[zhang-alvin]

@dloney, just to clarify, do you intend to build proteus through hashdist?

[dloney]

Hi Alvin. Yes, that's what I was hoping. It appears to jump over to the conda build system though when it fails with hashdisk.

[zhang-alvin]

Hi Alvin. Yes, that's what I was hoping. It appears to jump over to the conda build system though when it fails with hashdisk.

Could you also post the commands you used to start the build? If you used make develop, it looks like it's skipping the building of the dependencies https://github.com/erdc/proteus/blob/master/Makefile#L143-L154.

[cekees]

@dloney I'd also recommend excluding anaconda python from your path since my understanding is that conda overrides pip, and we use that in the proteus build process. Hashdist should be fine with the system python2 to execute the build. When starting from a failed build like this, it's probably worth manually removing any old prefix directory, such as llinux and/or linux2.

[dloney]

@zhang-alvin All I did was make develop within the conda environment, so I didn't modify anything from its default configuration. I started with clean environment and a new clone of proteus.

[dloney]

@cekees That makes sense. Even if you called pip within a conda environment, it would still target just that single directory. It's still strange that the build is throwing an error on making the folder though.

How does removing conda from the path and bashrc affect the ability to use conda environments from the terminal for other applications? Wouldn't one need to have a secondary terminal like the Anaconda prompt to run conda environments then on a machine using proteus?