installation problem

[elc...@lanl.gov]

I was trying to install the latest ATS version using amanzi master folder and the build_ATS_generic.sh. It installed all the libraries and failed to configure. I attached error message below.

-------------------------------------------
--
-- CMake: Configuring ATS build/install.
--
-- ----------------------------------------
-- Adding ats-regression-tests
-- Found PythonInterp: /usr/bin/python (found version "2.7.16")
/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '/Users/elchin/ats/amanzi-build-master-Debug/src/physics/ats/testing/ats-regression-tests/regression_tests.py': [Errno 2] No such file or directory
-- Found ATS tests:
CMake Error at src/physics/ats/testing/CMakeLists.txt:24 (string):
  string sub-command STRIP requires two arguments.


CMake Error at src/physics/ats/testing/CMakeLists.txt:25 (string):
  string sub-command REPLACE requires at least four arguments.


-- Found Python: /usr/bin/python 
-- Install Python tools and modules in: /Users/elchin/ats/amanzi-install-master-Debug/lib/python2.7/site-packages
-- Leaving create_tpl_export_file
-- Writing target file
-- Writing evaluator registration macro file
-- Configuring incomplete, errors occurred!
See also "/Users/elchin/ats/amanzi-build-master-Debug/CMakeFiles/CMakeOutput.log".
[Tue Nov 17 09:37:33 MST 2020] Amanzi configure complete
make: *** No targets specified and no makefile found.  Stop.
Amanzi Bootstrap ERROR: Failed to build Amanzi

[Sergi Molins Rafa]

Elchin

I also reported issues with ats-regression-tests and python yesterday. See https://groups.google.com/g/ats-users/c/MT_jSsE138A

I also saw your error in the course of my testing. 

Ethan provides some answers in the thread. I managed to build ats using point 3 in his response. I think he is still working through some of the issues.

Sergi

Sergi

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[elc...@lanl.gov]

I did what Ethan suggested in the Sergi's email. I also manually copied ats-regression-tests into build-master. Now it cannot import h5py. I installed h5py, and checked. I can import it when I am in ipython. For some reason, the python 2.7 does not see h5py.

File "/Users/elchin/ats/amanzi-build-master-Debug/src/physics/ats/testing/ats-regression-tests/regression_tests.py", line 23, in <module>
    import test_manager
  File "/Users/elchin/ats/repos/amanzi/src/physics/ats/tools/testing/test_manager.py", line 35, in <module>
    import h5py
ImportError: No module named h5py

-- Found ATS tests:
CMake Error at src/physics/ats/testing/CMakeLists.txt:24 (string):
  string sub-command STRIP requires two arguments.


CMake Error at src/physics/ats/testing/CMakeLists.txt:25 (string):
  string sub-command REPLACE requires at least four arguments.

-- Install Python tools and modules in: /Users/elchin/ats/amanzi-install-master-Debug/lib/python2.7/site-packages
-- Leaving create_tpl_export_file
-- Writing target file
-- Writing evaluator registration macro file
-- Configuring incomplete, errors occurred!
See also "/Users/elchin/ats/amanzi-build-master-Debug/CMakeFiles/CMakeOutput.log".

[Tue Nov 17 10:13:21 MST 2020] Amanzi configure complete

make: *** No targets specified and no makefile found.  Stop.
Amanzi Bootstrap ERROR: Failed to build Amanzi

[Sergi Molins Rafa]

Yes, this is a secondary problem. For me, there are 3 separate problems.

The main one is 

1- that the ats-regression-tests is not pulled correctly when using bootstrap.sh. (can be overcome by manual pull as described by Ethan in point 3)

The secondary ones are that 

2- I don't know how to disable this option (i.e. doing the ats-regression-tests) in bootstrap.sh

3- the build system always uses /usr/bin/python. This is a problem if /usr/bin/python is python2. If it is python3, it is also a problem because the system distribution usually does not have all the bells and whistles of a distribution like anaconda, including numpy, h5py, etc. 

Sergi

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[Sergi Molins Rafa]

Elchin,

I updated bootstrap.sh to deal with this. Try with new bootstrap.sh

Sergi

[Jafarov, Elchin]

Sergi,

I pulled the latest version, I also tried Konstantin's way. In both cases I am having the python related error, not finding h5py.

-E

---

From: Sergi Molins Rafa <smo...@lbl.gov>
Sent: Tuesday, November 17, 2020 12:39:28 PM
To: Jafarov, Elchin
Cc: Amanzi-ATS Users
Subject: [EXTERNAL] Re: installation problem

 

[Coon, Ethan]

I’m sorry for the confusion over this – I will be pushing a change to turn this off by default and enable with a bootstrap option.

 

1. Thanks for pushing the fix to bootstrap Sergi, I thought I had done that already but apparently not.  My own setup doesn’t rely on bootstrap to get the subrepo, so I missed it.  I sent an email around to a few people to check their setups too and get back to me if they had trouble, but you guys are too fast.
2. There isn’t currently a way to disable registering the tests (other than setting ENABLE_TESTING=False, which would turn off all Amanzi and ATS testing, and passing that as a cmake configure argument to bootstrap).  I’ll add an option.
3. I’m confused by this one.  I used cmake’s PythonInterp stuff, and it successfully finds my python3 anaconda installation that is in my path, and not the /usr/bin/python (which is also 2.7 on my mac, and further down in the path).  Let me do some more googling.

 

Elchin’s problem requires two things:

 

1. it shouldn’t require h5py just to register or run the tests, only to actually read their output and so check and see if the tests pass.  This needs to be fixed on my end.
2. if you actually want to run ATS’s regression testing, you need to install h5py.  “pip install h5py”, “conda install h5py” or any other typical python package manager should find it.

 

Ethan

 

-- 

-------------------------------------------------------------------------

Ethan Coon

Research Scientist

Oak Ridge National Laboratory

 

865-241-1296

https://www.ornl.gov/staff-profile/ethan-t-coon

-------------------------------------------------------------------------

 

 

 

From: ats-...@googlegroups.com <ats-...@googlegroups.com>
Date: Tuesday, November 17, 2020 at 12:33 PM
To: elc...@lanl.gov <elc...@lanl.gov>
Cc: Amanzi-ATS Users <ats-...@googlegroups.com>
Subject: [EXTERNAL] Re: installation problem

To view this discussion on the web visit https://groups.google.com/d/msgid/ats-users/CAP9Hfk4yX0Fg3PT%2B%2BKGVJp3bs1zfCri7RnVoHkxs0u%3DOPb3GOg%40mail.gmail.com.

[Sergi Molins Rafa]

Disregard my comments regarding the python installation. These issues seem only to be appearing when I was manually doing the git submodule update. Not sure why. It is picking up my anaconda build fine with the updated bootstrap.sh.

Thanks

Sergi