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PCMDI / pcmdi_metrics

Open-source Python package for Systematic Evaluation of Climate and Earth System Models
http://pcmdi.github.io/pcmdi_metrics/
BSD 3-Clause "New" or "Revised" License
97 stars 37 forks source link

Current master build is failing #279

Closed durack1 closed 8 years ago

durack1 commented 9 years ago

It seems the current master branch is failing the travis build tests

durack1 commented 8 years ago

Likely a duplicate of #277

doutriaux1 commented 8 years ago

@durack1 master builds and tests fine for me. Is this still valid?

durack1 commented 8 years ago

It seems we still have a red travis badge, so I assume that master still has issues..

durack1 commented 8 years ago

@doutriaux1 this is the error on OS X:

CMake Error at /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build.cmake:56 (message):
  CTEST_FULL_OUTPUT
   Command failed: 1
   'env' 'PYTHONPATH=' 'LD_LIBRARY_PATH=' '/Users/travis/build/PCMDI/_build/PCMDI_METRICS/bin/python' 'setup.py' 'build'
   From /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build-out.log
  -------------------------------------------------
  -------------------------------------------------
   From /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build-err.log
  -------------------------------------------------
  Traceback (most recent call last):
    File "setup.py", line 17, in <module>
      exec(init_file.read(), command_ns)
    File "<string>", line 8, in <module>
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uv-- [download 72% complete]
-- [download 43% complete]
-- [download 73% complete]
-- [download 74% complete]
-- [download 75% complete]
-- [download 44% complete]
-- [download 45% complete]
cdat_build/build/setuptools/setuptools/__init__.py", line 11, in <module>
      from setuptools.extension import Extension
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/setuptools/extension.py", line 5, in <module>
      from setuptools.dist import _get_unpatched
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/setuptools/dist.py", line 16, in <module>
      import pkg_resources
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 706, in <module>
      class Environment(object):
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line -- [download 76% complete]
-- [download 77% complete]
709, in Environment
      def __init__(self, search_path=None, platform=get_supported_platform(), python=PY_MAJOR):
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 148, in get_supported_platform
      plat = 'macosx-%s-%s' % ('.'.join(_macosx_vers()[:2]), m.group(3))
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 241, in _macosx_vers
      version = platform.mac_ver()[0]
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/platform.py", line 809, in mac_ver
      info = _mac_ver_xml()
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/platform.py", line 786, in _mac_ver_xml
      p-- [download 78% complete]
l = plistlib.readPlist(fn)
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plistlib.py", line 78, in readPlist
      rootObject = p.parse(pathOrFile)
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plistlib.py", line 401, in parse
      from xml.parsers.expat import ParserCreate
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/parsers/expat.py", line 4, in <module>
      from pyexpat import *
  ImportError: No module named pyexpat
  -------------------------------------------------
make[2]: *** [setuptools-prefix/src/setuptools-stamp/setuptools-build] Error 1
make[1]: *** [CMakeFiles/setuptools.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

This is a little weird as setuptools has the python dependency specified: https://github.com/UV-CDAT/uvcdat/blob/master/CMake/cdat_modules/setuptools_deps.cmake#L1

Seems like on OS X 10.10.5 and the built in Python 2.7.10 this module is installed:

[durack1ml:~] durack1% python 
Python 2.7.10 (default, Jul 14 2015, 19:46:27) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyexpat
>>>

Is there some race condition happening here?

durack1 commented 8 years ago

@doutriaux1 I just tested this on my LOFTER with OS X 10.10.5, XCode 6.1.1 and gfortran 5.2 and seems like we're doing well on the master branch:

*******************************
UVCDAT  - 2.2.0 - Install Success
Metrics - master - Install Success
*******************************
Please test as follows:
source /Users/durack1/Desktop/PCMDI_METRICS/bin/setup_runtime.sh or .csh
python /Users/durack1/Desktop/PCMDI_METRICS/tmp/metrics/test/test_suite.py
*******************************
Create your customized input_parameters.py (inspire yourself from examples in /Users/durack1/Desktop/PCMDI_METRICS/doc/pcmdi_input_parameters_sample.py
Once you have a parameter file run:
source /Users/durack1/Desktop/PCMDI_METRICS/bin/setup_runtime.sh or .csh
pcmdi_metrics_driver.py -p /path/to/your/edited/parameter_file.py
*******************************
Once everything is ok, you can safely remove the temporary directory: /Users/durack1/Desktop/PCMDI_METRICS/tmp
*******************************
For further information or suggestions please contact the PCMDI Metrics Team @ pcmdi-metrics@llnl.gov
*******************************

It'd be great to get the travis builds and badges back on track however..

durack1 commented 8 years ago

@doutriaux1 looks like it's OS X that is failing on travis and in particular it's a pyexpat dependency of setuptools which doesn't appear to be listed as a dependency

CMake Error at /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build.cmake:56 (message):
  CTEST_FULL_OUTPUT
   Command failed: 1
   'env' 'PYTHONPATH=' 'LD_LIBRARY_PATH=' '/Users/travis/build/PCMDI/_build/PCMDI_METRICS/bin/python' 'setup.py' 'build'
   From /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build-out.log
  -------------------------------------------------
  -------------------------------------------------
   From /Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/setuptools-prefix/src/setuptools-stamp/setuptools-build-err.log
  -------------------------------------------------
  Traceback (most recent call last):
    File "setup.py", line 17, in <module>
      exec(init_file.read(), command_ns)
    File "<string>", line 8, in <module>
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcd-- [download 31% complete]
at/uvcdat_build/build/setuptools/setuptools/__init__.py", line 11, in <module>
      from setuptools.extension import Extension
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/setuptools/extension.py", line 5, in <module>
      from setuptools.dist import _get_unpatched
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/setuptools/dist.py", line 16, in <module>
      import pkg_resources
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 706, in <module>
      class Environment(object):
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 709, in Environment
      def __init__(self, search_path=-- [download 32% complete]
-- [download 64% complete]
-- [download 65% complete]
None, platform=get_supported_platform(), python=PY_MAJOR):
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 148, in get_supported_platform
      plat = 'macosx-%s-%s' % ('.'.join(_macosx_vers()[:2]), m.group(3))
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/build/setuptools/pkg_resources.py", line 241, in _macosx_vers
      version = platform.mac_ver()[0]
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/platform.py", line 809, in mac_ver
      info = _mac_ver_xml()
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/py-- [download 66% complete]
-- [download 67% complete]
thon2.7/platform.py", line 786, in _mac_ver_xml
      pl = plistlib.readPlist(fn)
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plistlib.py", line 78, in readPlist
      rootObject = p.parse(pathOrFile)
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plistlib.py", line 401, in parse
      from xml.parsers.expat import ParserCreate
    File "/Users/travis/build/PCMDI/_build/PCMDI_METRICS/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/xml/parsers/expat.py", line 4, in <module>
      from pyexpat import *
  ImportError: No module named pyexpat

Is there an xml or pyexpat dependency for setuptools that needs to be added here to solve this persistent problem?

durack1 commented 8 years ago

@doutriaux1 it seems there's a failed install somewhere, on my vanilla (non-UV-CDAT) OS X 10.10.5 I get this:

[durack1ml:~] durack1% python
Python 2.7.10 (default, Jul 14 2015, 19:46:27) 
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyexpat
>>> pyexpat.__doc__
'Python wrapper for Expat parser.'
>>> pyexpat.__file__
'/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/pyexpat.so'

So there must be a dependency that isn't listed and therefore a race condition that is persistent with the pcmdi_metrics build?

It does seem that a "broken python install" tends to resonate somewhat - I wonder if there is some race condition being triggered repeatedly here?

durack1 commented 8 years ago

@jbeezley do you think the issue above is the same as garant with https://github.com/UV-CDAT/uvcdat/pull/1652

jbeezley commented 8 years ago

I don't think it is related.

doutriaux1 commented 8 years ago

can't use 5.2

doutriaux1 commented 8 years ago

travis changes expat disappeared from their macs breaking the builds for a while now...

durack1 commented 8 years ago

@doutriaux1 does this need to be added back in to the build, or can we get travis behaving better with an additional command line argument?

doutriaux1 commented 8 years ago

It's a travis thing. No idea how to tweak it.

doutriaux1 commented 8 years ago

it works on all macs I've seen.

durack1 commented 8 years ago

@doutriaux1 we might need to add a requirements.txt additional to the travis.yml

durack1 commented 8 years ago

@doutriaux1 ok, I'm lost I tried to debug the travis environment to see what's happening with pyexpat and it seems the system python has this available - from the OS X build:

> python --version
Python 2.7.5
> ( echo "import pyexpat" ; echo "print pyexpat.EXPAT_VERSION" ) | python
expat_2.1.0
> ( echo "import sys" ; echo "print sys.executable" ) | python
/usr/bin/python

So the build then installs it's own python which fails to include pyexpat, or at least it's not a valid library to import..

Any ideas? I have some working test code at https://github.com/PCMDI/pcmdi_metrics/pull/285

jservonnat commented 8 years ago

Just for your information, I've tried the install on Ciclad here at IPSL and it works.

durack1 commented 8 years ago

@jservonnat thanks for the heads up.. Yeah the issue we're hitting is specific to the test environment that travis provides for their OS X build machines.. The build is working fine using the standard environment on OS X, it'd just be nice to get the travis build tests correctly reporting passes..

jservonnat commented 8 years ago

@durack1 ok!

durack1 commented 8 years ago

@doutriaux1 ok I've run a bunch of tests within https://github.com/PCMDI/pcmdi_metrics/pull/285 and it would seem that the pyexpat import error that's causing the travis build failures is due to a mangled python install by the build - I've been able to load pyexpat using the travis system (python2.7.5), and in a pre-build built python2.7.10 - and I've also checked that this pre-build python2.7.10 can successfully build and install both setuptools1.4 (the version built within UV-CDAT 2.2.0) and the latest setuptools18.5.. So it's a build python issue - I wonder if there's a test to ensure that the build python is complete, or that the python build has completed before setuptools attempts to install..?

doutriaux1 commented 8 years ago

the system one has it because it';s just a binary that they stick there. THe headers seem to be gone form travis so our python cannot build with it.

durack1 commented 8 years ago

@doutriaux1 in the testing in #285 both the python2.7.10 build from source and the setuptools1.4 and setuptools18.5 both install successfully.. So it's a build-environment-specific issue..

I also turned off parallel (-j1) building to make sure things aren't clashing in order..

durack1 commented 8 years ago

@doutriaux1 logs should be broadcasted to the OS X tab at https://travis-ci.org/PCMDI/pcmdi_metrics/jobs/89563783

durack1 commented 8 years ago

And the faster breaking one https://travis-ci.org/PCMDI/pcmdi_metrics/builds/89565901

durack1 commented 8 years ago

@doutriaux1 here's the logs https://travis-ci.org/PCMDI/pcmdi_metrics/jobs/89734921#L1827

durack1 commented 8 years ago

@doutriaux1 @charlesdoutriaux this seems like the failure, there are quite a few failures on the travis OS X builds:

*** WARNING: renaming "pyexpat" since importing it failed: dlopen(build/lib.macosx-10.4-x86_64-2.7/pyexpat.so, 2): Symbol not found: _XML_ErrorString
  Referenced from: build/lib.macosx-10.4-x86_64-2.7/pyexpat.so
  Expected in: flat namespace
 in build/lib.macosx-10.4-x86_64-2.7/pyexpat.so

Not sure if this is available in python2.7.10 but could be worth a try - it was included in the python2.7.1 release to fix an issue with expat2.0.1 which looks eerily like our problem:

- Issue #7609: Add a ``--with-system-expat`` option that causes the system's
  expat library to be used for the pyexpat module instead of the one included
  with Python.
durack1 commented 8 years ago

@doutriaux1 @charlesdoutriaux just confirmed that --with-system-expat is available in python2.7.10 and running a test build with it to see if setuptools1.4 installs fine - I presume it will.. And this should be our travis OS X fix.. See https://github.com/PCMDI/pcmdi_metrics/pull/285 for info..

jservonnat commented 8 years ago

@durack1 @doutriaux1 anything new on #279 and #277 (related with #288 closed)? I really need to install a version of the MP with the units check on salinity... or would you advise another way to do it (rather than taking the last versions of the MP and UVCDAT)?

doutriaux1 commented 8 years ago

@jservonnat build seem t work for us provided you use uvcdat's master tag point. Last I tried test suite was ok. Not sure if it's on a branch or in master though.

durack1 commented 8 years ago

@jservonnat @doutriaux1 the salinity fix was implemented in April last year and is now in the master branch - see here.

Are you not getting this change?

jservonnat commented 8 years ago

I'm actually getting this change but the test fails. 

*******************************
UVCDAT  - master - Install Success
Metrics - master - Install Success
*******************************
Please test as follows:
source /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/bin/setup_runtime.sh or .csh
python /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/test_suite.py
*******************************
Create your customized input_parameters.py (inspire yourself from examples in /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/doc/pcmdi_input_parameters_sample.py
Once you have a parameter file run:
source /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/bin/setup_runtime.sh
pcmdi_metrics_driver.py -p /path/to/your/edited/parameter_file.py
*******************************
Once everything is ok, you can safely remove the temporary directory: /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp
*******************************
For further information or suggestions please contact the PCMDI Metrics Team @ pcmdi-metrics@llnl.gov
*******************************

jservon@ciclad-ng:/data/jservon/PMP_installs/latest_2016-01-12> source /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/bin/setup_runtime.sh
Successfully updated your environment to use UVCDAT
(changes are valid for this session/terminal only)
Version: 2.4.0.rc2-332-g6f64cc6
Location: /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS
jservon@ciclad-ng:/data/jservon/PMP_installs/latest_2016-01-12> python /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/test_suite.py

ERROR import vcs, skipping graphics test...
flake8 (test_flake8.TestFlake8) ... ok
test_from_parameter_file (test_from_param.TestFromParam) ...  parameter file ref is:  ['all']
 refs: [u'default']
 ref is:  [u'default']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 tos   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/numpy/ma/core.py:935: RuntimeWarning: overflow encountered in multiply
  result = self.f(da, db, *args, **kwargs)
 parameter file ref is:  ['all']
 refs: [u'default', u'alternate1', u'alternate2']
 ref is:  [u'default', u'alternate1', u'alternate2']
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
Fatal Python error: Couldn't create autoTLSkey mapping
Fatal Python error: Couldn't create autoTLSkey mapping
comparing: pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/installationTest/tos_2.5x2.5_esmf_linear_metrics.json
Failing line: -                    "bias_xy_djf_GLB": "0.29",

Failing line: -                    "bias_xy_djf_SHEX": "2.26",

Failing line: -                    "bias_xy_jja_SHEX": "0.70",

Failing line: -                    "bias_xy_mam_GLB": "0.13",

Failing line: -                    "bias_xy_mam_NHEX": "-0.95",

Failing line: -                    "bias_xy_son_NHEX": "-1.18",

Failing line: -                    "bias_xy_son_SHEX": "0.67",

Failing line: -                    "mae_xy_djf_NHEX": "1.30",

Failing line: -                    "mae_xy_jja_NHEX": "1.11",

Failing line: -                    "mae_xy_mam_NHEX": "1.18",

Failing line: -                    "mae_xy_son_NHEX": "1.32",

Failing line: -                    "rms_xy_ann_NHEX": "1.87",

Failing line: -                    "rms_xy_ann_SHEX": "1.61",

Failing line: -                    "rms_xy_djf_GLB": "1.83",

Failing line: -                    "rms_xy_djf_NHEX": "2.18",

Failing line: -                    "rms_xy_jja_TROPICS": "1.19",

Failing line: -                    "rms_xy_mam_NHEX": "1.98",

Failing line: -                    "rms_xy_son_NHEX": "2.09",

Failing line: -                    "rms_xy_son_TROPICS": "1.28",

Failing line: -                    "rms_xyt_ann_NHEX": "2.05",

Failing line: -                    "rms_xyt_ann_TROPICS": "1.30",

FAIL
test_from_parameter_file (test_from_param.TestFromParam) ...  parameter file ref is:  ['default']
 ref is:  ['default']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
 Error while processing variable tas:
    not all arguments converted during string formatting
ok
test_from_parameter_file (test_from_param.TestFromParam) ... CDMS system error: No such file or directory
CDMS I/O error: Opening file /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftflf_not_here_GFDL-ESM2G.nc
 No mask for  /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftflf_not_here_GFDL-ESM2G.nc
 parameter file ref is:  ['default']
 ref is:  ['default']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
 Error while processing variable tas:
    not all arguments converted during string formatting
ok
test_from_parameter_file (test_from_param.TestFromParam) ... CDMS system error: No such file or directory
CDMS I/O error: Opening file /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftflf_not_here_GFDL-ESM2G.nc
 No mask for  /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftflf_not_here_GFDL-ESM2G.nc
 parameter file ref is:  ['default']
 ref is:  ['default']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
 Error while processing variable tas:
    not all arguments converted during string formatting
ok
test_from_parameter_file (test_from_param.TestFromParam) ... CDMS system error: No such file or directory
CDMS I/O error: Opening file /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftlf_GFDL-ESM2G_fx_historical_r0i0p0_198501-200512-clim.nc
 No mask for  /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftlf_GFDL-ESM2G_fx_historical_r0i0p0_198501-200512-clim.nc
 Error while processing variable aVarThatIsNot:
    'aVarThatIsNot'
 parameter file ref is:  ['default']
 ref is:  ['default']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 tos   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    default
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/numpy/ma/core.py:935: RuntimeWarning: overflow encountered in multiply
  result = self.f(da, db, *args, **kwargs)
^@CDMS system error: No such file or directory
CDMS I/O error: Opening file /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/obs/fx/sftlf/UKMETOFFICE-HadISST-v1-1/sftlf_pcmdi-metrics_fx_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc
 Could not find obs mask, generating
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/cdms2/avariable.py:1088: Warning:
avariable.regrid: We chose regridMethod = linear for you among the following choices:
    'conserve' or 'linear' or 'patch'
  warnings.warn(message, Warning)
 OBS SHAPE IS  (12, 72, 144)
 Error while processing variable tos:
    not all arguments converted during string formatting
ok
test_from_parameter_file (test_from_param.TestFromParam) ...  parameter file ref is:  ['ERAINT']
 ref is:  ['ERAINT']
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    ERAINT
 OBS SHAPE IS  (12, 72, 144)
 tas   GFDL-ESM2G   (12, 72, 144)   (12, 72, 144)    ERAINT
Fatal Python error: Couldn't create autoTLSkey mapping
ok
test_from_parameter_file (test_from_param.TestFromParam) ... CDMS system error: No such file or directory
CDMS I/O error: Opening file /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftlf_GFDL-CM3_fx_historical_000101-010012-clim.nc
 No mask for  /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/data/sftlf_GFDL-CM3_fx_historical_000101-010012-clim.nc
 parameter file ref is:  ['JPL-Aquarius-v2']
 ref is:  ['JPL-Aquarius-v2']
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1241: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (srcMaskValues != None):
/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/lib/python2.7/site-packages/ESMP/src/ESMP_API.py:1248: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if (dstMaskValues != None):
 OBS SHAPE IS  (12, 72, 144)
 sos   GFDL-CM3   (12, 72, 144)   (12, 72, 144)    JPL-Aquarius-v2
 Error while processing variable sos:
    not all arguments converted during string formatting
ok

======================================================================
FAIL: test_from_parameter_file (test_from_param.TestFromParam)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/test_from_param.py", line 68, in test_from_parameter_file
    self.assertTrue(ok)
AssertionError: False is not true

----------------------------------------------------------------------
Ran 8 tests in 118.542s

FAILED (failures=1)

This is what I have in the output directory of the test:

jservon@ciclad-ng:/data/jservon/PMP_installs/latest_2016-01-12> ls pcmdi_install_test_results/metrics_results/*/*
pcmdi_install_test_results/metrics_results/gensftlfTest/errors_log.txt
pcmdi_install_test_results/metrics_results/installationTest/errors_log.txt
pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json
pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.txt
pcmdi_install_test_results/metrics_results/keep_going_on_error_varnameTest/errors_log.txt
pcmdi_install_test_results/metrics_results/nosftlfTest/errors_log.txt
pcmdi_install_test_results/metrics_results/obsByNameTest/errors_log.txt
pcmdi_install_test_results/metrics_results/salinityTest/errors_log.txt
pcmdi_install_test_results/metrics_results/unitsTest/errors_log.txt

And here is the version controlling section in my install_metrics.bash:

main() {
    ## Generic Build Parameters
    cmake_repo=git://cmake.org/cmake.git
    cmake_repo_http=http://cmake.org/cmake.git
    cmake_repo_https=https://cmake.org/cmake.git
    cmake_min_version=2.8.11
    cmake_max_version=2.9
    cmake_version=2.8.12
    force_install=0
    DEBUG=1
    cdat_repo=git://github.com/UV-CDAT/uvcdat.git
    cdat_repo_http=http://github.com/UV-CDAT/uvcdat.git
    cdat_repo_https=https://github.com/UV-CDAT/uvcdat.git
    #cdat_version="2.1.0"
    cdat_version="master"
    metrics_repo=git://github.com/PCMDI/pcmdi_metrics.git
    metrics_repo_http=http://github.com/PCMDI/pcmdi_metrics.git
    metrics_repo_https=https://github.com/PCMDI/pcmdi_metrics.git
    #metrics_checkout="v1.0.0"
    metrics_checkout="master"

Any thoughts?

durack1 commented 8 years ago

@jservonnat thanks for this, it's failing due to differences in the numbers calculated by the test, vs what we have in the repo for the test results - the number comparisons - so:

comparing: pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json /data/jservon/PMP_installs/latest_2016-01-12/PCMDI_METRICS/tmp/metrics/test/pcmdi/installationTest/tos_2.5x2.5_esmf_linear_metrics.json
Failing line: -                    "bias_xy_djf_GLB": "0.29", VS some number you calculate 
Failing line: -                    "bias_xy_djf_SHEX": "2.26", ditto
Failing line: -                    "bias_xy_jja_SHEX": "0.70", ditto
...

Can you post your pcmdi_install_test_results/metrics_results/installationTest/tos_2.5x2.5_esmf_linear_metrics.json file here too?

jservonnat commented 8 years ago

There it is:

{
    "References": {
        "default": {
            "RefName": "UKMETOFFICE-HadISST-v1-1",
            "MD5sum": "41833b403cad7052773dd933d1798a14",
            "period": "198002-200501",
            "filename": "tos_pcmdi-metrics_Omon_UKMETOFFICE-HadISST-v1-1_198002-200501-clim.nc",
            "shape": "(12, 180, 360)",
            "CMIP_CMOR_TABLE": "Omon",
            "RefTrackingDate": "Wed Jan 15 10:57:20 2014"
        }
    },
    "RegionalMasking": {
        "global": null
    },
    "GridInfo": {
        "GridResolution": [
            72,
            144
        ],
        "GridName": "2.5x2.5",
        "RegridMethod": "linear",
        "RegridTool": "esmf"
    },
    "GFDL-ESM2G": {
        "InputClimatologyFileName": "tos_GFDL-ESM2G_Omon_historical_r1i1p1_198501-200512-clim.nc",
        "SimulationDescription": {
            "Center": "N/A",
            "ModellingGroup": "NOAA GFDL",
            "ModelFreeSpace": "N/A",
            "MIPTable": "Omon",
            "creation_date": "2012-01-10T20:19:59Z",
            "ModelActivity": "CMIP5",
            "Experiment": "historical",
            "Realization": "r1i1p1",
            "Model": "GFDL-ESM2G",
            "Login": "N/A",
            "SimTrackingDate": "2012-01-10T20:19:59Z"
        },
        "defaultReference": {
            "source": "UKMETOFFICE-HadISST-v1-1",
            "r1i1p1": {
                "global": {
                    "bias_xy_ann_GLB": "-0.03",
                    "bias_xy_ann_NHEX": "-0.97",
                    "bias_xy_ann_SHEX": "1.33",
                    "bias_xy_ann_TROPICS": "-0.59",
                    "bias_xy_djf_GLB": "0.30",
                    "bias_xy_djf_NHEX": "-1.00",
                    "bias_xy_djf_SHEX": "2.27",
                    "bias_xy_djf_TROPICS": "-0.59",
                    "bias_xy_jja_GLB": "-0.22",
                    "bias_xy_jja_NHEX": "-0.86",
                    "bias_xy_jja_SHEX": "0.69",
                    "bias_xy_jja_TROPICS": "-0.57",
                    "bias_xy_mam_GLB": "0.14",
                    "bias_xy_mam_NHEX": "-0.94",
                    "bias_xy_mam_SHEX": "1.71",
                    "bias_xy_mam_TROPICS": "-0.55",
                    "bias_xy_son_GLB": "-0.34",
                    "bias_xy_son_NHEX": "-1.19",
                    "bias_xy_son_SHEX": "0.66",
                    "bias_xy_son_TROPICS": "-0.64",
                    "cor_xy_djf_GLB": "0.98",
                    "cor_xy_djf_NHEX": "0.97",
                    "cor_xy_djf_SHEX": "0.99",
                    "cor_xy_djf_TROPICS": "0.90",
                    "cor_xy_jja_GLB": "0.99",
                    "cor_xy_jja_NHEX": "0.99",
                    "cor_xy_jja_SHEX": "0.98",
                    "cor_xy_jja_TROPICS": "0.94",
                    "cor_xy_mam_GLB": "0.99",
                    "cor_xy_mam_NHEX": "0.98",
                    "cor_xy_mam_SHEX": "0.99",
                    "cor_xy_mam_TROPICS": "0.90",
                    "cor_xy_son_GLB": "0.99",
                    "cor_xy_son_NHEX": "0.99",
                    "cor_xy_son_SHEX": "0.98",
                    "cor_xy_son_TROPICS": "0.93",
                    "cor_xyt_ann_GLB": "0.99",
                    "cor_xyt_ann_NHEX": "0.98",
                    "cor_xyt_ann_SHEX": "0.98",
                    "cor_xyt_ann_TROPICS": "0.92",
                    "custom_ref_min": 271.27384426614753,
                    "mae_xy_ann_GLB": "1.15",
                    "mae_xy_ann_NHEX": "1.14",
                    "mae_xy_ann_SHEX": "1.46",
                    "mae_xy_ann_TROPICS": "0.89",
                    "mae_xy_djf_GLB": "1.53",
                    "mae_xy_djf_NHEX": "1.29",
                    "mae_xy_djf_SHEX": "2.31",
                    "mae_xy_djf_TROPICS": "0.99",
                    "mae_xy_jja_GLB": "1.01",
                    "mae_xy_jja_NHEX": "1.12",
                    "mae_xy_jja_SHEX": "1.00",
                    "mae_xy_jja_TROPICS": "0.95",
                    "mae_xy_mam_GLB": "1.30",
                    "mae_xy_mam_NHEX": "1.17",
                    "mae_xy_mam_SHEX": "1.74",
                    "mae_xy_mam_TROPICS": "1.00",
                    "mae_xy_son_GLB": "1.10",
                    "mae_xy_son_NHEX": "1.33",
                    "mae_xy_son_SHEX": "1.01",
                    "mae_xy_son_TROPICS": "1.02",
                    "rms_xy_ann_GLB": "1.42",
                    "rms_xy_ann_NHEX": "1.86",
                    "rms_xy_ann_SHEX": "1.62",
                    "rms_xy_ann_TROPICS": "1.10",
                    "rms_xy_djf_GLB": "1.84",
                    "rms_xy_djf_NHEX": "2.17",
                    "rms_xy_djf_SHEX": "2.41",
                    "rms_xy_djf_TROPICS": "1.24",
                    "rms_xy_jja_GLB": "1.35",
                    "rms_xy_jja_NHEX": "1.73",
                    "rms_xy_jja_SHEX": "1.36",
                    "rms_xy_jja_TROPICS": "1.20",
                    "rms_xy_mam_GLB": "1.63",
                    "rms_xy_mam_NHEX": "1.97",
                    "rms_xy_mam_SHEX": "1.90",
                    "rms_xy_mam_TROPICS": "1.30",
                    "rms_xy_son_GLB": "1.47",
                    "rms_xy_son_NHEX": "2.08",
                    "rms_xy_son_SHEX": "1.35",
                    "rms_xy_son_TROPICS": "1.29",
                    "rms_xyt_ann_GLB": "1.63",
                    "rms_xyt_ann_NHEX": "2.04",
                    "rms_xyt_ann_SHEX": "1.86",
                    "rms_xyt_ann_TROPICS": "1.31",
                    "some_custom": 1.5
                }
            }
        },
        "InputClimatologyMD5": "974a3339d34fcdd6a68d6e135f72cd78"
    },
durack1 commented 8 years ago

@jservonnat @doutriaux1 ok so we have:

metric: repo # | test #
"bias_xy_djf_GLB": "0.29" | 0.30
"bias_xy_djf_SHEX": "2.26" | 2.27
"bias_xy_jja_SHEX": "0.70" | 0.69
"bias_xy_mam_GLB": "0.13" | 0.14
"bias_xy_mam_NHEX": "-0.95" | -0.94
"bias_xy_son_NHEX": "-1.18" | -1.19
"bias_xy_son_SHEX": "0.67" | 0.66
"mae_xy_djf_NHEX": "1.30" | 1.29
"mae_xy_jja_NHEX": "1.11" | 1.12
"mae_xy_mam_NHEX": "1.18" | 1.17
...

And we just have a rounding issue - it's something that @doutriaux1 and I have been aware of and it's difficult to fix across all the systems we're currently trying to test for..

doutriaux1 commented 8 years ago

@durack1 I could try to parse the error string and do a diff on numbers... Or we could maybe increase the precision in json files to 3 digits. @gleckler1 what do you think. We would probably still run into the issue (less often though) but a diff at the 3rd digit probably would be less worrisome?

jservonnat commented 8 years ago

Ok so I'll carry on my tests without worrying too much about it. Thank you guys, I'll keep you in touch!

durack1 commented 8 years ago

@doutriaux1 got this issue too:

[ 84%] Performing install step for 'MyProxyClient'
CMake Error at /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/MyProxyClient-prefix/src/MyProxyClient-stamp/MyProxyClient-install.cmake:56 (message):
  CTEST_FULL_OUTPUT

   Command failed: 1
   'env' 'LD_LIBRARY_PATH=/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/paraview-.:' 'CFLAGS=-I/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/include -I/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/libffi-3.1/include   ' 'LDFLAGS=-L/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib -L/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64  -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64 -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib' 'PKG_CONFIG_PATH=/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/share/pkgconfig:/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/pkgconfig:' 'PYTHONPATH=/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib/python2.7/site-packages' 'LDFLAGS=-L/usr/lib64 -L/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib -L/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64  -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib64 -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib -Wl,-rpath,/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib' 'CFLAGS=-I/usr/include -I/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/include -I/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/Externals/lib/libffi-3.1/include   ' '/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/bin/python' 'setup.py' 'install' '--prefix=/export/durack1/160216_pcmdi_metrics/PCMDI_METRICS'
   From /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/MyProxyClient-prefix/src/MyProxyClient-stamp/MyProxyClient-install-out.log

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

  running install

  running bdist_egg

  running egg_info

  writing requirements to MyProxyClient.egg-info/requires.txt

  writing MyProxyClient.egg-info/PKG-INFO

  writing top-level names to MyProxyClient.egg-info/top_level.txt

  writing dependency_links to MyProxyClient.egg-info/dependency_links.txt

  writing entry points to MyProxyClient.egg-info/entry_points.txt

  reading manifest file 'MyProxyClient.egg-info/SOURCES.txt'

  writing manifest file 'MyProxyClient.egg-info/SOURCES.txt'

  installing library code to build/bdist.linux-x86_64/egg

  running install_lib

  running build_py

  creating build

  creating build/lib

  creating build/lib/myproxy

  copying myproxy/__init__.py -> build/lib/myproxy

  copying myproxy/client.py -> build/lib/myproxy

  copying myproxy/script.py -> build/lib/myproxy

  creating build/lib/myproxy/test

  copying myproxy/test/__init__.py -> build/lib/myproxy/test

  copying myproxy/test/test_myproxyclient.py -> build/lib/myproxy/test

  creating build/lib/myproxy/utils

  copying myproxy/utils/__init__.py -> build/lib/myproxy/utils

  copying myproxy/utils/openssl.py -> build/lib/myproxy/utils

  creating build/bdist.linux-x86_64

  creating build/bdist.linux-x86_64/egg

  creating build/bdist.linux-x86_64/egg/myproxy

  copying build/lib/myproxy/__init__.py ->
  build/bdist.linux-x86_64/egg/myproxy

  copying build/lib/myproxy/client.py -> build/bdist.linux-x86_64/egg/myproxy

  creating build/bdist.linux-x86_64/egg/myproxy/test

  copying build/lib/myproxy/test/__init__.py ->
  build/bdist.linux-x86_64/egg/myproxy/test

  copying build/lib/myproxy/test/test_myproxyclient.py ->
  build/bdist.linux-x86_64/egg/myproxy/test

  creating build/bdist.linux-x86_64/egg/myproxy/utils

  copying build/lib/myproxy/utils/__init__.py ->
  build/bdist.linux-x86_64/egg/myproxy/utils

  copying build/lib/myproxy/utils/openssl.py ->
  build/bdist.linux-x86_64/egg/myproxy/utils

  copying build/lib/myproxy/script.py -> build/bdist.linux-x86_64/egg/myproxy

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/__init__.py to
  __init__.pyc

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/client.py to client.pyc

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/test/__init__.py to
  __init__.pyc

  byte-compiling
  build/bdist.linux-x86_64/egg/myproxy/test/test_myproxyclient.py to
  test_myproxyclient.pyc

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/utils/__init__.py to
  __init__.pyc

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/utils/openssl.py to
  openssl.pyc

  byte-compiling build/bdist.linux-x86_64/egg/myproxy/script.py to script.pyc

  creating build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/PKG-INFO ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/SOURCES.txt ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/dependency_links.txt ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/entry_points.txt ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/not-zip-safe ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/requires.txt ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  copying MyProxyClient.egg-info/top_level.txt ->
  build/bdist.linux-x86_64/egg/EGG-INFO

  creating dist

  creating 'dist/MyProxyClient-1.3.0-py2.7.egg' and adding
  'build/bdist.linux-x86_64/egg' to it

  removing 'build/bdist.linux-x86_64/egg' (and everything under it)

  Processing MyProxyClient-1.3.0-py2.7.egg

  creating
  /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib/python2.7/site-packages/MyProxyClient-1.3.0-py2.7.egg

  Extracting MyProxyClient-1.3.0-py2.7.egg to
  /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib/python2.7/site-packages

  Adding MyProxyClient 1.3.0 to easy-install.pth file

  Installing myproxyclient script to
  /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/bin

  Installed
  /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/lib/python2.7/site-packages/MyProxyClient-1.3.0-py2.7.egg

  Processing dependencies for MyProxyClient==1.3.0

  Searching for cryptography>=0.7

  Reading https://pypi.python.org/simple/cryptography/

  Couldn't retrieve index page for 'cryptography'

  Scanning index of all packages (this may take a while)

  Reading https://pypi.python.org/simple/

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

   From /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/MyProxyClient-prefix/src/MyProxyClient-stamp/MyProxyClient-install-err.log

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

  Download error on https://pypi.python.org/simple/cryptography/: [SSL:
  CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some
  packages may not be found!

  Download error on https://pypi.python.org/simple/: [SSL:
  CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some
  packages may not be found!

  No local packages or download links found for cryptography>=0.7

  error: Could not find suitable distribution for
  Requirement.parse('cryptography>=0.7')

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

make[2]: *** [MyProxyClient-prefix/src/MyProxyClient-stamp/MyProxyClient-install] Error 1
make[1]: *** [CMakeFiles/MyProxyClient.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
-- FFMPEG build command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/FFMPEG-prefix/src/FFMPEG-stamp/FFMPEG-build-*.log

[ 84%] Performing install step for 'FFMPEG'
-- FFMPEG install command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/FFMPEG-prefix/src/FFMPEG-stamp/FFMPEG-install-*.log

[ 84%] Completed 'FFMPEG'
[ 84%] Built target FFMPEG
-- SCIPY configure command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/SCIPY-prefix/src/SCIPY-stamp/SCIPY-configure-*.log

[ 85%] Performing build step for 'SCIPY'
-- ESMF build command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/ESMF-prefix/src/ESMF-stamp/ESMF-build-*.log

[ 85%] Performing install step for 'ESMF'
-- ESMF install command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/ESMF-prefix/src/ESMF-stamp/ESMF-install-*.log

[ 86%] Completed 'ESMF'
[ 86%] Built target ESMF
-- SCIPY build command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/SCIPY-prefix/src/SCIPY-stamp/SCIPY-build-*.log

[ 87%] Performing install step for 'SCIPY'
-- SCIPY install command succeeded.  See also /export/durack1/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat_build/SCIPY-prefix/src/SCIPY-stamp/SCIPY-install-*.log

[ 87%] Completed 'SCIPY'
[ 87%] Built target SCIPY
make: *** [all] Error 2
 ERROR: Could not compile (make) cdat code
~/160216_pcmdi_metrics/PCMDI_METRICS/tmp/uvcdat/uvcdat ~/160216_pcmdi_metrics/PCMDI_METRICS/tmp/metrics

Sorry...
This action did not complete successfully
Please try to re-run this task until successful before continuing further

 ERROR: Could not compile (make) cdat code
~/160216_pcmdi_metrics/PCMDI_METRICS/tmp/metrics

Sorry...
This action did not complete successfully
Please try to re-run this task until successful before continuing further
durack1 commented 8 years ago

@doutriaux1 it's likely cryptography needs to be added as a dependency of MyProxyClient here

durack1 commented 8 years ago

This is a duplicate of the upstream https://github.com/UV-CDAT/uvcdat/issues/1838

durack1 commented 8 years ago

@doutriaux1 https://github.com/UV-CDAT/uvcdat/pull/1840 should fix the standing issues that I was having - if you can then implement the test tolerances I think we're set and all tests should also pass - and then we can finally close this issue after nearly 6 months

durack1 commented 8 years ago

Actually @doutriaux1 this is what I get now:

Ran 8 tests in 8.877s
FAILED (failures=5)

So we're almost good on ocean (we've got some missing test files, and also need to update after @gleckler1 tweaked the obs.json - see the attached log file - this is the current difference between master and climo_script [climo_script passes]), and the tolerances do need to be implemented so that @jservonnat can get the tests passing on his environment

160217_pcmdi_metrics-testlog.txt