{"action":"created","issue":{"url":"https://api.github.com/repos/sherpa/sherpa/issues/507","repository_url":"https://api.github.com/repos/sherpa/sherpa","labels_url":"https://api.github.com/repos/sherpa/sherpa/issues/507/labels{/name}","comments_url":"https://api.github.com/repos/sherpa/sherpa/issues/507/comments","events_url":"https://api.github.com/repos/sherpa/sherpa/issues/507/events","html_url":"https://github.com/sherpa/sherpa/issues/507","id":367451421,"node_id":"MDU6SXNzdWUzNjc0NTE0MjE=","number":507,"title":"pileup test fails with XSPEC: covariance matrix is different","user":{"login":"DougBurke","id":224638,"node_id":"MDQ6VXNlcjIyNDYzOA==","avatar_url":"https://avatars3.githubusercontent.com/u/224638?v=4","gravatar_id":"","url":"https://api.github.com/users/DougBurke","html_url":"https://github.com/DougBurke","followers_url":"https://api.github.com/users/DougBurke/followers","following_url":"https://api.github.com/users/DougBurke/following{/other_user}","gists_url":"https://api.github.com/users/DougBurke/gists{/gist_id}","starred_url":"https://api.github.com/users/DougBurke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DougBurke/subscriptions","organizations_url":"https://api.github.com/users/DougBurke/orgs","repos_url":"https://api.github.com/users/DougBurke/repos","events_url":"https://api.github.com/users/DougBurke/events{/privacy}","received_events_url":"https://api.github.com/users/DougBurke/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-10-06T12:09:02Z","updated_at":"2018-10-19T17:38:12Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"# Summary\r\n\r\nThe replacement of the Fortran optimisation code with C++ has lead to the pileup test to fail with XSPEC 12.9.1p. The errors are in the diagonal elements of the covariance matrix; the best-fit parameters and statistic are the same (within the error tolerance). What is is about my system that is different enough to the Travis tests?\r\n\r\n# Details\r\n\r\nI have master checked out - i.e. 3540951 - built against XSPEC 12.9.1p\r\n\r\n```\r\n% git rev-parse HEAD\r\n354095107245d5190c6cfe54741c5f4c2d4f87f9\r\n% python -c 'from sherpa.astro import xspec; print(xspec.get_xsversion());'\r\n12.9.1p\r\n``` \r\n\r\nThe pileup test fails with:\r\n\r\n```\r\n% python setup.py test -a sherpa/astro/tests/test_astro.py::test_threads::test_pileup\r\nrunning sherpa_config\r\nwarning: sherpa_config: built configure string['./configure', '--prefix=/home/djburke/sherpa/sherpa-fix-sphinx-docs/build', '--with-pic', '--enable-standalone', '--disable-maintainer-mode', '--enable-stuberrorlib', '--disable-shared', '--enable-shared=libgrp,stklib', '--enable-fftw', '--enable-region', '--enable-group', '--enable-stk', '--enable-wcs']\r\n\r\nrunning xspec_config\r\nFound XSPEC version: 12.9.1p\r\nrunning develop\r\nrunning build_scripts\r\nrunning egg_info\r\nrunning build_src\r\nbuild_src\r\nbuilding extension \"sherpa.estmethods._est_funcs\" sources\r\nbuilding extension \"sherpa.utils._utils\" sources\r\nbuilding extension \"sherpa.models._modelfcts\" sources\r\nbuilding extension \"sherpa.optmethods._saoopt\" sources\r\nbuilding extension \"sherpa.optmethods._tstoptfct\" sources\r\nbuilding extension \"sherpa.stats._statfcts\" sources\r\nbuilding extension \"sherpa.utils.integration\" sources\r\nbuilding extension \"sherpa.astro.models._modelfcts\" sources\r\nbuilding extension \"sherpa.astro.utils._pileup\" sources\r\nbuilding extension \"sherpa.astro.utils._utils\" sources\r\nbuilding extension \"sherpa.utils._psf\" sources\r\nbuilding extension \"sherpa.astro.utils._wcs\" sources\r\nbuilding extension \"sherpa.astro.utils._region\" sources\r\nbuilding extension \"sherpa.astro.xspec._xspec\" sources\r\nbuilding data_files sources\r\nbuild_src: building npy-pkg config files\r\nwriting sherpa.egg-info/PKG-INFO\r\nwriting dependency_links to sherpa.egg-info/dependency_links.txt\r\nwriting entry points to sherpa.egg-info/entry_points.txt\r\nwriting requirements to sherpa.egg-info/requires.txt\r\nwriting top-level names to sherpa.egg-info/top_level.txt\r\nreading manifest file 'sherpa.egg-info/SOURCES.txt'\r\nreading manifest template 'MANIFEST.in'\r\nwriting manifest file 'sherpa.egg-info/SOURCES.txt'\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\nCreating /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages/sherpa.egg-link (link to .)\r\nsherpa 4.10.0+177.g3540951.dirty is already the active version in easy-install.pth\r\nInstalling sherpa_smoke script to /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/bin\r\nInstalling sherpa_test script to /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/bin\r\n\r\nInstalled /home/djburke/sherpa/sherpa-fix-sphinx-docs\r\nProcessing dependencies for sherpa==4.10.0+177.g3540951.dirty\r\nSearching for six==1.11.0\r\nBest match: six 1.11.0\r\nAdding six 1.11.0 to easy-install.pth file\r\n\r\nUsing /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages\r\nSearching for numpy==1.15.2\r\nBest match: numpy 1.15.2\r\nAdding numpy 1.15.2 to easy-install.pth file\r\n\r\nUsing /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages\r\nFinished processing dependencies for sherpa==4.10.0+177.g3540951.dirty\r\nrunning test\r\nSearching for pytest-xvfb\r\nBest match: pytest-xvfb 1.1.0\r\nProcessing pytest_xvfb-1.1.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/pytest_xvfb-1.1.0-py3.6.egg\r\nSearching for mock\r\nBest match: mock 2.0.0\r\nProcessing mock-2.0.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/mock-2.0.0-py3.6.egg\r\nSearching for pyvirtualdisplay>=0.2.1\r\nBest match: PyVirtualDisplay 0.2.1\r\nProcessing PyVirtualDisplay-0.2.1-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/PyVirtualDisplay-0.2.1-py3.6.egg\r\nSearching for pbr>=0.11\r\nBest match: pbr 4.3.0\r\nProcessing pbr-4.3.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/pbr-4.3.0-py3.6.egg\r\nSearching for EasyProcess\r\nBest match: EasyProcess 0.2.3\r\nProcessing EasyProcess-0.2.3-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/EasyProcess-0.2.3-py3.6.egg\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\n======================================================================= test session starts ========================================================================\r\nplatform linux -- Python 3.6.6, pytest-3.8.1, py-1.6.0, pluggy-0.7.1\r\nrootdir: /home/djburke/sherpa/sherpa-fix-sphinx-docs, inifile: pytest.ini\r\nplugins: xvfb-1.1.0, remotedata-0.3.0, openfiles-0.3.0, doctestplus-0.1.3, arraydiff-0.2\r\ncollected 1 item                                                                                                                                                   \r\n\r\nsherpa/astro/tests/test_astro.py F                                                                                                                           [100%]\r\n\r\n============================================================================= FAILURES =============================================================================\r\n_____________________________________________________________________ test_threads.test_pileup _____________________________________________________________________\r\n\r\nself = <test_astro.test_threads testMethod=test_pileup>\r\n\r\n    @requires_fits\r\n    @requires_xspec\r\n    def test_pileup(self):\r\n        self.run_thread('pileup')\r\n    \r\n        fr = ui.get_fit_results()\r\n        covarerr = sqrt(fr.extra_output['covar'].diagonal())\r\n>       assert covarerr[0] == approx(684.056 , rel=1e-4)\r\nE       AssertionError: assert 694.3746848979197 == 684.056 ± 6.8e-02\r\nE        +  where 684.056 ± 6.8e-02 = approx(684.056, rel=0.0001)\r\n\r\nsherpa/astro/tests/test_astro.py:218: AssertionError\r\n----------------------------------------------------------------------- Captured stdout call -----------------------------------------------------------------------\r\n Solar Abundance Vector set to angr:  Anders E. & Grevesse N. Geochimica et Cosmochimica Acta 53, 197 (1989)\r\n Cross Section Table set to bcmc:  Balucinska-Church and McCammon, 1998\r\n===================================================================== 1 failed in 0.67 seconds =====================================================================\r\n```\r\n\r\nI am using python=3.6,numpy=1.15, built with gcc 7.3.0.\r\n\r\nIf I switch to a commit before the great-Fortran-removal then the test passes - that is with\r\n\r\n```\r\n% git checkout 03e3fb5ad872470fae79c4e8433c9ee42ef74441\r\nNote: checking out '03e3fb5ad872470fae79c4e8433c9ee42ef74441'.\r\n\r\nYou are in 'detached HEAD' state. You can look around, make experimental\r\nchanges and commit them, and you can discard any commits you make in this\r\nstate without impacting any branches by performing another checkout.\r\n\r\nIf you want to create a new branch to retain commits you create, you may\r\ndo so (now or later) by using -b with the checkout command again. Example:\r\n\r\n  git checkout -b <new-branch-name>\r\n\r\nHEAD is now at 03e3fb5 Add doc-build status to README.md\r\n```\r\n\r\nI get the following from the test:\r\n\r\n```\r\n% python setup.py test -a sherpa/astro/tests/test_astro.py::test_threads::test_pileup\r\nrunning sherpa_config\r\nwarning: sherpa_config: built configure string['./configure', '--prefix=/home/djburke/sherpa/sherpa-fix-sphinx-docs/build', '--with-pic', '--enable-standalone', '--disable-maintainer-mode', '--enable-stuberrorlib', '--disable-shared', '--enable-shared=libgrp,stklib', '--enable-fftw', '--enable-region', '--enable-group', '--enable-stk', '--enable-wcs']\r\n\r\nrunning xspec_config\r\nFound XSPEC version: 12.9.1p\r\nrunning develop\r\nrunning build_scripts\r\nrunning egg_info\r\nrunning build_src\r\nbuild_src\r\nbuilding extension \"sherpa.estmethods._est_funcs\" sources\r\nbuilding extension \"sherpa.utils._utils\" sources\r\nbuilding extension \"sherpa.models._modelfcts\" sources\r\nbuilding extension \"sherpa.optmethods._saoopt\" sources\r\nbuilding extension \"sherpa.optmethods._tstoptfct\" sources\r\nbuilding extension \"sherpa.stats._statfcts\" sources\r\nbuilding extension \"sherpa.utils.integration\" sources\r\nbuilding extension \"sherpa.astro.models._modelfcts\" sources\r\nbuilding extension \"sherpa.astro.utils._pileup\" sources\r\nbuilding extension \"sherpa.astro.utils._utils\" sources\r\nbuilding extension \"sherpa.optmethods._minpack\" sources\r\nf2py options: []\r\n  adding 'build/src.linux-x86_64-3.6/sherpa/optmethods/src/minpack/fortranobject.c' to sources.\r\n  adding 'build/src.linux-x86_64-3.6/sherpa/optmethods/src/minpack' to include_dirs.\r\n  adding 'sherpa/optmethods/src/minpack/_minpack-f2pywrappers.f' to sources.\r\nbuilding extension \"sherpa.optmethods._minim\" sources\r\nf2py options: []\r\n  adding 'build/src.linux-x86_64-3.6/sherpa/optmethods/src/fortranobject.c' to sources.\r\n  adding 'build/src.linux-x86_64-3.6/sherpa/optmethods/src' to include_dirs.\r\nbuilding extension \"sherpa.utils._psf\" sources\r\nbuilding extension \"sherpa.astro.utils._wcs\" sources\r\nbuilding extension \"sherpa.astro.utils._region\" sources\r\nbuilding extension \"sherpa.astro.xspec._xspec\" sources\r\nbuilding data_files sources\r\nbuild_src: building npy-pkg config files\r\nwriting sherpa.egg-info/PKG-INFO\r\nwriting dependency_links to sherpa.egg-info/dependency_links.txt\r\nwriting entry points to sherpa.egg-info/entry_points.txt\r\nwriting requirements to sherpa.egg-info/requires.txt\r\nwriting top-level names to sherpa.egg-info/top_level.txt\r\nreading manifest file 'sherpa.egg-info/SOURCES.txt'\r\nreading manifest template 'MANIFEST.in'\r\nwriting manifest file 'sherpa.egg-info/SOURCES.txt'\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\nget_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'\r\ncustomize Gnu95FCompiler\r\nFound executable /usr/bin/gfortran\r\ncustomize Gnu95FCompiler\r\ncustomize Gnu95FCompiler using build_ext\r\nCreating /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages/sherpa.egg-link (link to .)\r\nsherpa 4.10.0+149.g03e3fb5.dirty is already the active version in easy-install.pth\r\nInstalling sherpa_smoke script to /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/bin\r\nInstalling sherpa_test script to /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/bin\r\n\r\nInstalled /home/djburke/sherpa/sherpa-fix-sphinx-docs\r\nProcessing dependencies for sherpa==4.10.0+149.g03e3fb5.dirty\r\nSearching for six==1.11.0\r\nBest match: six 1.11.0\r\nAdding six 1.11.0 to easy-install.pth file\r\n\r\nUsing /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages\r\nSearching for numpy==1.15.2\r\nBest match: numpy 1.15.2\r\nAdding numpy 1.15.2 to easy-install.pth file\r\n\r\nUsing /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs/lib/python3.6/site-packages\r\nFinished processing dependencies for sherpa==4.10.0+149.g03e3fb5.dirty\r\nrunning test\r\nSearching for pytest-xvfb\r\nBest match: pytest-xvfb 1.1.0\r\nProcessing pytest_xvfb-1.1.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/pytest_xvfb-1.1.0-py3.6.egg\r\nSearching for mock\r\nBest match: mock 2.0.0\r\nProcessing mock-2.0.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/mock-2.0.0-py3.6.egg\r\nSearching for pyvirtualdisplay>=0.2.1\r\nBest match: PyVirtualDisplay 0.2.1\r\nProcessing PyVirtualDisplay-0.2.1-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/PyVirtualDisplay-0.2.1-py3.6.egg\r\nSearching for pbr>=0.11\r\nBest match: pbr 4.3.0\r\nProcessing pbr-4.3.0-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/pbr-4.3.0-py3.6.egg\r\nSearching for EasyProcess\r\nBest match: EasyProcess 0.2.3\r\nProcessing EasyProcess-0.2.3-py3.6.egg\r\n\r\nUsing /home/djburke/sherpa/sherpa-fix-sphinx-docs/.eggs/EasyProcess-0.2.3-py3.6.egg\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\nget_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'\r\ncustomize Gnu95FCompiler\r\ncustomize Gnu95FCompiler\r\ncustomize Gnu95FCompiler using build_ext\r\n======================================================================= test session starts ========================================================================\r\nplatform linux -- Python 3.6.6, pytest-3.8.1, py-1.6.0, pluggy-0.7.1\r\nrootdir: /home/djburke/sherpa/sherpa-fix-sphinx-docs, inifile: pytest.ini\r\nplugins: xvfb-1.1.0, remotedata-0.3.0, openfiles-0.3.0, doctestplus-0.1.3, arraydiff-0.2\r\ncollected 1 item                                                                                                                                                   \r\n\r\nsherpa/astro/tests/test_astro.py .                                                                                                                           [100%]\r\n\r\n===================================================================== 1 passed in 0.63 seconds =====================================================================\r\n```\r\n\r\nThen again, comparing this test in the two versions shows that the error comes from a check of the covariance matrix, which wasn't available in the Fortran version:\r\n\r\n```\r\n% git diff -r 354095107245d5190c6cfe54741c5f4c2d4f87f9 sherpa/astro/tests/test_astro.py\r\n...\r\n@@ -214,28 +190,22 @@ class test_threads(SherpaTestCase):\r\n         self.run_thread('pileup')\r\n \r\n         fr = ui.get_fit_results()\r\n-        covarerr = sqrt(fr.extra_output['covar'].diagonal())\r\n-        assert covarerr[0] == approx(684.056 , rel=1e-4)\r\n-        assert covarerr[1] == approx(191.055, rel=1e-3)\r\n-        assert covarerr[2] == approx(0.632061, rel=1e-3)\r\n-        assert covarerr[3] == approx(0.290159, rel=1e-3)\r\n-        assert covarerr[4] == approx(1.62529, rel=1e-3)\r\n-        assert fr.statval == approx(53.6112, rel=1e-4)\r\n-        assert fr.rstat == approx(1.44895, rel=1e-4)\r\n-        assert fr.qval == approx(0.0379417, rel=1e-4)\r\n+        self.assertEqualWithinTol(fr.statval, 53.6112, 1e-4)\r\n+        self.assertEqualWithinTol(fr.rstat, 1.44895, 1e-4)\r\n+        self.assertEqualWithinTol(fr.qval, 0.0379417, 1e-4)\r\n         self.assertEqual(fr.numpoints, 42)\r\n         self.assertEqual(fr.dof, 37)\r\n \r\n         jdp = self.locals['jdp']\r\n-        assert jdp.alpha.val == approx(0.522593, rel=1e-1)\r\n-        assert jdp.f.val == approx(0.913458, rel=1e-2)\r\n+        self.assertEqualWithinTol(jdp.alpha.val, 0.522593, 1e-1)\r\n+        self.assertEqualWithinTol(jdp.f.val, 0.913458, 1e-2)\r\n \r\n         abs1 = self.locals['abs1']\r\n-        assert abs1.nh.val == approx(6.12101, rel=1e-2)\r\n+        self.assertEqualWithinTol(abs1.nh.val, 6.12101, 1e-2)\r\n \r\n         power = self.locals['power']\r\n-        assert power.gamma.val == approx(1.41887, rel=1e-2)\r\n-        assert power.ampl.val == approx(0.00199457, rel=1e-2)\r\n+        self.assertEqualWithinTol(power.gamma.val, 1.41887, 1e-2)\r\n+        self.assertEqualWithinTol(power.ampl.val, 0.00199457, 1e-2)\r\n \r\n         # Issue #294 was a problem with serializing the pileup model\r\n         # after a fit in Python 3 (but not Python 2). Add some basic\r\n@@ -264,21 +234,16 @@ class test_threads(SherpaTestCase):\r\n...\r\n```\r\n\r\nAs a check, I went back to the 354095107245d5190c6cfe54741c5f4c2d4f87f9 commit and commented out the five checks of the diagonal elements of the covariance matrix and the test passed. Instrumenting the test to display the diagonal terms gives me\r\n\r\n```\r\n>       assert covarerr[0] == approx(684.056 , rel=1e-4)\r\nE       AssertionError: assert 694.3746848979197 == 684.056 ± 6.8e-02\r\nE        +  where 684.056 ± 6.8e-02 = approx(684.056, rel=0.0001)\r\n\r\nsherpa/astro/tests/test_astro.py:221: AssertionError\r\n----------------------------------------------------------------------- Captured stdout call -----------------------------------------------------------------------\r\n - covarerr[0] = 694.3746848979197\r\n - covarerr[1] = 192.13254192587013\r\n - covarerr[2] = 0.6322390421678051\r\n - covarerr[3] = 0.29017303370770375\r\n - covarerr[4] = 1.7174108323954933\r\n```\r\n \r\nwhich can be compared to the values from the test:\r\n\r\n```\r\n        assert covarerr[0] == approx(684.056 , rel=1e-4)\r\n        assert covarerr[1] == approx(191.055, rel=1e-3)\r\n        assert covarerr[2] == approx(0.632061, rel=1e-3)\r\n        assert covarerr[3] == approx(0.290159, rel=1e-3)\r\n        assert covarerr[4] == approx(1.62529, rel=1e-3)\r\n```\r\n\r\nLooking at the test thread I see that it moves the fit parameters to \"the best-fit location\" before fitting, to save time in the test. So maybe there's something here that means that the optimiser hasn't been able to adequately describe the search surface, and hence the covariance matrix. This still doesn't explain why I see it and the Travis tests don't.\r\n\r\nThe test uses the `xswabs` and `powlaw1d` models. I would be surprised if there were significant differences in the `xswabs` model between XSPEC 12.9.1p and whatever versions we use on Travis.\r\n\r\nFor reference:\r\n\r\n```\r\n% conda list\r\n# packages in environment at /home/djburke/miniconda3/envs/sherpa-fix-sphinx-docs:\r\n#\r\n# Name                    Version                   Build  Channel\r\nastropy                   3.0.4            py36h14c3975_0  \r\natomicwrites              1.2.1                    py36_0  \r\nattrs                     18.2.0           py36h28b3542_0  \r\nbackcall                  0.1.0                    py36_0  \r\nblas                      1.0                         mkl  \r\nca-certificates           2018.03.07                    0  \r\ncertifi                   2018.8.24                py36_1  \r\ndecorator                 4.3.0                    py36_0  \r\nintel-openmp              2019.0                      118  \r\nipython                   7.0.1            py36h39e3cac_0  \r\nipython_genutils          0.2.0                    py36_0  \r\njedi                      0.12.1                   py36_0  \r\nlibedit                   3.1.20170329         h6b74fdf_2  \r\nlibffi                    3.2.1                hd88cf55_4  \r\nlibgcc-ng                 8.2.0                hdf63c60_1  \r\nlibgfortran-ng            7.3.0                hdf63c60_0  \r\nlibstdcxx-ng              8.2.0                hdf63c60_1  \r\nmkl                       2019.0                      118  \r\nmkl_fft                   1.0.6            py36h7dd41cf_0  \r\nmkl_random                1.0.1            py36h4414c95_1  \r\nmore-itertools            4.3.0                    py36_0  \r\nncurses                   6.1                  hf484d3e_0  \r\nnumpy                     1.15.2           py36h1d66e8a_1  \r\nnumpy-base                1.15.2           py36h81de0dd_1  \r\nopenssl                   1.0.2p               h14c3975_0  \r\nparso                     0.3.1                    py36_0  \r\npexpect                   4.6.0                    py36_0  \r\npickleshare               0.7.5                    py36_0  \r\npip                       10.0.1                   py36_0  \r\npluggy                    0.7.1            py36h28b3542_0  \r\nprompt_toolkit            2.0.5                    py36_0  \r\npsutil                    5.4.7            py36h14c3975_0  \r\nptyprocess                0.6.0                    py36_0  \r\npy                        1.6.0                    py36_0  \r\npygments                  2.2.0                    py36_0  \r\npytest                    3.8.1                    py36_0  \r\npytest-arraydiff          0.2              py36h39e3cac_0  \r\npytest-astropy            0.4.0                    py36_0  \r\npytest-doctestplus        0.1.3                    py36_0  \r\npytest-openfiles          0.3.0                    py36_0  \r\npytest-remotedata         0.3.0                    py36_0  \r\npython                    3.6.6                hc3d631a_0  \r\nreadline                  7.0                  h7b6447c_5  \r\nsetuptools                40.4.3                   py36_0  \r\nsherpa                    4.10.0+177.g3540951.dirty           <pip>\r\nsimplegeneric             0.8.1                    py36_2  \r\nsix                       1.11.0                   py36_1  \r\nsqlite                    3.25.2               h7b6447c_0  \r\ntk                        8.6.8                hbc83047_0  \r\ntraitlets                 4.3.2                    py36_0  \r\nwcwidth                   0.1.7                    py36_0  \r\nwheel                     0.32.0                   py36_0  \r\nxz                        5.2.4                h14c3975_4  \r\nzlib                      1.2.11               ha838bed_2  \r\n```"},"comment":{"url":"https://api.github.com/repos/sherpa/sherpa/issues/comments/431440655","html_url":"https://github.com/sherpa/sherpa/issues/507#issuecomment-431440655","issue_url":"https://api.github.com/repos/sherpa/sherpa/issues/507","id":431440655,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMTQ0MDY1NQ==","user":{"login":"olaurino","id":5692321,"node_id":"MDQ6VXNlcjU2OTIzMjE=","avatar_url":"https://avatars2.githubusercontent.com/u/5692321?v=4","gravatar_id":"","url":"https://api.github.com/users/olaurino","html_url":"https://github.com/olaurino","followers_url":"https://api.github.com/users/olaurino/followers","following_url":"https://api.github.com/users/olaurino/following{/other_user}","gists_url":"https://api.github.com/users/olaurino/gists{/gist_id}","starred_url":"https://api.github.com/users/olaurino/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olaurino/subscriptions","organizations_url":"https://api.github.com/users/olaurino/orgs","repos_url":"https://api.github.com/users/olaurino/repos","events_url":"https://api.github.com/users/olaurino/events{/privacy}","received_events_url":"https://api.github.com/users/olaurino/received_events","type":"User","site_admin":false},"created_at":"2018-10-19T17:38:12Z","updated_at":"2018-10-19T17:38:12Z","author_association":"MEMBER","body":"No luck with ubuntu 14, xspec 12.9.1 and conda's gcc 7.3, the test is OK.\r\n\r\nOn the other hand I can reproduce the issue on ubuntu 18, with the system's gcc 7.3 compilers.\r\n\r\nJust to be sure I also installed the conda's 7.3 compilers (so the very same as above), and I can also reproduce the issue.\r\n\r\nIt's kind of puzzling, because xspec is pre-built (I am using the conda binaries used to test on Travis), the conda compilers are exactly the same in the ubuntu 14 and 18 cases. Why would one see a difference between ubuntu 14 and ubuntu 18 everything else being equal?\r\n\r\nThe python modules link a few system libraries, like `libm` and `libpthread`. Is it possible a change in these libraries can explain the differences we see?\r\n\r\nTime for another red pill, I guess."}}
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