{"action":"created","issue":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551","labels_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/labels{/name}","comments_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/comments","events_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551/events","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/551","id":119748746,"number":551,"title":"2 failures and 1 error while performing the tests","user":{"login":"ashkurti","id":6951871,"avatar_url":"https://avatars.githubusercontent.com/u/6951871?v=3","gravatar_id":"","url":"https://api.github.com/users/ashkurti","html_url":"https://github.com/ashkurti","followers_url":"https://api.github.com/users/ashkurti/followers","following_url":"https://api.github.com/users/ashkurti/following{/other_user}","gists_url":"https://api.github.com/users/ashkurti/gists{/gist_id}","starred_url":"https://api.github.com/users/ashkurti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashkurti/subscriptions","organizations_url":"https://api.github.com/users/ashkurti/orgs","repos_url":"https://api.github.com/users/ashkurti/repos","events_url":"https://api.github.com/users/ashkurti/events{/privacy}","received_events_url":"https://api.github.com/users/ashkurti/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2015-12-01T16:03:02Z","updated_at":"2015-12-02T09:27:44Z","closed_at":null,"body":"Hi MDAnalysis developers!!\r\n\r\nAny advice on the following error and failures will be much appreciated. I am aiming to get everything working before contributing to the MDAnalysis code with some analysis enhancements.\r\n```\r\n======================================================================\r\nERROR: MDAnalysisTests.coordinates.test_trz.TestTRZWriter2.test_writer_trz_from_other\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/nose/case.py\", line 197, in runTest\r\n    self.test(*self.arg)\r\n  File \"MDAnalysisTests/coordinates/test_trz.py\", line 189, in test_writer_trz_from_other\r\n    u2 = mda.Universe(two_water_gro, outfile)\r\n  File \"/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py\", line 3791, in __init__\r\n    \"Error: {2}\".format(self.filename, parser, err))\r\nIOError: Failed to load from the topology file MDAnalysisTests/data/two_water_gro.gro with parser <class 'MDAnalysis.topology.GROParser.GROParser'>.\r\nError: [Errno 5] Cannot open file or stream in mode='r'.: \"'MDAnalysisTests/data/two_water_gro.gro'\"\r\n-------------------- >> begin captured stderr << ---------------------\r\n/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRZ.py:539: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory\r\n  \"\".format(\", \".join(faked_attrs)))\r\n/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRZ.py:547: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. \r\n  warnings.warn(\"Timestep didn't have velocity information, \"\r\n\r\n--------------------- >> end captured stderr << ----------------------\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/two_water_gro.gro...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/Amber/bala.ncdf...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmp2QChD0/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading MDAnalysisTests/data/Amber/tz2.truncoct.nc...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmpdfdaTZ/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n----------------------------------------------------------------------\r\nRan 3275 tests in 983.183s\r\n\r\nFAILED (KNOWNFAIL=3, errors=1, failures=2)\r\n```"},"comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/comments/161233550","html_url":"https://github.com/MDAnalysis/mdanalysis/issues/551#issuecomment-161233550","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/551","id":161233550,"user":{"login":"ashkurti","id":6951871,"avatar_url":"https://avatars.githubusercontent.com/u/6951871?v=3","gravatar_id":"","url":"https://api.github.com/users/ashkurti","html_url":"https://github.com/ashkurti","followers_url":"https://api.github.com/users/ashkurti/followers","following_url":"https://api.github.com/users/ashkurti/following{/other_user}","gists_url":"https://api.github.com/users/ashkurti/gists{/gist_id}","starred_url":"https://api.github.com/users/ashkurti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ashkurti/subscriptions","organizations_url":"https://api.github.com/users/ashkurti/orgs","repos_url":"https://api.github.com/users/ashkurti/repos","events_url":"https://api.github.com/users/ashkurti/events{/privacy}","received_events_url":"https://api.github.com/users/ashkurti/received_events","type":"User","site_admin":false},"created_at":"2015-12-02T09:27:44Z","updated_at":"2015-12-02T09:27:44Z","body":"@orbeckst and @hainm thanks for your tips.\r\n\r\nI ran again now: \r\n```\r\n./mda_nosetests -v --with-memleak ./coordinates/test_netcdf.py\r\n```\r\nAnd I get two failures. The output produced is this:\r\n```\r\n[MDAPCAvenv] ardita@moriarty 390% ./mda_nosetests -v --with-memleak ./coordinates/test_netcdf.py\r\ntest_amber_proteinselection (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_full_slice (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_initial_frame_is_0 (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_load_prm (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_metadata (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_n_atoms (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_n_frames (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_periodic (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_rewind (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\ntest_slice_iteration (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\nTest that coordinate arrays are filled as soon as the trajectory ... ok\r\ntest_sum_centres_of_geometry (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReader) ... ok\r\nCheck forces on first frame ... ok\r\nCheck forces on second frame ... ok\r\nCheck positions on first frame ... ok\r\nCheck positions on second frame ... ok\r\nCheck time on first frame ... ok\r\nCheck time on second frame ... ok\r\ntest_amber_proteinselection (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_full_slice (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_initial_frame_is_0 (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_load_prm (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_metadata (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_n_atoms (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_n_frames (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_periodic (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_rewind (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_slice_iteration (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\nTest that coordinate arrays are filled as soon as the trajectory ... ok\r\ntest_sum_centres_of_geometry (MDAnalysisTests.coordinates.test_netcdf.TestNCDFReaderTZ2) ... ok\r\ntest_OtherWriter (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... ok\r\ntest_TRR2NCDF (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... ok\r\ntest to write NCDF from AtomGroup (Issue 116) ... ok\r\ntest_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter) ... FAIL\r\ntest_OtherWriter (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... ok\r\ntest_TRR2NCDF (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... ok\r\ntest to write NCDF from AtomGroup (Issue 116) ... ok\r\ntest_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2) ... FAIL\r\ntest_pos (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok\r\ntest_pos_force (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok\r\ntest_pos_vel (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok\r\ntest_pos_vel_force (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterVelsForces) ... ok\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriter)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/users/ardita/MDAPCA/mdanalysis/testsuite/MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA/mdanalysis/testsuite/MDAnalysisTests/data/Amber/bala.ncdf...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmp_zaQSW/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n======================================================================\r\nFAIL: test_write_trajectory (MDAnalysisTests.coordinates.test_netcdf.TestNCDFWriterTZ2)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/users/ardita/MDAPCA/mdanalysis/testsuite/MDAnalysisTests/coordinates/test_netcdf.py\", line 139, in test_write_trajectory\r\n    'ncdf coord output not float32')\r\nAssertionError: ncdf coord output not float32\r\n-------------------- >> begin captured logging << --------------------\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA/mdanalysis/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.nc...\r\nMDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /tmp/tmpkfCo6j/ncdf-writer-1.ncdf...\r\n--------------------- >> end captured logging << ---------------------\r\n\r\n----------------------------------------------------------------------\r\nRan 42 tests in 15.233s\r\n\r\nFAILED (failures=2)\r\n```"}}