{"action":"created","issue":{"url":"https://api.github.com/repos/lofar-astron/prefactor/issues/36","repository_url":"https://api.github.com/repos/lofar-astron/prefactor","labels_url":"https://api.github.com/repos/lofar-astron/prefactor/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/lofar-astron/prefactor/issues/36/comments","events_url":"https://api.github.com/repos/lofar-astron/prefactor/issues/36/events","html_url":"https://github.com/lofar-astron/prefactor/issues/36","id":149172865,"number":36,"title":"Problem with HDF5 versions","user":{"login":"TMCantwell","id":6649797,"avatar_url":"https://avatars.githubusercontent.com/u/6649797?v=3","gravatar_id":"","url":"https://api.github.com/users/TMCantwell","html_url":"https://github.com/TMCantwell","followers_url":"https://api.github.com/users/TMCantwell/followers","following_url":"https://api.github.com/users/TMCantwell/following{/other_user}","gists_url":"https://api.github.com/users/TMCantwell/gists{/gist_id}","starred_url":"https://api.github.com/users/TMCantwell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TMCantwell/subscriptions","organizations_url":"https://api.github.com/users/TMCantwell/orgs","repos_url":"https://api.github.com/users/TMCantwell/repos","events_url":"https://api.github.com/users/TMCantwell/events{/privacy}","received_events_url":"https://api.github.com/users/TMCantwell/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-18T14:48:08Z","updated_at":"2016-04-18T15:18:46Z","closed_at":null,"body":"The current version of LOFAR software that I am running is 2.15. \r\n\r\nThe script is crashing when trying to fit the clock correction due to some issue with HDF5 versions which I have not been able to resolve. I was wondering if this problem has been encountered before and if a solution has been found?\r\n\r\nWe tried uninstalling pyTables from usr/local/lofar-2_15 and reinstalling them using pip install --install-option='--hdf5=/usr/local/hdf5-1.8.15-patch1' tables==3.2.1.1 . However this failed with error: option --hdf5 not recognized.\r\n\r\nI’ve attached the log file from the script as well as other useful information. My paths are also pasted below in case these are important.\r\n\r\n\r\nPATH:\r\n\r\n/usr/local/casapy-42.2.30986-1-64b/bin:/usr/local/casapy/bin/:/usr/local/lofar-2_15/lofar/release/bin:/usr/local/lofar-2_15/lofar/release/sbin:/usr/local/lofar-2_15/local/release/bin:/usr/local/lofar-2_15/local/release/bin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin\r\n\r\nPYTHONPATH:\r\n\r\n/home/cantwell/lib/python2.7/site-packages/:/home/cantwell/lib/python2.7/site-packages/:/usr/local/lofar-2_15/local/release/lib/python2.7/site-packages:/usr/local/lofar-2_15/lofar/release/lib/python2.7/site-packages:/usr/local/lofar-2_15/local/release/lib/python2.7/site-packages:/usr/local/lofar-2_15/local/release/lib/python2.7/site-packages\r\n\r\nLD_LIBRARY_PATH:\r\n\r\n/usr/local/hdf5-1.8.15-patch1/lib/:/usr/local/lofar-2_15/lofar/release/lib64:/usr/local/lofar-2_15/lofar/release/lib:/usr/local/lofar-2_15/local/release/lib:/usr/local/lofar-2_15/local/release/lib64:/usr/local/lofar-2_15/local/release/lib:/usr/local/lofar-2_15/local/release/lib64\r\n\r\n[Pipeline_log.txt](https://github.com/lofar-astron/prefactor/files/224001/Pipeline_log.txt)\r\n[pipeline_cfg.txt](https://github.com/lofar-astron/prefactor/files/224003/pipeline_cfg.txt)\r\n\r\n[Pre-Facet-Cal-3C295_parset.txt](https://github.com/lofar-astron/prefactor/files/224007/Pre-Facet-Cal-3C295_parset.txt)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/lofar-astron/prefactor/issues/comments/211426883","html_url":"https://github.com/lofar-astron/prefactor/issues/36#issuecomment-211426883","issue_url":"https://api.github.com/repos/lofar-astron/prefactor/issues/36","id":211426883,"user":{"login":"AHorneffer","id":900708,"avatar_url":"https://avatars.githubusercontent.com/u/900708?v=3","gravatar_id":"","url":"https://api.github.com/users/AHorneffer","html_url":"https://github.com/AHorneffer","followers_url":"https://api.github.com/users/AHorneffer/followers","following_url":"https://api.github.com/users/AHorneffer/following{/other_user}","gists_url":"https://api.github.com/users/AHorneffer/gists{/gist_id}","starred_url":"https://api.github.com/users/AHorneffer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AHorneffer/subscriptions","organizations_url":"https://api.github.com/users/AHorneffer/orgs","repos_url":"https://api.github.com/users/AHorneffer/repos","events_url":"https://api.github.com/users/AHorneffer/events{/privacy}","received_events_url":"https://api.github.com/users/AHorneffer/received_events","type":"User","site_admin":false},"created_at":"2016-04-18T15:18:45Z","updated_at":"2016-04-18T15:18:45Z","body":"My suggestion is to fully kick out one of the two installations of HDF5. PyTables (and thus LoSoTo) should work with either of them, just not with both of them mixed together.\r\n\r\nThe best approach depends on your local setup. (The HDF5 installation in /usr/local/lofar-2_15/local/release seems to be done by root, so maybe that's harder for you to remove. Another question is which libraries are used by casacore?)\r\n"}}