{"action":"created","issue":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1459","repository_url":"https://api.github.com/repos/Amber-MD/pytraj","labels_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1459/labels{/name}","comments_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1459/comments","events_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1459/events","html_url":"https://github.com/Amber-MD/pytraj/issues/1459","id":332983732,"node_id":"MDU6SXNzdWUzMzI5ODM3MzI=","number":1459,"title":"PyPI/Conda binaries incompatible with recent glibc versions?","user":{"login":"Olllom","id":30830507,"node_id":"MDQ6VXNlcjMwODMwNTA3","avatar_url":"https://avatars2.githubusercontent.com/u/30830507?v=4","gravatar_id":"","url":"https://api.github.com/users/Olllom","html_url":"https://github.com/Olllom","followers_url":"https://api.github.com/users/Olllom/followers","following_url":"https://api.github.com/users/Olllom/following{/other_user}","gists_url":"https://api.github.com/users/Olllom/gists{/gist_id}","starred_url":"https://api.github.com/users/Olllom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Olllom/subscriptions","organizations_url":"https://api.github.com/users/Olllom/orgs","repos_url":"https://api.github.com/users/Olllom/repos","events_url":"https://api.github.com/users/Olllom/events{/privacy}","received_events_url":"https://api.github.com/users/Olllom/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-06-16T12:22:09Z","updated_at":"2018-06-18T14:33:48Z","closed_at":null,"author_association":"NONE","body":"We are having trouble installing pytraj (2.0.3) on recent Ubuntu versions (18.0.4).\r\n\r\n```\r\nImportError while importing test module '/home/ubuntu/coffe-master/tests/misc/test_mk_torsion_conformers.py'.\r\nHint: make sure your test modules/packages have valid Python names.\r\nTraceback:\r\ntests/misc/test_mk_torsion_conformers.py:8: in <module>\r\n    from coffe.analysis import pdb_reader\r\ncoffe/analysis/pdb_reader.py:12: in <module>\r\n    import pytraj as pt\r\n../.local/lib/python2.7/site-packages/pytraj-2.0.3-py2.7-linux-x86_64.egg/pytraj/__init__.py:24: in <module>\r\n    from .utils.misc import info\r\n../.local/lib/python2.7/site-packages/pytraj-2.0.3-py2.7-linux-x86_64.egg/pytraj/utils/misc.py:7: in <module>\r\n    from pytraj.core.c_options import set_world_silent\r\n../.local/lib/python2.7/site-packages/pytraj-2.0.3-py2.7-linux-x86_64.egg/pytraj/core/__init__.py:2: in <module>\r\n    from .topology_objects import Atom, Residue, Molecule\r\nE   ImportError: /home/ubuntu/.local/lib/python2.7/site-packages/pytraj-2.0.3-py2.7-linux-x86_64.egg/pytraj/core/../.libs/libresolv-2-c4c53def.5.so: symbol __res_maybe_init version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference\r\n```\r\n\r\nAs far as I understand this, the binaries were compiled using glibc < 2.26, while Ubuntu 18.0.4, by default, comes with glibc 2.27. \r\n\r\n`ldd Version:ldd (Ubuntu GLIBC 2.27-3ubuntu1) 2.27`\r\nhttps://sourceware.org/glibc/wiki/Release/2.26#Removal_of_.27xlocale.h.27\r\n\r\nOr am I missing something?\r\nDo you see any way to fix this, other than manually downgrading glibc on my system?"},"comment":{"url":"https://api.github.com/repos/Amber-MD/pytraj/issues/comments/398075278","html_url":"https://github.com/Amber-MD/pytraj/issues/1459#issuecomment-398075278","issue_url":"https://api.github.com/repos/Amber-MD/pytraj/issues/1459","id":398075278,"node_id":"MDEyOklzc3VlQ29tbWVudDM5ODA3NTI3OA==","user":{"login":"hainm","id":4451957,"node_id":"MDQ6VXNlcjQ0NTE5NTc=","avatar_url":"https://avatars2.githubusercontent.com/u/4451957?v=4","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"created_at":"2018-06-18T14:33:48Z","updated_at":"2018-06-18T14:33:48Z","author_association":"CONTRIBUTOR","body":"> Are you still going to fix the distributed binaries using a more recent version of auditwheel?\r\n\r\nhi, that's my guess but the error might due to the docker image I used to build pytraj. The image is based on the one from manylinux (https://github.com/pypa/manylinux#docker-images).\r\nWe used centos 5 image to build ambertools.\r\n\r\nI will definitely fix the error but I am not sure I can make it happen soon. For now, please use ambertools. Thanks.\r\n"}}
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