{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/yank/issues/346","repository_url":"https://api.github.com/repos/choderalab/yank","labels_url":"https://api.github.com/repos/choderalab/yank/issues/346/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/yank/issues/346/comments","events_url":"https://api.github.com/repos/choderalab/yank/issues/346/events","html_url":"https://github.com/choderalab/yank/issues/346","id":136161017,"number":346,"title":"Cluster MPI run issues","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-24T19:23:49Z","updated_at":"2016-04-12T08:19:33Z","closed_at":null,"body":"When I installed `yank-dev` via anaconda cloud, I ran into a `glibc` incompatibility issue:\r\n```\r\nIteration 2 / 200\r\n2016-02-24 14:16:44,345: Mixing replicas...\r\nTraceback (most recent call last):\r\n  File \"/cbio/jclab/home/chodera/miniconda/bin/yank\", line 9, in <module>\r\n    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/cli.py\", line 105, in main\r\n    dispatched = getattr(commands, command).dispatch(args)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/commands/script.py\", line 34, in dispatch\r\n    yaml_builder.build_experiment()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1203, in build_experiment\r\n    self._run_experiment(combination, output_dir)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1778, in _run_experiment\r\n    yank.run()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yank.py\", line 451, in run\r\n    simulation.run(niterations_to_run=niterations_to_run)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 840, in run\r\n    self._mix_replicas()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1559, in _mix_replicas\r\n    self._mix_all_replicas_cython()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1474, in _mix_all_replicas_cython\r\n    from mixing._mix_replicas import _mix_replicas_cython\r\nImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/mixing/_mix_replicas.so)\r\nTraceback (most recent call last):\r\n  File \"/cbio/jclab/home/chodera/miniconda/bin/yank\", line 9, in <module>\r\n    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/cli.py\", line 105, in main\r\n    dispatched = getattr(commands, command).dispatch(args)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/commands/script.py\", line 34, in dispatch\r\nTraceback (most recent call last):\r\n  File \"/cbio/jclab/home/chodera/miniconda/bin/yank\", line 9, in <module>\r\nTraceback (most recent call last):\r\n  File \"/cbio/jclab/home/chodera/miniconda/bin/yank\", line 9, in <module>\r\n    yaml_builder.build_experiment()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1203, in build_experiment\r\nTraceback (most recent call last):\r\n  File \"/cbio/jclab/home/chodera/miniconda/bin/yank\", line 9, in <module>\r\n    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()\r\n    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/cli.py\", line 105, in main\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/cli.py\", line 105, in main\r\n    load_entry_point('yank==0.9.0', 'console_scripts', 'yank')()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/cli.py\", line 105, in main\r\n    dispatched = getattr(commands, command).dispatch(args)\r\n    dispatched = getattr(commands, command).dispatch(args)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/commands/script.py\", line 34, in dispatch\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/commands/script.py\", line 34, in dispatch\r\n    yaml_builder.build_experiment()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1203, in build_experiment\r\n    dispatched = getattr(commands, command).dispatch(args)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/commands/script.py\", line 34, in dispatch\r\n    yaml_builder.build_experiment()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1203, in build_experiment\r\n    yaml_builder.build_experiment()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1203, in build_experiment\r\n    self._run_experiment(combination, output_dir)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1778, in _run_experiment\r\n    self._run_experiment(combination, output_dir)\r\n    self._run_experiment(combination, output_dir)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1778, in _run_experiment\r\n    self._run_experiment(combination, output_dir)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1778, in _run_experiment\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yamlbuild.py\", line 1778, in _run_experiment\r\n    yank.run()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yank.py\", line 451, in run\r\n    simulation.run(niterations_to_run=niterations_to_run)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 840, in run\r\n    yank.run()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yank.py\", line 451, in run\r\n    yank.run()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yank.py\", line 451, in run\r\n    yank.run()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/yank.py\", line 451, in run\r\n    simulation.run(niterations_to_run=niterations_to_run)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 843, in run\r\n    simulation.run(niterations_to_run=niterations_to_run)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 843, in run\r\n    simulation.run(niterations_to_run=niterations_to_run)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 843, in run\r\n    self._mix_replicas()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1543, in _mix_replicas\r\n    self._propagate_replicas()\r\n    self._propagate_replicas()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/sampling.py\", line 656, in _propagate_replicas\r\n    self._propagate_replicas()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/sampling.py\", line 656, in _propagate_replicas\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/sampling.py\", line 656, in _propagate_replicas\r\n    ReplicaExchange._propagate_replicas(self)\r\n    ReplicaExchange._propagate_replicas(self)\r\n    ReplicaExchange._propagate_replicas(self)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1288, in _propagate_replicas\r\n    self.replica_states = self.mpicomm.bcast(self.replica_states, root=0)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1288, in _propagate_replicas\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1288, in _propagate_replicas\r\n  File \"MPI/Comm.pyx\", line 1276, in mpi4py.MPI.Comm.bcast (src/mpi4py.MPI.c:108819)\r\n    self._propagate_replicas_mpi()\r\n    self._propagate_replicas_mpi()\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in _propagate_replicas_mpi\r\n    self._propagate_replicas_mpi()\r\n  File \"MPI/msgpickle.pxi\", line 613, in mpi4py.MPI.PyMPI_bcast (src/mpi4py.MPI.c:47032)\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in _propagate_replicas_mpi\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in _propagate_replicas_mpi\r\nmpi4py.MPI.Exception    replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\n    replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in <genexpr>\r\n    replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in <genexpr>\r\n  File \"/cbio/jclab/home/chodera/miniconda/lib/python2.7/site-packages/yank-0.9.0-py2.7-linux-x86_64.egg/yank/repex.py\", line 1231, in <genexpr>\r\n    replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\n    replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\nTypeError:     replica_lookup = dict( (self.replica_states[replica_index], replica_index) for replica_index in range(self.nstates) ) # replica_lookup[state_index] is the replica index currently at state 'state_index' # Python 2.6 compatible\r\n'NoneType' object has no attribute '__getitem__'\r\nTypeError: 'NoneType' object has no attribute '__getitem__'\r\nTypeError: 'NoneType' object has no attribute '__getitem__'\r\n\r\n=====================================================================================\r\n=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES\r\n=   EXIT CODE: 11\r\n=   CLEANING UP REMAINING PROCESSES\r\n=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES\r\n=====================================================================================\r\n[proxy:0:1@gpu-1-13.local] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:928): assert (!closed) failed\r\n[proxy:0:1@gpu-1-13.local] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status\r\n[proxy:0:1@gpu-1-13.local] main (./pm/pmiserv/pmip.c:226): demux engine error waiting for event\r\n[mpiexec@gpu-1-12.local] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated badly; aborting\r\n[mpiexec@gpu-1-12.local] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion\r\n[mpiexec@gpu-1-12.local] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:191): launcher returned error waiting for completion\r\n[mpiexec@gpu-1-12.local] main (./ui/mpich/mpiexec.c:405): process manager error waiting for completion\r\n```\r\nIt looks like the newest travis docker build framework may be using a too-recent version of `linux`.\r\n\r\nThe easiest way to fix this might be to revert to the old precise penguin build framework by setting `sudo: true` in [`.travis.yml`](https://github.com/choderalab/yank/blob/master/.travis.yml#L2)."},"comment":{"url":"https://api.github.com/repos/choderalab/yank/issues/comments/208776741","html_url":"https://github.com/choderalab/yank/issues/346#issuecomment-208776741","issue_url":"https://api.github.com/repos/choderalab/yank/issues/346","id":208776741,"user":{"login":"hlfsimko","id":6966675,"avatar_url":"https://avatars.githubusercontent.com/u/6966675?v=3","gravatar_id":"","url":"https://api.github.com/users/hlfsimko","html_url":"https://github.com/hlfsimko","followers_url":"https://api.github.com/users/hlfsimko/followers","following_url":"https://api.github.com/users/hlfsimko/following{/other_user}","gists_url":"https://api.github.com/users/hlfsimko/gists{/gist_id}","starred_url":"https://api.github.com/users/hlfsimko/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hlfsimko/subscriptions","organizations_url":"https://api.github.com/users/hlfsimko/orgs","repos_url":"https://api.github.com/users/hlfsimko/repos","events_url":"https://api.github.com/users/hlfsimko/events{/privacy}","received_events_url":"https://api.github.com/users/hlfsimko/received_events","type":"User","site_admin":false},"created_at":"2016-04-12T08:19:33Z","updated_at":"2016-04-12T08:19:33Z","body":"I encounter the same issue. Is the recommended solution still to change the setting `sudo: true` in `.travis.yml`?"}}