{"action":"closed","issue":{"url":"https://api.github.com/repos/NCPP/ocgis/issues/475","repository_url":"https://api.github.com/repos/NCPP/ocgis","labels_url":"https://api.github.com/repos/NCPP/ocgis/issues/475/labels{/name}","comments_url":"https://api.github.com/repos/NCPP/ocgis/issues/475/comments","events_url":"https://api.github.com/repos/NCPP/ocgis/issues/475/events","html_url":"https://github.com/NCPP/ocgis/issues/475","id":285179536,"node_id":"MDU6SXNzdWUyODUxNzk1MzY=","number":475,"title":"\"Cannot allocate memory\" error","user":{"login":"aaschwanden","id":120698,"node_id":"MDQ6VXNlcjEyMDY5OA==","avatar_url":"https://avatars0.githubusercontent.com/u/120698?v=4","gravatar_id":"","url":"https://api.github.com/users/aaschwanden","html_url":"https://github.com/aaschwanden","followers_url":"https://api.github.com/users/aaschwanden/followers","following_url":"https://api.github.com/users/aaschwanden/following{/other_user}","gists_url":"https://api.github.com/users/aaschwanden/gists{/gist_id}","starred_url":"https://api.github.com/users/aaschwanden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aaschwanden/subscriptions","organizations_url":"https://api.github.com/users/aaschwanden/orgs","repos_url":"https://api.github.com/users/aaschwanden/repos","events_url":"https://api.github.com/users/aaschwanden/events{/privacy}","received_events_url":"https://api.github.com/users/aaschwanden/received_events","type":"User","site_admin":false},"labels":[{"id":16307170,"node_id":"MDU6TGFiZWwxNjMwNzE3MA==","url":"https://api.github.com/repos/NCPP/ocgis/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2017-12-30T02:47:17Z","updated_at":"2018-06-01T15:57:14Z","closed_at":"2018-06-01T15:57:14Z","author_association":"NONE","body":"Hi,\r\n\r\nI'm trying to run OCGIS on an HPC cluster that uses SLURM and has dedicated post-procssing nodes (http://www.gi.alaska.edu/research-computing-systems/hpc).\r\n\r\nThis sometimes works, but more often it doesn't. Running my script on the login node, I get the following warning:\r\n\r\n```\r\n--------------------------------------------------------------------------\r\nAn MPI process has executed an operation involving a call to the\r\n\"fork()\" system call to create a child process.  Open MPI is currently\r\noperating in a condition that could result in memory corruption or\r\nother system errors; your MPI job may hang, crash, or produce silent\r\ndata corruption.  The use of fork() (or system() or other calls that\r\ncreate child processes) is strongly discouraged.  \r\n\r\nThe process that invoked fork was:\r\n\r\n  Local host:          chinook01 (PID 19077)\r\n  MPI_COMM_WORLD rank: 0\r\n\r\nIf you are *absolutely sure* that your application will successfully\r\nand correctly survive a call to fork(), you may disable this warning\r\nby setting the mpi_warn_on_fork MCA parameter to 0.\r\n\r\n```\r\n\r\nbut running the same on the post-processing node, it bails most of the time with:\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/u1/uaf/aaschwanden/base/gris-analysis/basins/extract_basins.py\", line 6, in <module>\r\n    import ocgis\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/ocgis-2.1.0.dev1-py2.7.egg/ocgis/__init__.py\", line 8, in <module>\r\n    from ocgis.vmachine.core import vm, OcgVM\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/ocgis-2.1.0.dev1-py2.7.egg/ocgis/vmachine/core.py\", line 5, in <module>\r\n    from ocgis.base import AbstractOcgisObject\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/ocgis-2.1.0.dev1-py2.7.egg/ocgis/base.py\", line 10, in <module>\r\n    from ocgis.util.helpers import get_iter\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/ocgis-2.1.0.dev1-py2.7.egg/ocgis/util/helpers.py\", line 18, in <module>\r\n    from shapely.geometry import Point\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/Shapely-1.6.3-py2.7-linux-x86_64.egg/shapely/geometry/__init__.py\", line 4, in <module>\r\n    from .base import CAP_STYLE, JOIN_STYLE\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/Shapely-1.6.3-py2.7-linux-x86_64.egg/shapely/geometry/base.py\", line 17, in <module>\r\n    from shapely.coords import CoordinateSequence\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/Shapely-1.6.3-py2.7-linux-x86_64.egg/shapely/coords.py\", line 8, in <module>\r\n    from shapely.geos import lgeos\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/Shapely-1.6.3-py2.7-linux-x86_64.egg/shapely/geos.py\", line 75, in <module>\r\n    _lgeos = load_dll('geos_c', fallbacks=alt_paths)\r\n  File \"/u1/uaf/aaschwanden/.local/lib/python2.7/site-packages/Shapely-1.6.3-py2.7-linux-x86_64.egg/shapely/geos.py\", line 28, in load_dll\r\n    lib = find_library(libname)\r\n  File \"/usr/local/pkg/lang/Python/2.7.12-pic-intel-2016b/lib/python2.7/ctypes/util.py\", line 237, in find_library\r\n    return _findSoname_ldconfig(name) or _get_soname(_findLib_gcc(name))\r\n  File \"/usr/local/pkg/lang/Python/2.7.12-pic-intel-2016b/lib/python2.7/ctypes/util.py\", line 226, in _findSoname_ldconfig\r\n    f = os.popen('LC_ALL=C LANG=C /sbin/ldconfig -p 2>/dev/null')\r\nOSError: [Errno 12] Cannot allocate memory\r\n```\r\n\r\nAt first I considered this a glitch in our HPC system that we are not able to track down, but now I've come across some posts that relate this error to the use of \"fork\" in python:\r\n\r\nhttps://stackoverflow.com/questions/20111242/how-to-avoid-errno-12-cannot-allocate-memory-errors-caused-by-using-subprocess\r\n\r\nso I've decided to post it here because it happens during the initialization of OCGIS.\r\n\r\nI understand that the information provided here may be insufficient to diagnose the problem, and I'd be happy to share additional debugging info.\r\n\r\nThanks."}}
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