{"action":"closed","issue":{"url":"https://api.github.com/repos/aowen87/TicketTester/issues/1859","repository_url":"https://api.github.com/repos/aowen87/TicketTester","labels_url":"https://api.github.com/repos/aowen87/TicketTester/issues/1859/labels{/name}","comments_url":"https://api.github.com/repos/aowen87/TicketTester/issues/1859/comments","events_url":"https://api.github.com/repos/aowen87/TicketTester/issues/1859/events","html_url":"https://github.com/aowen87/TicketTester/issues/1859","id":390039469,"node_id":"MDU6SXNzdWUzOTAwMzk0Njk=","number":1859,"title":"Crash in mdserver when reading Exodus data on Mac.","user":{"login":"aowen87","id":11658578,"node_id":"MDQ6VXNlcjExNjU4NTc4","avatar_url":"https://avatars0.githubusercontent.com/u/11658578?v=4","gravatar_id":"","url":"https://api.github.com/users/aowen87","html_url":"https://github.com/aowen87","followers_url":"https://api.github.com/users/aowen87/followers","following_url":"https://api.github.com/users/aowen87/following{/other_user}","gists_url":"https://api.github.com/users/aowen87/gists{/gist_id}","starred_url":"https://api.github.com/users/aowen87/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aowen87/subscriptions","organizations_url":"https://api.github.com/users/aowen87/orgs","repos_url":"https://api.github.com/users/aowen87/repos","events_url":"https://api.github.com/users/aowen87/events{/privacy}","received_events_url":"https://api.github.com/users/aowen87/received_events","type":"User","site_admin":false},"labels":[{"id":1158143536,"node_id":"MDU6TGFiZWwxMTU4MTQzNTM2","url":"https://api.github.com/repos/aowen87/TicketTester/labels/bug","name":"bug","color":"d73a4a","default":true},{"id":1158144329,"node_id":"MDU6TGFiZWwxMTU4MTQ0MzI5","url":"https://api.github.com/repos/aowen87/TicketTester/labels/crash","name":"crash","color":"4682B4","default":false},{"id":1158144223,"node_id":"MDU6TGFiZWwxMTU4MTQ0MjIz","url":"https://api.github.com/repos/aowen87/TicketTester/labels/likelihood%20medium","name":"likelihood medium","color":"003152","default":false},{"id":1158143970,"node_id":"MDU6TGFiZWwxMTU4MTQzOTcw","url":"https://api.github.com/repos/aowen87/TicketTester/labels/reviewed","name":"reviewed","color":"008ECC","default":false},{"id":1158144312,"node_id":"MDU6TGFiZWwxMTU4MTQ0MzEy","url":"https://api.github.com/repos/aowen87/TicketTester/labels/severity%20high","name":"severity high","color":"0F52BA","default":false},{"id":1158144364,"node_id":"MDU6TGFiZWwxMTU4MTQ0MzY0","url":"https://api.github.com/repos/aowen87/TicketTester/labels/wrong%20results","name":"wrong results","color":"73C2FB","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/aowen87/TicketTester/milestones/2","html_url":"https://github.com/aowen87/TicketTester/milestone/2","labels_url":"https://api.github.com/repos/aowen87/TicketTester/milestones/2/labels","id":3890070,"node_id":"MDk6TWlsZXN0b25lMzg5MDA3MA==","number":2,"title":"2.13.0","description":null,"creator":{"login":"aowen87","id":11658578,"node_id":"MDQ6VXNlcjExNjU4NTc4","avatar_url":"https://avatars0.githubusercontent.com/u/11658578?v=4","gravatar_id":"","url":"https://api.github.com/users/aowen87","html_url":"https://github.com/aowen87","followers_url":"https://api.github.com/users/aowen87/followers","following_url":"https://api.github.com/users/aowen87/following{/other_user}","gists_url":"https://api.github.com/users/aowen87/gists{/gist_id}","starred_url":"https://api.github.com/users/aowen87/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aowen87/subscriptions","organizations_url":"https://api.github.com/users/aowen87/orgs","repos_url":"https://api.github.com/users/aowen87/repos","events_url":"https://api.github.com/users/aowen87/events{/privacy}","received_events_url":"https://api.github.com/users/aowen87/received_events","type":"User","site_admin":false},"open_issues":0,"closed_issues":44,"state":"open","created_at":"2018-12-11T17:10:59Z","updated_at":"2018-12-12T02:34:13Z","due_on":null,"closed_at":null},"comments":0,"created_at":"2018-12-12T02:34:08Z","updated_at":"2018-12-12T02:34:12Z","closed_at":"2018-12-12T02:34:12Z","author_association":"OWNER","body":"I run into a problem on Mac where we build HDF4 and NETCDF as shared libraries. When I try and read an Exodus file, the mdserver crashes. Run visit -o foo.exo Apparently, things are going fine through the NETCDF library and then when trying to call NC_var_shape, the mdserver crashes. The reported crash is inside libmfhdf.dylib, which is an HDF4 shared library! That file is defining some NETCDF functions!!! IT seems to me that HDF4 should not be defining HDF4 functions. Also, we don't link the Exodus or NETCDF readers with HDF4. IF we load any HDF4 plugins (like Enzo or ZeusMP) then the NC_var_shape from HDF4 is being called instead of the symbol from libnetcdf.6.dylib. Maybe libmfhdf could be patched in build_visit so it does not define NETCDF symbols. <code><pre> optimusprime:lib bjw$ nm libmfhdf.dylib | grep \"NC_var_shape\" 0000000000018f30 T _NC_var_shape (lldb) bt * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x452) * frame #0: 0x00000001087e10ad libmfhdf.dylib`NC_var_shape + 381 frame #1: 0x00000001092889f4 libnetcdf.6.dylib`nc_get_NC + 3556 frame #2: 0x0000000109269cb8 libnetcdf.6.dylib`nc3__open_mp + 216 frame #3: 0x00000001092563a0 libnetcdf.6.dylib`nc_open_file + 560 frame #4: 0x00000001091d5d59 libMExodusDatabase.dylib`avtExodusFileFormat::GetFileHandle(this=0x00000001040353d0) at avtExodusFileFormat.C:1568 frame #5: 0x00000001091d7c84 libMExodusDatabase.dylib`avtExodusFileFormat::GetTimesteps(this=0x00000001040353d0, ntimes=0x00007fff5fbf7194, times=0x0000000000000000) at avtEx </pre></code>\n\n\n\n\n\n-----------------------REDMINE MIGRATION-----------------------\nThis ticket was migrated from Redmine. As such, not all \ninformation was able to be captured in the transition. Below is\na complete record of the original redmine ticket.\n\nTicket number: 2896\nStatus: Resolved\nProject: VisIt\nTracker: Bug\nPriority: Normal\nSubject: Crash in mdserver when reading Exodus data on Mac.\nAssigned to: Brad Whitlock\nCategory: \nTarget version: 2.13.0\nAuthor: Brad Whitlock\nStart: 08/23/2017\nDue date: \n% Done: 100\nEstimated time: \nCreated: 08/23/2017 06:21 pm\nUpdated: 08/23/2017 06:56 pm\nLikelihood: 3 - Occasional\nSeverity: 4 - Crash / Wrong Results\nFound in version: 2.12.3\nImpact: \nExpected Use: \nOS: OSX\nSupport Group: Any\nDescription:\n I run into a problem on Mac where we build HDF4 and NETCDF as shared libraries. When I try and read an Exodus file, the mdserver crashes. Run visit -o foo.exo Apparently, things are going fine through the NETCDF library and then when trying to call NC_var_shape, the mdserver crashes. The reported crash is inside libmfhdf.dylib, which is an HDF4 shared library! That file is defining some NETCDF functions!!! IT seems to me that HDF4 should not be defining HDF4 functions. Also, we don't link the Exodus or NETCDF readers with HDF4. IF we load any HDF4 plugins (like Enzo or ZeusMP) then the NC_var_shape from HDF4 is being called instead of the symbol from libnetcdf.6.dylib. Maybe libmfhdf could be patched in build_visit so it does not define NETCDF symbols. <code><pre> optimusprime:lib bjw$ nm libmfhdf.dylib | grep \"NC_var_shape\" 0000000000018f30 T _NC_var_shape (lldb) bt * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x452) * frame #0: 0x00000001087e10ad libmfhdf.dylib`NC_var_shape + 381 frame #1: 0x00000001092889f4 libnetcdf.6.dylib`nc_get_NC + 3556 frame #2: 0x0000000109269cb8 libnetcdf.6.dylib`nc3__open_mp + 216 frame #3: 0x00000001092563a0 libnetcdf.6.dylib`nc_open_file + 560 frame #4: 0x00000001091d5d59 libMExodusDatabase.dylib`avtExodusFileFormat::GetFileHandle(this=0x00000001040353d0) at avtExodusFileFormat.C:1568 frame #5: 0x00000001091d7c84 libMExodusDatabase.dylib`avtExodusFileFormat::GetTimesteps(this=0x00000001040353d0, ntimes=0x00007fff5fbf7194, times=0x0000000000000000) at avtEx </pre></code>\n\nComments:\nI changed bv_hdf4.sh to include disable-netcdf so it would not have NETCDF symbols in it anymore. This should avoid a conflict when loading NETCDF/Exodus data on Mac.\n"}}
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