{"action":"created","issue":{"url":"https://api.github.com/repos/veg/hyphy/issues/483","repository_url":"https://api.github.com/repos/veg/hyphy","labels_url":"https://api.github.com/repos/veg/hyphy/issues/483/labels{/name}","comments_url":"https://api.github.com/repos/veg/hyphy/issues/483/comments","events_url":"https://api.github.com/repos/veg/hyphy/issues/483/events","html_url":"https://github.com/veg/hyphy/issues/483","id":185983407,"number":483,"title":"HYPHYMPI not running on CentOS 6.8","user":{"login":"ArtPoon","id":1109328,"avatar_url":"https://avatars.githubusercontent.com/u/1109328?v=3","gravatar_id":"","url":"https://api.github.com/users/ArtPoon","html_url":"https://github.com/ArtPoon","followers_url":"https://api.github.com/users/ArtPoon/followers","following_url":"https://api.github.com/users/ArtPoon/following{/other_user}","gists_url":"https://api.github.com/users/ArtPoon/gists{/gist_id}","starred_url":"https://api.github.com/users/ArtPoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ArtPoon/subscriptions","organizations_url":"https://api.github.com/users/ArtPoon/orgs","repos_url":"https://api.github.com/users/ArtPoon/repos","events_url":"https://api.github.com/users/ArtPoon/events{/privacy}","received_events_url":"https://api.github.com/users/ArtPoon/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-28T17:56:41Z","updated_at":"2016-10-28T18:01:34Z","closed_at":null,"body":"I can build HYPHYMPI on a fresh install of Ubuntu using the following workflow:\r\n1. `git clone https://github.com/veg/hyphy.git`\r\n2. `sudo apt install libopenmpi-dev`\r\n3. `sudo apt install cmake`\r\n4. `cd hyphy; cmake .`\r\n5. `make MPI`\r\n6. `sudo make install`\r\n\r\nbut I'm having trouble building in CentOS 6.8 (Scyld CW kernel 2.6.32-642.6.1.el6.684g0000.x86_64).  The first issue I ran into is that `yum install cmake` installs an older cmake (2.8.12.2) that is not supported by HyPhy, so I compiled the latest release of cmake (3.6.2).  I loaded the openmpi/gnu/2.0.1 Scyld module and ran through the `cmake; make MPI; sudo make install` process.  \r\n\r\nIf I run the resulting binary as a serial process, then it seems to function okay; for example, running `./HYPHYMPI Examples/SimpleAnalyses/HKY85.bf` returns the expected output.  However, if I run `mpirun -np 4 ./HYPHYMPI Examples/SimpleAnalyses/HKY85.bf`, then the output from four separate instances of HyPhy are written to the console.  Next, I wrote a little test script:\r\n```\r\nfprintf (stdout, MPI_NODE_COUNT);\r\n```\r\nand confirmed that if I invoke the script with `mpirun -np 4 test.bf` I get the following output:\r\n```\r\n1\r\n\r\n1\r\n\r\n1\r\n\r\n1\r\n\r\n```\r\n\r\nI'm going to try compiling with MPICH next and will report back.\r\n"},"comment":{"url":"https://api.github.com/repos/veg/hyphy/issues/comments/256987591","html_url":"https://github.com/veg/hyphy/issues/483#issuecomment-256987591","issue_url":"https://api.github.com/repos/veg/hyphy/issues/483","id":256987591,"user":{"login":"ArtPoon","id":1109328,"avatar_url":"https://avatars.githubusercontent.com/u/1109328?v=3","gravatar_id":"","url":"https://api.github.com/users/ArtPoon","html_url":"https://github.com/ArtPoon","followers_url":"https://api.github.com/users/ArtPoon/followers","following_url":"https://api.github.com/users/ArtPoon/following{/other_user}","gists_url":"https://api.github.com/users/ArtPoon/gists{/gist_id}","starred_url":"https://api.github.com/users/ArtPoon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ArtPoon/subscriptions","organizations_url":"https://api.github.com/users/ArtPoon/orgs","repos_url":"https://api.github.com/users/ArtPoon/repos","events_url":"https://api.github.com/users/ArtPoon/events{/privacy}","received_events_url":"https://api.github.com/users/ArtPoon/received_events","type":"User","site_admin":false},"created_at":"2016-10-28T18:01:34Z","updated_at":"2016-10-28T18:01:34Z","body":"Same result.  \r\n```\r\n$ module unload openmpi/gnu\r\n$ module load mpich/gnu\r\n$ make clean\r\n$ cmake .\r\n$ make MPI\r\n$ ./HYPHYMPI test.bf\r\n1\r\n\r\n$ which mpirun\r\n/opt/scyld/mpich/3.2/gnu/bin/mpirun\r\n$ mpirun -np 4 ./HYPHYMPI test.bf\r\n1\r\n\r\n1\r\n\r\n1\r\n\r\n1\r\n\r\n```\r\n"}}
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