{"action":"created","issue":{"url":"https://api.github.com/repos/NixOS/nixpkgs/issues/34580","repository_url":"https://api.github.com/repos/NixOS/nixpkgs","labels_url":"https://api.github.com/repos/NixOS/nixpkgs/issues/34580/labels{/name}","comments_url":"https://api.github.com/repos/NixOS/nixpkgs/issues/34580/comments","events_url":"https://api.github.com/repos/NixOS/nixpkgs/issues/34580/events","html_url":"https://github.com/NixOS/nixpkgs/pull/34580","id":294178130,"number":34580,"title":"openmpi: fix broken modules, disable dsos","user":{"login":"markuskowa","id":26470037,"avatar_url":"https://avatars1.githubusercontent.com/u/26470037?v=4","gravatar_id":"","url":"https://api.github.com/users/markuskowa","html_url":"https://github.com/markuskowa","followers_url":"https://api.github.com/users/markuskowa/followers","following_url":"https://api.github.com/users/markuskowa/following{/other_user}","gists_url":"https://api.github.com/users/markuskowa/gists{/gist_id}","starred_url":"https://api.github.com/users/markuskowa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/markuskowa/subscriptions","organizations_url":"https://api.github.com/users/markuskowa/orgs","repos_url":"https://api.github.com/users/markuskowa/repos","events_url":"https://api.github.com/users/markuskowa/events{/privacy}","received_events_url":"https://api.github.com/users/markuskowa/received_events","type":"User","site_admin":false},"labels":[{"id":731735423,"url":"https://api.github.com/repos/NixOS/nixpkgs/labels/10.rebuild-darwin:%2011-100","name":"10.rebuild-darwin: 11-100","color":"fbca04","default":false},{"id":731734101,"url":"https://api.github.com/repos/NixOS/nixpkgs/labels/10.rebuild-linux:%2011-100","name":"10.rebuild-linux: 11-100","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-02-04T07:49:22Z","updated_at":"2018-02-17T07:31:26Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/NixOS/nixpkgs/pulls/34580","html_url":"https://github.com/NixOS/nixpkgs/pull/34580","diff_url":"https://github.com/NixOS/nixpkgs/pull/34580.diff","patch_url":"https://github.com/NixOS/nixpkgs/pull/34580.patch"},"body":"###### Motivation for this change\r\nSome modules fail to resolve some symbols which seem to reside in other modules. This problem can be solved disabling `mca-dso`. All modules are then linked into one library thus eliminating the problem (see https://www.open-mpi.org/faq/?category=building#avoid-dso). \r\n\r\n```\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_btl_openib: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_btl_openib.so: undefined symbol: mca_mpool_grdma_evict (ignored)\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_dynamic: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_dynamic.so: undefined symbol: ompi_io_ompio_allgatherv_array (ignored)\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_individual: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_individual.so: undefined symbol: mca_io_ompio_file_write (ignored)\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_static: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_static.so: undefined symbol: ompi_io_ompio_allgather_array (ignored)\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_two_phase: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_two_phase.so: undefined symbol: ompi_io_ompio_set_aggregator_props (ignored)\r\n[lf5:23608] mca: base: component_find: unable to open /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_ylib: /nix/store/igiz5k6hyn9lc2704ipbbpfm77424cib-openmpi-1.10.7/lib/openmpi/mca_fcoll_ylib.so: undefined symbol: ompi_io_ompio_scatter_data (ignored)\r\n```\r\n\r\n\r\n###### Things done\r\n\r\n<!-- Please check what applies. Note that these are not hard requirements but merely serve as information for reviewers. -->\r\n\r\n- [x] Tested using sandboxing ([nix.useSandbox](http://nixos.org/nixos/manual/options.html#opt-nix.useSandbox) on NixOS, or option `build-use-sandbox` in [`nix.conf`](http://nixos.org/nix/manual/#sec-conf-file) on non-NixOS)\r\n- Built on platform(s)\r\n   - [x] NixOS\r\n   - [ ] macOS\r\n   - [ ] other Linux distributions\r\n- [ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside [nixos/tests](https://github.com/NixOS/nixpkgs/blob/master/nixos/tests))\r\n- [ ] Tested compilation of all pkgs that depend on this change using `nix-shell -p nox --run \"nox-review wip\"`\r\n- [x] Tested execution of all binary files (usually in `./result/bin/`)\r\n- [x] Fits [CONTRIBUTING.md](https://github.com/NixOS/nixpkgs/blob/master/.github/CONTRIBUTING.md).\r\n\r\n---\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/NixOS/nixpkgs/issues/comments/366423798","html_url":"https://github.com/NixOS/nixpkgs/pull/34580#issuecomment-366423798","issue_url":"https://api.github.com/repos/NixOS/nixpkgs/issues/34580","id":366423798,"user":{"login":"GrahamcOfBorg","id":25447658,"avatar_url":"https://avatars2.githubusercontent.com/u/25447658?v=4","gravatar_id":"","url":"https://api.github.com/users/GrahamcOfBorg","html_url":"https://github.com/GrahamcOfBorg","followers_url":"https://api.github.com/users/GrahamcOfBorg/followers","following_url":"https://api.github.com/users/GrahamcOfBorg/following{/other_user}","gists_url":"https://api.github.com/users/GrahamcOfBorg/gists{/gist_id}","starred_url":"https://api.github.com/users/GrahamcOfBorg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GrahamcOfBorg/subscriptions","organizations_url":"https://api.github.com/users/GrahamcOfBorg/orgs","repos_url":"https://api.github.com/users/GrahamcOfBorg/repos","events_url":"https://api.github.com/users/GrahamcOfBorg/events{/privacy}","received_events_url":"https://api.github.com/users/GrahamcOfBorg/received_events","type":"User","site_admin":false},"created_at":"2018-02-17T07:31:26Z","updated_at":"2018-02-17T07:31:26Z","author_association":"NONE","body":"Success on x86_64-linux [(full log)](https://logs.nix.ci/?key=nixos/nixpkgs.34580&attempt_id=463c6561-1de4-4459-a915-9c8ef4f8ff02)\n\n<details><summary>Partial log (click to expand)</summary><p>\n\n```\n********************************************************************************\nExecuting cythonize()\n/tmp/nix-build-python3.6-h5py-2.7.1.drv-0/h5py-2.7.1/h5py/h5p.pyx: cannot find cimported module 'mpi4py.mpi_c'\n....................................s................x.........................s.........................................x....................................s....................................ss.....................................................ss...................ssssss.................................................................x....x........................x.....x.................................................ssss..............\n----------------------------------------------------------------------\nRan 446 tests in 0.709s\n\nOK (skipped=17, expected failures=6)\n/nix/store/rlrdq6k2vj7h4r7r0dalllsk66d39d59-openmpi-3.0.0\n/nix/store/p63dminb4g3zavwg4axbx7wscy4qfv8d-python3.6-h5py-2.7.1\n```\n</p></details>\n\n"}}
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