{"action":"created","issue":{"url":"https://api.github.com/repos/I2PC/scipion/issues/357","repository_url":"https://api.github.com/repos/I2PC/scipion","labels_url":"https://api.github.com/repos/I2PC/scipion/issues/357/labels{/name}","comments_url":"https://api.github.com/repos/I2PC/scipion/issues/357/comments","events_url":"https://api.github.com/repos/I2PC/scipion/issues/357/events","html_url":"https://github.com/I2PC/scipion/issues/357","id":138934794,"number":357,"title":"cannot configure scipion with openmpi installed in custom paths ?","user":{"login":"pescobar","id":103797,"avatar_url":"https://avatars.githubusercontent.com/u/103797?v=3","gravatar_id":"","url":"https://api.github.com/users/pescobar","html_url":"https://github.com/pescobar","followers_url":"https://api.github.com/users/pescobar/followers","following_url":"https://api.github.com/users/pescobar/following{/other_user}","gists_url":"https://api.github.com/users/pescobar/gists{/gist_id}","starred_url":"https://api.github.com/users/pescobar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pescobar/subscriptions","organizations_url":"https://api.github.com/users/pescobar/orgs","repos_url":"https://api.github.com/users/pescobar/repos","events_url":"https://api.github.com/users/pescobar/events{/privacy}","received_events_url":"https://api.github.com/users/pescobar/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/I2PC/scipion/labels/install","name":"install","color":"bfe5bf"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":17,"created_at":"2016-03-07T09:48:35Z","updated_at":"2016-03-09T22:38:07Z","closed_at":null,"body":"Hi,\r\n\r\nI am trying to install scipion in my cluster and I found some issues when trying to use my openmpi installation in a custom path. \r\n\r\nBefore the installation I have defined `MPI_INCLUDE` and `MPI_LIBDIR`\r\n\r\n```\r\n[escobar@login11 ]$ env |egrep ^MPI\r\nMPI_INCLUDE=/scicore/soft/apps/OpenMPI/1.6.4-GCC-4.7.2/include\r\nMPI_LIBDIR=/scicore/soft/apps/OpenMPI/1.6.4-GCC-4.7.2/lib\r\n```\r\n\r\nVariables `LD_LIBRARY_PATH`, `PATH`, `CPATH` are also correctly defined when loading the openmpi module but still when I run `./scipion config` I get this error:\r\n\r\n```\r\nChecking paths in /scicore/home/scicore/escobar/soft-compilation/test-scipion/src/scipion/config/scipion.conf ...\r\n  Path to MPI_LIBDIR (/usr/lib64/mpi/gcc/openmpi/lib) should exist but it doesn't.\r\n  Path to MPI_INCLUDE (/usr/lib64/mpi/gcc/openmpi/include) should exist but it doesn't.\r\n  Cannot find file: /usr/lib64/mpi/gcc/openmpi/include/mpi.h\r\nErrors found.\r\n```\r\n\r\nIs there any way to force scipion to use the openmpi libraries in my custom paths? I have checked that if I hardcode the paths in scipion.conf it works but I would like to avoid hardcoding paths so if I want to use a different openmpi version the installation procedure keeps the same and I it's easier to automatize. Is this possible?\r\n\r\nI am testing with `scipion_v1.0.0_2016-02-20_linux64.tgz`\r\n\r\nthanks in advance for your help.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/I2PC/scipion/issues/comments/194546338","html_url":"https://github.com/I2PC/scipion/issues/357#issuecomment-194546338","issue_url":"https://api.github.com/repos/I2PC/scipion/issues/357","id":194546338,"user":{"login":"pescobar","id":103797,"avatar_url":"https://avatars.githubusercontent.com/u/103797?v=3","gravatar_id":"","url":"https://api.github.com/users/pescobar","html_url":"https://github.com/pescobar","followers_url":"https://api.github.com/users/pescobar/followers","following_url":"https://api.github.com/users/pescobar/following{/other_user}","gists_url":"https://api.github.com/users/pescobar/gists{/gist_id}","starred_url":"https://api.github.com/users/pescobar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pescobar/subscriptions","organizations_url":"https://api.github.com/users/pescobar/orgs","repos_url":"https://api.github.com/users/pescobar/repos","events_url":"https://api.github.com/users/pescobar/events{/privacy}","received_events_url":"https://api.github.com/users/pescobar/received_events","type":"User","site_admin":false},"created_at":"2016-03-09T22:38:07Z","updated_at":"2016-03-09T22:38:07Z","body":"I opened this issue to ask if paths to mpi libs can be passed as arguments or env vars during the installation. You clarified that this is  not possible so I think it's fine to close it."}}