{"action":"created","issue":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/329","labels_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/329/labels{/name}","comments_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/329/comments","events_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/329/events","html_url":"https://github.com/cBio/cbio-cluster/issues/329","id":110715730,"number":329,"title":"Relion install","user":{"login":"goldgury","id":15054814,"avatar_url":"https://avatars.githubusercontent.com/u/15054814?v=3","gravatar_id":"","url":"https://api.github.com/users/goldgury","html_url":"https://github.com/goldgury","followers_url":"https://api.github.com/users/goldgury/followers","following_url":"https://api.github.com/users/goldgury/following{/other_user}","gists_url":"https://api.github.com/users/goldgury/gists{/gist_id}","starred_url":"https://api.github.com/users/goldgury/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/goldgury/subscriptions","organizations_url":"https://api.github.com/users/goldgury/orgs","repos_url":"https://api.github.com/users/goldgury/repos","events_url":"https://api.github.com/users/goldgury/events{/privacy}","received_events_url":"https://api.github.com/users/goldgury/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":92,"created_at":"2015-10-09T18:45:30Z","updated_at":"2015-10-19T21:03:05Z","closed_at":null,"body":"Hello,\r\nwe need to install Relion\r\n\r\nhttp://www2.mrc-lmb.cam.ac.uk/groups/scheres/relion13_tutorial.pdf\r\n\r\non Hal cluster. Assistance will be much appreciated. \r\n\r\nRegards,\r\n\r\nYehuda "},"comment":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/comments/149346797","html_url":"https://github.com/cBio/cbio-cluster/issues/329#issuecomment-149346797","issue_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/329","id":149346797,"user":{"login":"goldgury","id":15054814,"avatar_url":"https://avatars.githubusercontent.com/u/15054814?v=3","gravatar_id":"","url":"https://api.github.com/users/goldgury","html_url":"https://github.com/goldgury","followers_url":"https://api.github.com/users/goldgury/followers","following_url":"https://api.github.com/users/goldgury/following{/other_user}","gists_url":"https://api.github.com/users/goldgury/gists{/gist_id}","starred_url":"https://api.github.com/users/goldgury/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/goldgury/subscriptions","organizations_url":"https://api.github.com/users/goldgury/orgs","repos_url":"https://api.github.com/users/goldgury/repos","events_url":"https://api.github.com/users/goldgury/events{/privacy}","received_events_url":"https://api.github.com/users/goldgury/received_events","type":"User","site_admin":false},"created_at":"2015-10-19T21:03:05Z","updated_at":"2015-10-19T21:03:05Z","body":"Now the output looks the way it should \r\n\r\nmpirun --machinefile $PBS_NODEFILE `which relion_refine_mpi` --o Class2D/run3a --i merged3e.star --particle_diameter 340 --angpix 2.82 --ctf --iter 25 --tau2_fudge 1.5 --K 50 --flatten_solvent  --zero_mask  --strict_highres_exp 12 --oversampling 1 --psi_step 10 --offset_range 10 --offset_step 4 --norm --scale  --j 1 --memory_per_thread 4 \r\n- === RELION MPI setup ===\r\n + Number of MPI processes             = 16\r\n + Master  (0) runs on host            = gpu-1-9.local\r\n + Slave     1 runs on host            = gpu-1-9.local\r\n + Slave     2 runs on host            = gpu-1-9.local\r\n + Slave     3 runs on host            = gpu-1-9.local\r\n + Slave     4 runs on host            = gpu-1-9.local\r\n + Slave     5 runs on host            = gpu-1-9.local\r\n + Slave     6 runs on host            = gpu-1-9.local\r\n + Slave     7 runs on host            = gpu-1-9.local\r\n + Slave     8 runs on host            = gpu-1-9.local\r\n + Slave     9 runs on host            = gpu-1-9.local\r\n + Slave    10 runs on host            = gpu-1-9.local\r\n + Slave    11 runs on host            = gpu-1-9.local\r\n + Slave    12 runs on host            = gpu-1-9.local\r\n + Slave    13 runs on host            = gpu-1-9.local\r\n + Slave    14 runs on host            = gpu-1-9.local\r\n + Slave    15 runs on host            = gpu-1-9.local\r\n =================\r\n Running in double precision. \r\n Estimating initial noise spectra \r\n  24/  24 sec ............................................................~~(,_,\">\r\nWARNING: There are only 2 particles in group 131\r\nWARNING: There are only 3 particles in group 142\r\nWARNING: There are only 4 particles in group 161\r\nWARNING: There are only 1 particles in group 163\r\nWARNING: There are only 1 particles in group 165\r\nWARNING: There are only 2 particles in group 174\r\nWARNING: There are only 2 particles in group 175\r\nWARNING: There are only 1 particles in group 176\r\nWARNING: There are only 4 particles in group 177\r\nWARNING: There are only 1 particles in group 178\r\nWARNING: There are only 1 particles in group 179\r\n"}}