{"action":"created","issue":{"url":"https://api.github.com/repos/JuliaLang/julia/issues/10056","labels_url":"https://api.github.com/repos/JuliaLang/julia/issues/10056/labels{/name}","comments_url":"https://api.github.com/repos/JuliaLang/julia/issues/10056/comments","events_url":"https://api.github.com/repos/JuliaLang/julia/issues/10056/events","html_url":"https://github.com/JuliaLang/julia/issues/10056","id":56412979,"number":10056,"title":"HDF5 reading  in parallel loop : WARNING: Module HDF5 not defined on process 4, fatal error ...","user":{"login":"paulanalyst","id":7359510,"avatar_url":"https://avatars.githubusercontent.com/u/7359510?v=3","gravatar_id":"","url":"https://api.github.com/users/paulanalyst","html_url":"https://github.com/paulanalyst","followers_url":"https://api.github.com/users/paulanalyst/followers","following_url":"https://api.github.com/users/paulanalyst/following{/other_user}","gists_url":"https://api.github.com/users/paulanalyst/gists{/gist_id}","starred_url":"https://api.github.com/users/paulanalyst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulanalyst/subscriptions","organizations_url":"https://api.github.com/users/paulanalyst/orgs","repos_url":"https://api.github.com/users/paulanalyst/repos","events_url":"https://api.github.com/users/paulanalyst/events{/privacy}","received_events_url":"https://api.github.com/users/paulanalyst/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-02-03T17:55:41Z","updated_at":"2015-02-03T18:56:02Z","closed_at":null,"body":"               _\r\n   _       _ _(_)_     |  A fresh approach to technical computing\r\n  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org\r\n   _ _   _| |_  __ _   |  Type \"help()\" for help.\r\n  | | | | | | |/ _` |  |\r\n  | | |_| | | | (_| |  |  Version 0.4.0-dev+2847 (2015-01-21 18:34 UTC)\r\n _/ |\\__'_|_|_|\\__'_|  |  Commit fc61385 (12 days old master)\r\n|__/                   |  x86_64-w64-mingw32\r\n\r\njulia> using HDF5\r\n\r\njulia> addprocs(5)\r\n5-element Array{Any,1}:\r\n 2\r\n 3\r\n 4\r\n 5\r\n 6\r\n\r\njulia> using HDF5,JLD\r\n\r\njulia> fil=h5open(\"labels_F.h5\");obj=fil[\"F\"];k,l=size(obj);close(fil);\r\n\r\njulia> procs()\r\n6-element Array{Int64,1}:\r\n 1\r\n 2\r\n 3\r\n 4\r\n 5\r\n 6\r\n\r\njulia> ranking=@parallel (sum) for i=-l:-1\r\n       vec(h5read(\"labels_punkty.h5\",\"mygroup/punkty\",(:,i*-1)))\r\n       if mod(i,40)==0 println(i); end;\r\n       end\r\nWARNING: Module HDF5 not defined on process 4\r\nWARNING: Module HDF5 not defined on process 2\r\nfatal error on 4: fatal error on 2: WARNING: Module HDF5 not defined on process 3\r\nWARNING: Module HDF5 not defined on process 6\r\nfatal error on 3: fatal error on 6: WARNING: Module HDF5 not defined on process 5\r\nERROR: UndefVarError: HDF5 not defined\r\n in deserialize at serialize.jl:377\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:395\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in anonymous at task.jl:839\r\nfatal error on 5: ERROR: UndefVarError: HDF5 not defined\r\n in deserialize at serialize.jl:377\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:395\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in anonymous at task.jl:839\r\nERROR: UndefVarError: HDF5 not defined\r\n in deserialize at serialize.jl:377\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:395\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in anonymous at task.jl:839\r\nERROR: UndefVarError: HDF5 not defined\r\n in deserialize at serialize.jl:377\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:395\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in anonymous at task.jl:839\r\nERROR: UndefVarError: HDF5 not defined\r\n in deserialize at serialize.jl:377\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:395\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in deserialize at serialize.jl:335\r\n in anonymous at serialize.jl:355\r\n in ntuple at tuple.jl:30\r\n in deserialize_tuple at serialize.jl:355\r\n in handle_deserialize at serialize.jl:347\r\n in deserialize at serialize.jl:405\r\n in handle_deserialize at serialize.jl:352\r\n in anonymous at task.jl:839\r\nWorker 4 terminated.\r\nWorker 5 terminated.Worker 6 terminated.Worker 3 terminated.Worker 2 terminated.\r\n\r\n\r\n\r\nERROR: ProcessExitedException()\r\n in wait at task.jl:288\r\n in wait at task.jl:198\r\n in wait_full at multi.jl:586\r\n in remotecall_fetch at multi.jl:686\r\n in call_on_owner at multi.jl:733\r\n in fetch at multi.jl:741\r\n in _mapreduce at reduce.jl:135\r\n in preduce at multi.jl:1667\r\n\r\nPaul"},"comment":{"url":"https://api.github.com/repos/JuliaLang/julia/issues/comments/72711046","html_url":"https://github.com/JuliaLang/julia/issues/10056#issuecomment-72711046","issue_url":"https://api.github.com/repos/JuliaLang/julia/issues/10056","id":72711046,"user":{"login":"paulanalyst","id":7359510,"avatar_url":"https://avatars.githubusercontent.com/u/7359510?v=3","gravatar_id":"","url":"https://api.github.com/users/paulanalyst","html_url":"https://github.com/paulanalyst","followers_url":"https://api.github.com/users/paulanalyst/followers","following_url":"https://api.github.com/users/paulanalyst/following{/other_user}","gists_url":"https://api.github.com/users/paulanalyst/gists{/gist_id}","starred_url":"https://api.github.com/users/paulanalyst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulanalyst/subscriptions","organizations_url":"https://api.github.com/users/paulanalyst/orgs","repos_url":"https://api.github.com/users/paulanalyst/repos","events_url":"https://api.github.com/users/paulanalyst/events{/privacy}","received_events_url":"https://api.github.com/users/paulanalyst/received_events","type":"User","site_admin":false},"created_at":"2015-02-03T18:56:01Z","updated_at":"2015-02-03T18:56:01Z","body":"now:               _\r\n   _       _ _(_)_     |  A fresh approach to technical computing\r\n  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org\r\n   _ _   _| |_  __ _   |  Type \"help()\" for help.\r\n  | | | | | | |/ _` |  |\r\n  | | |_| | | | (_| |  |  Version 0.4.0-dev+2847 (2015-01-21 18:34 UTC)\r\n _/ |\\__'_|_|_|\\__'_|  |  Commit fc61385 (13 days old master)\r\n|__/                   |  x86_64-w64-mingw32\r\n\r\njulia> addprocs(5)\r\n5-element Array{Any,1}:\r\n 2\r\n 3\r\n 4\r\n 5\r\n 6\r\n\r\njulia>  using HDF5,JLD\r\n\r\njulia> fil=h5open(\"labels_F.h5\");obj=fil[\"F\"];k,l=size(obj);close(fil);\r\n\r\njulia>  procs()\r\n6-element Array{Int64,1}:\r\n 1\r\n 2\r\n 3\r\n 4\r\n 5\r\n 6\r\n\r\njulia> ranking=@parallel (sum) for i=-l:-1\r\n       vec(h5read(\"labels_punkty.h5\",\"mygroup/punkty\",(:,i*-1)))\r\n       if mod(i,40)==0 println(i); end;\r\n       end\r\nexception on exception on exception on 54: : exception on 2exception on : 6: 3: ERROR: MethodError: `sum` has no m\r\nethod matching sum(::Void, ::Void)\r\nClosest candidates are:\r\n  sum(!Matched::BitArray{N}, ::Any)\r\n  sum(!Matched::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(!Matched::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in anonymous at no file:3\r\n in anonymous at multi.jl:1528\r\n in anonymous at multi.jl:844\r\n in run_work_thunk at multi.jl:603\r\n in run_work_thunk at multi.jl:612\r\n in anonymous at task.jl:6\r\nERROR: MethodError: `sum` has no method matching sum(::Void, ::Void)\r\nClosest candidates are:\r\n  sum(!Matched::BitArray{N}, ::Any)\r\n  sum(!Matched::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(!Matched::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in anonymous at no file:3\r\n in anonymous at multi.jl:1528\r\n in anonymous at multi.jl:844\r\n in run_work_thunk at multi.jl:603\r\n in run_work_thunk at multi.jl:612\r\n in anonymous at task.jl:6\r\nERROR: MethodError: `sum` has no method matching sum(::Void, ::Void)\r\nClosest candidates are:\r\n  sum(!Matched::BitArray{N}, ::Any)\r\n  sum(!Matched::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(!Matched::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in anonymous at no file:3\r\n in anonymous at multi.jl:1528\r\n in anonymous at multi.jl:844\r\n in run_work_thunk at multi.jl:603\r\n in run_work_thunk at multi.jl:612\r\n in anonymous at task.jl:6\r\nERROR: MethodError: `sum` has no method matching sum(::Void, ::Void)\r\nClosest candidates are:\r\n  sum(!Matched::BitArray{N}, ::Any)\r\n  sum(!Matched::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(!Matched::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in anonymous at no file:3\r\n in anonymous at multi.jl:1528\r\n in anonymous at multi.jl:844\r\n in run_work_thunk at multi.jl:603\r\n in run_work_thunk at multi.jl:612\r\n in anonymous at task.jl:6\r\nERROR: MethodError: `sum` has no method matching sum(::Void, ::Void)\r\nClosest candidates are:\r\n  sum(!Matched::BitArray{N}, ::Any)\r\n  sum(!Matched::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(!Matched::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in anonymous at no file:3\r\n in anonymous at multi.jl:1528\r\n in anonymous at multi.jl:844\r\n in run_work_thunk at multi.jl:603\r\n in run_work_thunk at multi.jl:612\r\n in anonymous at task.jl:6\r\nERROR: MethodError: `sum` has no method matching sum(::MethodError, ::MethodError)\r\nClosest candidates are:\r\n  sum(::BitArray{N}, ::Any)\r\n  sum(::Union(Func{1},DataType,Function), ::Any)\r\n  sum{T}(::Base.SparseMatrix.SparseMatrixCSC{T,Ti<:Integer}, ::Any)\r\n  ...\r\n\r\n in _mapreduce at reduce.jl:137\r\n in preduce at multi.jl:1667\r\n\r\nPaul"}}