Hello,
I have this pipeline to run a simulation on a SGE cluster (see below).
Basically I activate the same environment @everywhere and later load packages from the env.
The problem is that now Julia fails in activating the environment
using Pkg
PATH = joinpath(@__DIR__,"cluster_test")
Pkg.activate(PATH)
using ClusterManagers, Distributed, Logging
@info "Activating: $PATH"
addprocs_sge(5)
@everywhere using Distributed, Pkg
@everywhere Pkg.activate($PATH)
for worker in workers()
@spawnat worker (print("$myid()"))
end
The script return this error on @everywhere Pkg.activate($PATH)
$ julia _research/runtests.jl [11:03:24]
Activating project at `~/Documents/Research/phd_project/spiking/Tripod/_research/cluster_test`
[ Info: Activating: /home/alequa/Documents/Research/phd_project/spiking/Tripod/_research/cluster_test
Job 3940105 in queue.
Running.
Activating project at `~/Documents/Research/phd_project/spiking/Tripod/_research/cluster_test`
ERROR: LoadError: On worker 5:
IOError: close: Unknown system error -116 (Unknown system error -116)
Stacktrace:
[1] uv_error
@ ./libuv.jl:100 [inlined]
[2] close
@ ./filesystem.jl:141 [inlined]
[3] close
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:340
[4] #mkpidlock#7
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:95
[5] mkpidlock
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:90 [inlined]
[6] mkpidlock
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
[7] write_env_usage
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:539
[8] EnvCache
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:377
[9] EnvCache
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:356 [inlined]
[10] add_snapshot_to_undo
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:2189
[11] add_snapshot_to_undo
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:2185 [inlined]
[12] #activate#310
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1973
[13] activate
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1932
[14] top-level scope
@ none:1
[15] eval
@ ./boot.jl:385
[16] #invokelatest#2
@ ./essentials.jl:892
[17] invokelatest
@ ./essentials.jl:889
[18] #114
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:303
[19] run_work_thunk
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:70
[20] run_work_thunk
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:79
[21] #100
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/process_messages.jl:88
...and 1 more exception.
Stacktrace:
[1] sync_end(c::Channel{Any})
@ Base ./task.jl:448
[2] macro expansion
@ ./task.jl:480 [inlined]
[3] remotecall_eval(m::Module, procs::Vector{Int64}, ex::Expr)
@ Distributed ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/macros.jl:219
[4] top-level scope
@ ~/.julia/juliaup/julia-1.10.4+0.x64.linux.gnu/share/julia/stdlib/v1.10/Distributed/src/macros.jl:203
in expression starting at /home/alequa/Documents/Research/phd_project/spiking/Tripod/_research/runtests.jl:10
FAIL: 1
With this TOML
name = "cluster_test"
[deps]
ClusterManagers = "34f1f09b-3a8b-5176-ab39-66d58a4d544e"
DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
[compat]
DrWatson = "2.15.0"
julia = "1.10.4"