implemented running_jobs

Author: louisponet

docs/src/guide/jobs.md

@@ -66,6 +66,7 @@ Loading all [`DFJobs`](@ref DFJob) that contain a given `fuzzy` can be done thro
 ```@docs
 registered_jobs
 load_jobs
+running_jobs
 ```
 ### Versioning
 

src/API.jl

@@ -18,10 +18,10 @@ export gencalc_scf, gencalc_vcrelax, gencalc_nscf, gencalc_bands, gencalc_projwf
 include("jobAPI.jl")
 #Basic Job Control Functionality
 export save, submit, abort, set_flow!, set_headerword!, isrunning, last_running_calculation,
-       last_submission,
+       last_submission, 
        progressreport, set_serverdir!, set_localdir!, structure, scale_cell!, volume,
        switch_version!, version, versions, registered_jobs, rm_version!, rm_versions!,
-       rm_tmp_dirs!, cleanup, load_jobs, last_version
+       rm_tmp_dirs!, cleanup, load_jobs, last_version, running_jobs
 
 #Basic Interaction with DFCalculations inside DFJob
 export set_cutoffs!

src/calculation.jl

@@ -148,7 +148,6 @@ end
 
 rm_outfiles(calc::DFCalculation) = rm.(outfiles(calc))
 
-
 include("qe/calculation.jl")
 include("elk/calculation.jl")
 include("wannier90/calculation.jl")

src/execs.jl

@@ -228,3 +228,24 @@ function exec(calculation::DFCalculation, exec::String)
     return getfirst(x -> occursin(exec, x.exec), calculation.execs)
 end
 exec(job::DFJob, exec::String) = getfirst(x -> occursin(exec, x.exec), execs(job))
+
+
+function Base.string(e::Exec)
+    direxec = joinpath(e.dir, e.exec)
+    str = "$direxec"
+    for flag in e.flags
+        str *= " $(join(fill('-', flag.minus_count)))$(flag.symbol)"
+        if !isa(flag.value, AbstractString)
+            for v in flag.value
+                str *= " $v"
+            end
+        else
+            str *= " $(flag.value)"
+        end
+    end
+    return str
+end
+    
+
+
+

src/fileio.jl

@@ -180,21 +180,8 @@ function writetojob(f, job, calculations::Vector{DFCalculation{Elk}}; kwargs...)
     return calculations
 end
 
-function writeexec(f, exec::Exec)
-    direxec = joinpath(exec.dir, exec.exec)
-    write(f, "$direxec")
-    for flag in exec.flags
-        write(f, " $(join(fill('-', flag.minus_count)))$(flag.symbol)")
-        if !isa(flag.value, AbstractString)
-            for v in flag.value
-                write(f, " $v")
-            end
-        else
-            write(f, " $(flag.value)")
-        end
-    end
-    return write(f, " ")
-end
+writeexec(f, exec::Exec) = 
+    write(f, string(exec) * " ")
 
 function writetojob(f, job, calculation::DFCalculation; kwargs...)
     filename   = infilename(calculation)

src/job.jl

@@ -220,17 +220,33 @@ is_slurm_job(job::DFJob) = haskey(job.metadata, :slurmid)
 """
     isrunning(job::DFJob; print=true)
 
-If the job was submitted through a scheduler like `slurm`,
-this will return whether the job is queued or running.
+Returns whether a job is running or not. If the job was
+submitted using `slurm`, a `QUEUED` status also counts as
+running.
 
-**Note:**
-For now only `slurm` is supported as scheduler.
+!!! note:
+    For now only `slurm` is supported as scheduler.
 """
 function isrunning(job::DFJob; print = true)
+    n = now()
     if is_slurm_job(job)
         return slurm_isrunning(job)
+    else
+        u = username()
+        l = last_running_calculation(job)
+        l === nothing && return false
+        codeexec = execs(l)[end].exec
+        try 
+            pids = parse.(Int, split(read(`pgrep $codeexec`, String)))
+            if isempty(pids)
+                return false
+            end
+            pwd = split(strip(read(`pwdx $(pids[end])`, String)))[end]
+            return abspath(pwd) == job.local_dir
+        catch
+            return false
+        end
     end
-    print && @warn "Job scheduler unknown."
     return false
 end
 

src/jobAPI.jl

@@ -63,6 +63,7 @@ function submit(job::DFJob; server = job.server, server_dir = job.server_dir, kw
             job.metadata[:slurmid] = sbatch(job)
             save_metadata(job)
         catch
+            pop!(job.metadata, :slurmid, nothing)
             run(job)
         end
     end
@@ -171,6 +172,9 @@ function set_localdir!(job::DFJob, dir::AbstractString; copy = false)
     if !isabspath(dir)
         dir = abspath(dir)
     end
+    if dir[end] == '/'
+        dir = dir[1:end-1]
+    end
     if copy
         verify_or_create(dir)
         cp(job, dir; temp = true)

src/registry.jl

@@ -36,16 +36,16 @@ end
 maybe_register_job(job::DFJob) = maybe_register_job(job.local_dir)
 
 """
-    registered_jobs(fuzzy::AbstractString)
+    registered_jobs(fuzzy::AbstractString = "")
 
-Lists all the known [`DFJob](@ref) directories that contain `fuzzy`.
+Lists all the known [`DFJobs`](@ref DFJob) directories that contain `fuzzy`.
 Intended to be used as:
 ```julia
 job_dirs = registered_jobs("NiO")
 job = DFJob(job_dirs[1])
 ```
 """
-registered_jobs(fuzzy::AbstractString) = filter(x -> occursin(fuzzy, x), JOB_REGISTRY)
+registered_jobs(fuzzy::AbstractString = "") = (cleanup_job_registry(; print=false); filter(x -> occursin(fuzzy, x), JOB_REGISTRY))
 
 """
     load_jobs(fuzzy::AbstractString)
@@ -55,7 +55,6 @@ Loads all the known [`DFJobs`](@ref DFJob) whose `local_dir` contains `fuzzy`.
 load_jobs(fuzzy::AbstractString) = DFJob.(registered_jobs(fuzzy))
 
 function request_job(job_dir::String)
-    cleanup_job_registry(; print = false)
     function timestamp(jobdir)
         if ispath(joinpath(jobdir, ".metadata.jld2"))
             md = load(joinpath(jobdir, ".metadata.jld2"))["metadata"]
@@ -88,3 +87,13 @@ function request_job(job_dir::String)
         @error err_msg
     end
 end
+
+"""
+    running_jobs(fuzzy::AbstractString = "")
+
+Loads all [`DFJobs`](@ref DFJob) that are currently running.
+"""
+function running_jobs(fuzzy::AbstractString = "")
+    jobs = load_jobs(fuzzy)
+    return filter(isrunning, jobs)
+end

src/utils.jl

@@ -203,3 +203,5 @@ end
 yesterday() = today() - Day(1)
 lastweek()  = today() - Week(1)
 lastmonth() = today() - Month(1)
+
+username() = read(`whoami`, String)