Fixed slurm_isrunning and reading 3D arrays from input

louisponet · May 21, 2021 · 39c35e4 · 39c35e4
1 parent 517b9d6
commit 39c35e4
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Showing 2 changed files with 9 additions and 13 deletions.
diff --git a/src/qe/fileio.jl b/src/qe/fileio.jl
@@ -783,22 +783,20 @@ function qe_read_input(filename; execs=[Exec("pw.x")], run=true, structure_name=
             if !haskey(parsed_flags, sym)
                 if typ <: AbstractMatrix
                     parsed_flags[sym] = length(parsedval) == 1 ? zeros(eltype(typ), ntyp, 10) : fill(zeros(eltype(typ), length(parsedval)), ntyp, 10) #arbitrary limit
-                else
+                elseif typ <: AbstractVector
                     parsed_flags[sym] = length(parsedval) == 1 ? zeros(eltype(typ), ntyp) : fill(zeros(eltype(typ), length(parsedval)), ntyp)
+                else
+                    dims = fill(nat, ndims(typ)-1)
+                    parsed_flags[sym] = zeros(eltype(typ), dims..., 3) 
                 end
             end
-            if length(ids) == 1
-                parsed_flags[sym][ids[1]] = length(parsedval) == 1 ? parsedval[1] : parsedval
-            else
-                parsed_flags[sym][ids[1], ids[2]] = length(parsedval) == 1 ? parsedval[1] : parsedval
-            end
+            parsed_flags[sym][ids...] =  length(parsedval) == 1 ? parsedval[1] : parsedval
         end
         structure = extract_structure!(structure_name, parsed_flags, cell_block, atsyms, atom_block, pseudos)
         delete!.((parsed_flags,), [:ibrav, :nat, :ntyp, :A, :celldm_1, :celldm])
         delete!.((parsed_flags,), [:Hubbard_U, :Hubbard_J0, :Hubbard_alpha, :Hubbard_beta, :Hubbard_J])
         delete!.((parsed_flags,), [:starting_magnetization, :angle1, :angle2]) #hubbard and magnetization flags
-    # elseif haskey(parsed_flags, :celldm) && parsed_flags[:celldm] != 
-
+
     else
         structure = nothing
     end

diff --git a/src/serverAPI.jl b/src/serverAPI.jl
@@ -68,12 +68,10 @@ function slurm_isrunning(job::DFJob)
     runslocal_assert(job)
     id = slurm_jobid(job)
     if id != -1
-        if slurm_process_command(`sacct -j $id --format=state`)[1] == "RUNNING"
-            return true
-        else
-            return false
-        end
+        line = getfirst(x -> occursin("JobState", x), slurm_process_command(`scontrol show job $id`))
+        return split(split(line)[1], "=")[2] == "RUNNING"
     else
+        @warn "No jobid found. Was your job submitted through slurm?"
         return false
     end
 end