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#1 Fix submission fail due to values of time or cpu being 0.
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@zieglerSe
zieglerSe committed Oct 25, 2023
1 parent 37fe2bb commit d57620e
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Showing 5 changed files with 21 additions and 298 deletions.
12 changes: 0 additions & 12 deletions src/Slurmi/Environment.fs
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71 changes: 0 additions & 71 deletions src/Slurmi/HelperFunctions.fs
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33 changes: 20 additions & 13 deletions src/Slurmi/Job.fs
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Original file line number Diff line number Diff line change
@@ -1,9 +1,5 @@
namespace Slurmi
//#r "nuget: DynamicObj, 2.0.0"
//#r "nuget: Fli, 1.10.0"

// #r "nuget: Slurmi"
////// .Split "\n") // Replace("\r","\n"))
open DynamicObj
open System.Runtime.InteropServices
open Fli
Expand All @@ -26,14 +22,22 @@ type TimeClock =
}
with
override this.ToString() =
let hourString = sprintf "%02d" this.hour
let minuteString = sprintf "%02d" this.minute
let secondString =
match this.second with
| Some(s) -> sprintf ":%02d" s
| None -> ""
sprintf "%s:%s%s" hourString minuteString secondString

if this = {hour = 0; minute = 0; second = Some 0} then
let hourString = sprintf "%02d" this.hour
let minuteString = sprintf "01"
let secondString =
match this.second with
| Some(s) -> sprintf ":%02d" s
| None -> ""
sprintf "%s:%s%s" hourString minuteString secondString
else
let hourString = sprintf "%02d" this.hour
let minuteString = sprintf "%02d" this.minute
let secondString =
match this.second with
| Some(s) -> sprintf ":%02d" s
| None -> ""
sprintf "%s:%s%s" hourString minuteString secondString

type TimeFormat1 =
{
Expand Down Expand Up @@ -1711,7 +1715,10 @@ type LongCommand (jobName: string) =
static member SetCPUsPerTask
([<Optional; DefaultParameterValue(null)>]?CPUsPerTask:int) =
(fun (job: LongCommand) ->
CPUsPerTask |> DynObj.setValueOpt job "cpus-per-task"
if CPUsPerTask = (Some 0) then
Some 1 |> DynObj.setValueOpt job "cpus-per-task"
else
CPUsPerTask |> DynObj.setValueOpt job "cpus-per-task"
job
)
static member tryGetCPUsPerTask (job: LongCommand) =
Expand Down
2 changes: 0 additions & 2 deletions src/Slurmi/Slurmi.fsproj
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,9 @@

<ItemGroup>
<Compile Include="Process.fs" />
<Compile Include="Environment.fs" />
<Compile Include="Dependency.fs" />
<Compile Include="Job.fs" />
<Compile Include="Workflow.fs" />
<Compile Include="HelperFunctions.fs" />
</ItemGroup>

<ItemGroup>
Expand Down
201 changes: 1 addition & 200 deletions src/Slurmi/Workflow.fs
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
namespace Slurmi

open DynamicObj
open System.Runtime.InteropServices
open Fli
open Graphoscope
open System.Collections.Generic
Expand Down Expand Up @@ -103,14 +101,13 @@ module Workflow =
()

member this.checkAllForWorked (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobs:string ) (workedOn:List<string>) =
printfn "working on %A rn " jobs
this.checkForWorkedBash graph jobs workedOn
if (this.hasSuccessors graph jobs) then
let successors = this.getSuccessors graph jobs

successors |> Seq.iter (fun x -> this.checkAllForWorked graph (fst x) workedOn)
else
printfn "no successors"
()


member this.submitAll (graph:FGraph<string,JobWithDep,KindOfDependency>) (workedOn:List<string>)=
Expand Down Expand Up @@ -188,199 +185,3 @@ module Workflow =
Graph = WFGraph.createGraphFromJobList jobList
}
}

//namespace Slurmi

//open DynamicObj
//open System.Runtime.InteropServices
//open Fli
//open Graphoscope
//open System.Collections.Generic

//module Workflow =

// let callToTerminalCMD (command:string) =
// let processResponse =
// cli {
// Shell CMD
// Command command
// }
// |> Command.execute
// // processResponse.Text
// processResponse
// let callToTerminalBash (command:string) =
// let processResponse =
// cli {
// Shell BASH
// Command command
// }
// |> Command.execute
// // processResponse.Text
// processResponse

// let matchOutput x =
// match x with
// | Some value -> value
// | None -> failwith "No output"

// let getResultFromCall (command:string) =
// (callToTerminalCMD (command)).Text
// |> matchOutput

// let getResultFromCallBASH (command:string) =
// (callToTerminalBash (command)).Text
// |> matchOutput


// type JobWithDep =

// {
// JobInfo : Job
// AllOrAny : TypeOfDep
// DependingOn : (Job*KindOfDependency) list

// }


// let createGraphFromJobList (input: JobWithDep list)=
// let g = FGraph.empty<string,JobWithDep,KindOfDependency>
// input
// |> List.iter (
// fun jobWithDep ->
// //FGraph.addElement jobWithDep.JobInfo.Name jobWithDep.DependingOn jobWithDep.DependingOn |> ignore
// jobWithDep.JobInfo.OnlyKey |> OnlyKey.SetParsable true |> ignore
// jobWithDep.DependingOn
// |> List.iter (fun (job,dep) -> FGraph.addElement job.Name (input|> List.find (fun x -> x.JobInfo.Name = job.Name)) jobWithDep.JobInfo.Name jobWithDep dep g |> ignore))

// g

// let sendToTerminalAndReceiveJobID (job:JobWithDep)=
// // job
// // set parsable
// job.JobInfo.OnlyKey |> OnlyKey.SetParsable true |> ignore

// let res = getResultFromCallBASH (job.JobInfo.formatProcess)
// // submit
// // get return
// job.JobInfo |> Job.SetJobID res |> ignore
// // set as Job ID


// let sendToTerminalAndReceiveJobIDCMD (job:JobWithDep)=
// // job
// // set parsable
// job.JobInfo.OnlyKey |> OnlyKey.SetParsable true |> ignore

// let res = getResultFromCall (job.JobInfo.formatProcess)
// // submit
// // get return
// job.JobInfo |> Job.SetJobID res |> ignore
// // set as Job ID


// let getNodesWithoutDependencies (graph:FGraph<string,JobWithDep,KindOfDependency>) =
// graph.Keys
// |> Seq.map (fun x -> ((graph.Item x) |> fun (a,b,c) -> b), graph.Item x |> (FContext.predecessors) |> Seq.length)
// |> Seq.filter (fun x -> (snd x = 0 ) )
// |> Seq.map fst

// let getPredecessors (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobToSearch:string) =
// (graph.Item (jobToSearch)) |> FContext.predecessors



// let hasPredecessors (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobToSearch:string) =
// if (getPredecessors graph jobToSearch |> Seq.length > 0) then true else false


// let getSuccessors (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobToSearch:string) =
// (graph.Item (jobToSearch)) |> FContext.successors
// let hasSuccessors (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobToSearch:string) =
// if (getSuccessors graph jobToSearch |> Seq.length > 0) then true else false


// let arePredecessorsWorkedAlready (graph:FGraph<string,JobWithDep,KindOfDependency>)(jobToLook:string) (workedOn:List<string>) =
// let predecessors = getPredecessors graph jobToLook
// let predecessorsWorked = predecessors |> Seq.toArray |> Array.forall (fun x -> workedOn.Contains (fst x))
// predecessorsWorked

// let getJob (graph:FGraph<string,JobWithDep,KindOfDependency>) (job:string )=
// let name,job,kind = graph.[job]
// job

// let getKind (graph:FGraph<string,JobWithDep,KindOfDependency>) (job:string )=
// let name,job,kind = graph.[job]
// kind

// let getDependencies (graph:FGraph<string,JobWithDep,KindOfDependency>) (job:string )=
// let name,job,kind = graph.[job]
// name

// let getIdFromJobWithDep (jwd:JobWithDep) =
// jwd.JobInfo |> Job.tryGetJobID

// let getJobId (graph:FGraph<string,JobWithDep,KindOfDependency>) (job:string)=
// let job = getJob graph job
// let jid = job.JobInfo |> Job.tryGetJobID
// jid.Value |> string


// let formatDep (graph:FGraph<string,JobWithDep,KindOfDependency>) (job:string) =
// let deps = (getDependencies graph job) |> Seq.map (fun x ->(KindOfDependency.toString x.Value)+(getJobId graph x.Key)) |> Seq.toArray
// let jobInfo = getJob graph job
// let command = deps |> String.concat (jobInfo.AllOrAny |> TypeOfDep.toString)
// printfn "%A" command
// jobInfo.JobInfo.TwoDashes |> LongCommand.SetDependency command |> ignore

// let checkForWorked (graph:FGraph<string,JobWithDep,KindOfDependency>)(jobToLook:string) (workedOn:List<string>)=
// if (arePredecessorsWorkedAlready graph jobToLook workedOn) then

// if workedOn.Contains jobToLook
// then printfn "already worked on %A "jobToLook
// else
// printfn "added %A" jobToLook
// let jtwo = getJob graph jobToLook

// formatDep graph jobToLook
// jtwo.JobInfo |> Job.SetJobID (getResultFromCallBASH (jtwo.JobInfo.produceCall)) |> ignore

// workedOn.Add jobToLook
// else
// printfn "false"

// let rec checkAllForWorked (graph:FGraph<string,JobWithDep,KindOfDependency>) (jobs:string ) (workedOn:List<string>) =
// printfn "working on %A rn " jobs
// checkForWorked graph jobs workedOn
// if (hasSuccessors graph jobs) then
// let successors = getSuccessors graph jobs

// successors |> Seq.iter (fun x -> checkAllForWorked graph (fst x) workedOn)
// else
// printfn "no successors"






// let formatCallWithDep (job:JobWithDep)=
// let jobInfo = job.JobInfo
// let localStr = new System.Text.StringBuilder()
// localStr.Append ("#!/bin/bash \n") |> ignore
// localStr.Append ("#SBATCH ") |> ignore
// localStr.AppendFormat (sprintf "-J %s " jobInfo.Name) |> ignore
// localStr.Append (jobInfo.formatOneDash) |> ignore
// localStr.Append (jobInfo.formatTwoDashes) |> ignore
// localStr.Append (jobInfo.formatOnlyKey) |> ignore
// localStr.Append ("\n") |> ignore
// if jobInfo |> Job.tryGetEnvironment |> Option.isSome then
// localStr.Append (jobInfo.formatEnv) |> ignore
// localStr.Append jobInfo.formatProcess |> ignore
// localStr.ToString()


// let submitAll (graph:FGraph<string,JobWithDep,KindOfDependency>) (workedOn:List<string>)=
// let firstNodes =
// getNodesWithoutDependencies graph
// |> Seq.toArray
// firstNodes |> Array.map (fun x -> checkAllForWorked graph x.JobInfo.Name workedOn) |> ignore

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