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Fixing parallelization issue #26

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31337e2
Fixing parallelization issue
Klemet Aug 17, 2026
0f1fe2a
Stamp builds with sub-version for the parallelization fix
Klemet Aug 18, 2026
b538961
Remove redundant on-site MaturePresent check in WardSeedDispersal
Klemet Aug 19, 2026
7eda3e2
Use striped site locks to bound memory and remove Initialize-time all…
Klemet Aug 19, 2026
a962f4a
Revert build-layout and lib hint changes; drop hardcoded SHA stamp
Klemet Aug 19, 2026
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122 changes: 88 additions & 34 deletions src/Reproduction.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,24 @@ public static class Delegates
private static ISiteVar<bool> noEstablish;
private static IPlanting planting;

// We must synchronize access to each site's cohort list: while one
// worker thread adds/removes cohorts at a site, another thread may be
// reading (iterating) that same site's cohort list during seed
// dispersal, which would otherwise crash with a "collection was
// modified during enumeration" error.
//
// Instead of one lock object per active site (about 128 MB of lock
// objects on a 4-million-cell landscape, spent even when running with a
// single thread), we use a small fixed set of "striped" locks. Each
// site maps to a stripe via "data index % SiteLockCount" (see
// GetSiteLock below), so memory stays O(1).
//
// SiteLockCount only needs to be comfortably larger than the number of
// worker threads (ThreadCount). Collisions are then rare and harmless.
private const int SiteLockCount = 1024;

private static readonly object[] siteLocks = CreateSiteLocks();

private static Delegates.AddNewCohort addNewCohort;
private static Delegates.SufficientResources lightMethod = ReproductionDefaults.SufficientResources;
private static Delegates.Establish estbMethod = ReproductionDefaults.Establish;
Expand Down Expand Up @@ -370,50 +388,81 @@ public static void EnableEstablishment(ActiveSite site)
}
//---------------------------------------------------------------------

/// <summary>
/// Returns the lock object that guards a site's cohort collection.
///
/// IMPORTANT — DO NOT NEST THESE LOCKS.
/// These locks are "striped": many different sites share the same lock
/// object. That is fine as long as each lock is taken on its own and
/// released before the next one is taken (which is how all the current
/// code behaves).
///
/// Never put a GetSiteLock(...) lock INSIDE another GetSiteLock(...)
/// lock. If a future change ever modifies two sites' cohorts at once,
/// take the two locks one after the other, not one inside the other.
/// Nesting them can deadlock: the simulation then freezes silently with
/// no error message, which is very hard to diagnose.
/// </summary>
internal static object GetSiteLock(ActiveSite site)
{
return siteLocks[(int)(site.DataIndex % SiteLockCount)];
}

/// <summary>
/// Creates the fixed, striped set of lock objects.
/// </summary>
private static object[] CreateSiteLocks()
{
var locks = new object[SiteLockCount];
for (int i = 0; i < locks.Length; i++)
locks[i] = new object();
return locks;
}
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/// <summary>
/// Does the appropriate forms of reproduction at a site.
/// </summary>
public static void Reproduce(ActiveSite site, ThreadSafeRandom randomGen = null)
{
if(noEstablish[site])
if (noEstablish[site])
return;

bool plantingOccurred = planting.TryAt(site);
//bool plantingOccurred = false;
//for (int index = 0; index < speciesDataset.Count; ++index)
//{
// if (planting[site].Get(index))
// {
// ISpecies species = speciesDataset[index];
// if (PlantingEstablish(species, site))
// {
// AddNewCohort(species, site);
// plantingOccurred = true;
// }
// }
//}
object siteLock = GetSiteLock(site);

bool plantingOccurred;
lock (siteLock)
{
plantingOccurred = planting.TryAt(site);
}

bool sufficientLight;

bool serotinyOccurred = false;
if (! plantingOccurred) {
for (int index = 0; index < speciesDataset.Count; ++index) {
if (serotiny[site].Get(index)) {
if (!plantingOccurred)
{
for (int index = 0; index < speciesDataset.Count; ++index)
{
if (serotiny[site].Get(index))
{
ISpecies species = speciesDataset[index];
sufficientLight = SufficientResources(species, site);
if (sufficientLight && Establish(species, site)) {
// Temp set propBiomass to 1.0
AddNewCohort(species, site,"serotiny", 1.0);
if (sufficientLight && Establish(species, site))
{
lock (siteLock)
{
AddNewCohort(species, site, "serotiny", 1.0);
}
serotinyOccurred = true;
if (isDebugEnabled)
log.DebugFormat("site {0}: {1} post-fire regenerated",
site.Location, species.Name);
}
else {
else
{
if (isDebugEnabled)
log.DebugFormat("site {0}: {1} post-fire regen failed: {2}",
site.Location, species.Name,
! sufficientLight ? "insufficient light"
!sufficientLight ? "insufficient light"
: "didn't establish");
}
}
Expand All @@ -422,25 +471,32 @@ public static void Reproduce(ActiveSite site, ThreadSafeRandom randomGen = null)
serotiny[site].SetAll(false);

bool speciesResprouted = false;
if (! serotinyOccurred) {
for (int index = 0; index < speciesDataset.Count; ++index) {
if (resprout[site].Get(index)) {
if (!serotinyOccurred)
{
for (int index = 0; index < speciesDataset.Count; ++index)
{
if (resprout[site].Get(index))
{
ISpecies species = speciesDataset[index];
sufficientLight = SufficientResources(species, site);
if (sufficientLight &&
((randomGen == null ? Model.Core.NextDouble() : randomGen.NextDouble()) < species.VegReprodProb)) {
// Temp set propBiomass to 1.0
AddNewCohort(species, site, "resprout",1.0);
((randomGen == null ? Model.Core.NextDouble() : randomGen.NextDouble()) < species.VegReprodProb))
{
lock (siteLock)
{
AddNewCohort(species, site, "resprout", 1.0);
}
speciesResprouted = true;
if (isDebugEnabled)
log.DebugFormat("site {0}: {1} resprouted",
site.Location, species.Name);
}
else {
else
{
if (isDebugEnabled)
log.DebugFormat("site {0}: {1} resprouting failed: {2}",
site.Location, species.Name,
! sufficientLight ? "insufficient light"
!sufficientLight ? "insufficient light"
: "random # >= probability");
}
}
Expand All @@ -449,10 +505,8 @@ public static void Reproduce(ActiveSite site, ThreadSafeRandom randomGen = null)
resprout[site].SetAll(false);

planting.NotTriedAt(site);
if (! plantingOccurred && ! serotinyOccurred && ! speciesResprouted)
if (!plantingOccurred && !serotinyOccurred && !speciesResprouted)
seeding.Do(site, randomGen);


}


Expand Down
45 changes: 13 additions & 32 deletions src/Seeding.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -27,42 +27,23 @@ public Seeding(SeedingAlgorithm seedingAlgorithm)

public void Do(ActiveSite site, ThreadSafeRandom randomGen = null)
{
// Accumulate seedling density if using demographic seeding
//if (seedingAlgorithm.GetType() == typeof(DemographicSeeding.Algorithm))
//{
// for (int i = 0; i < Model.Core.Species.Count; i++)
// {
// ISpecies species = Model.Core.Species[i];
// bool established;
// double seedlingProportion = 1.0;
// seedingAlgorithm(species, site, out established, out seedlingProportion);
// if(established)
// {
// // Temp set propBiomass to 1.0
// Reproduction.AddNewCohort(species, site, seedlingProportion);
// if (isDebugEnabled)
// log.DebugFormat("site {0}: seeded {1}",
// site.Location, species.Name);
// }
// }
//}
//else
//{
for (int i = 0; i < Model.Core.Species.Count; i++)
for (int i = 0; i < Model.Core.Species.Count; i++)
{
ISpecies species = Model.Core.Species[i];
bool established;
double seedlingProportion = 1.0;
seedingAlgorithm(species, site, out established, out seedlingProportion, randomGen);
if (established)
{
ISpecies species = Model.Core.Species[i];
bool established;
double seedlingProportion = 1.0 ;
seedingAlgorithm(species, site, out established, out seedlingProportion, randomGen);
if (established)
lock (Reproduction.GetSiteLock(site))
{
Reproduction.AddNewCohort(species, site,"seed", seedlingProportion);
if (isDebugEnabled)
log.DebugFormat("site {0}: seeded {1}",
site.Location, species.Name);
Reproduction.AddNewCohort(species, site, "seed", seedlingProportion);
}
if (isDebugEnabled)
log.DebugFormat("site {0}: seeded {1}",
site.Location, species.Name);
}
//}
}
}

//---------------------------------------------------------------------
Expand Down
38 changes: 25 additions & 13 deletions src/WardSeedDispersal.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ public static void Algorithm(ISpecies species,
{
established = false;
seedlingProportion = 1;

if (species.EffectiveSeedDist == Universal)
{
UniversalDispersal.Algorithm(species, site, out established, out seedlingProportion);
Expand Down Expand Up @@ -77,10 +78,13 @@ public static void Algorithm(ISpecies species,
{
Site neighbor = site.GetNeighbor(reloc.Location);
if (neighbor != null && neighbor.IsActive)
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
lock (Reproduction.GetSiteLock((ActiveSite)neighbor))
{
established = true;
break;
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
{
established = true;
break;
}
}
}

Expand All @@ -91,21 +95,27 @@ public static void Algorithm(ISpecies species,
if (rCol == 0)
neighbor = site.GetNeighbor(new RelativeLocation(0, rRow));
if (neighbor != null && neighbor.IsActive)
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
lock (Reproduction.GetSiteLock((ActiveSite)neighbor))
{
established = true;
break;
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
{
established = true;
break;
}
}
}

if (dispersalProb > uniformProb)
{
Site neighbor = site.GetNeighbor(new RelativeLocation(rRow * -1, rCol * -1));
if (neighbor != null && neighbor.IsActive)
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
lock (Reproduction.GetSiteLock((ActiveSite)neighbor))
{
established = true;
break;
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
{
established = true;
break;
}
}
}

Expand All @@ -115,13 +125,15 @@ public static void Algorithm(ISpecies species,
if (rCol == 0)
neighbor = site.GetNeighbor(new RelativeLocation(0, rRow * -1));
if (neighbor != null && neighbor.IsActive)
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
lock (Reproduction.GetSiteLock((ActiveSite)neighbor))
{
established = true;
break;
if (Reproduction.MaturePresent(species, (ActiveSite)neighbor))
{
established = true;
break;
}
}
}

} // end foreach relativelocation
}

Expand Down
12 changes: 6 additions & 6 deletions src/library-succession.csproj
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,11 @@
<AssemblyProduct>Landis.Library.Succession-v10</AssemblyProduct>
<AssemblyCompany>LANDIS-II Foundation</AssemblyCompany>
<AssemblyCopyright>LANDIS-II Foundation</AssemblyCopyright>
<!-- AssemblyVersion deliberately held at 10.0 for binary binding compatibility
with existing references; Version/FileVersion carry the human-readable stamp. -->
<AssemblyVersion>10.0</AssemblyVersion>
<Version>10.0</Version>
<FileVersion>10.0</FileVersion>
<Version>10.1.0</Version>
<FileVersion>10.1.0</FileVersion>
<AssemblyDescription>Input Parameters Library for LANDIS-II</AssemblyDescription>
<TargetFramework>netstandard2.0</TargetFramework>
<GeneratePackageOnBuild>false</GeneratePackageOnBuild>
Expand All @@ -26,19 +28,17 @@
<AppendTargetFrameworkToOutputPath>false</AppendTargetFrameworkToOutputPath>
<CopyLocalLockFileAssemblies>true</CopyLocalLockFileAssemblies>
</PropertyGroup>

<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">


<OutputPath></OutputPath>
<!--<OutputPath>bin\Debug\</OutputPath>-->

</PropertyGroup>

<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
<OutputPath></OutputPath>
</PropertyGroup>



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<ItemGroup>
<!--<PackageReference Include="Accord" Version="3.8.0" />-->
<PackageReference Include="Accord.Statistics" Version="3.8.0" />
Expand Down