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Speedier gptmd again #2448

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Speedier gptmd again #2448

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f74d88e
update to gptmd engine
trishorts Dec 5, 2024
1e7544e
increment mods added
trishorts Dec 5, 2024
8b4d010
scores a property
trishorts Dec 5, 2024
5ddc279
eliminate unneccesary else
trishorts Dec 5, 2024
eff37a8
eliminate spaces
trishorts Dec 5, 2024
62a782d
thread safe increment
trishorts Dec 5, 2024
8ea589f
Merge remote-tracking branch 'upstream/master' into speedierGptmd
trishorts Dec 9, 2024
6600c84
might be more stable might not
trishorts Dec 9, 2024
db19d0b
Merge branch 'master' into speedierGptmd
trishorts Dec 12, 2024
50f2843
Update GptmdEngine.cs
trishorts Jan 30, 2025
e347f26
Merge branch 'master' into speedierGptmd
trishorts Jan 31, 2025
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19 changes: 15 additions & 4 deletions MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -65,9 +65,8 @@ public static bool ModFits(Modification attemptToLocalize, IBioPolymer protein,

protected override MetaMorpheusEngineResults RunSpecific()
{
var modDict = new ConcurrentDictionary<string, ConcurrentBag<Tuple<int, Modification>>>();
var mergedDictionaries = new ConcurrentDictionary<string, ConcurrentBag<Tuple<int, Modification>>>();
int modsAdded = 0;

int maxThreadsPerFile = CommonParameters.MaxThreadsToUsePerFile;
var psms = AllIdentifications.Where(b => b.FdrInfo.QValueNotch <= 0.05 && !b.IsDecoy).ToList();
if (psms.Any() == false)
Expand All @@ -76,6 +75,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
}
Parallel.ForEach(Partitioner.Create(0, psms.Count), new ParallelOptions() { MaxDegreeOfParallelism = maxThreadsPerFile }, (range) =>
{
var modDict = new ConcurrentDictionary<string, ConcurrentBag<Tuple<int, Modification>>>();
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This doesn't need to be concurrent, as it is created inside the parallel loop, i.e., one per thread

for (int i = range.Item1; i < range.Item2; i++)
{
foreach (var pepWithSetMods in psms[i].BestMatchingBioPolymersWithSetMods.Select(v => v.Peptide as PeptideWithSetModifications))
Expand Down Expand Up @@ -173,10 +173,21 @@ protected override MetaMorpheusEngineResults RunSpecific()
}
}
}
foreach (var kvp in modDict)
{
mergedDictionaries.AddOrUpdate(kvp.Key, kvp.Value, (key, oldValue) =>
{
foreach (var item in kvp.Value)
{
oldValue.Add(item);
}
return oldValue;
});
}
});

// Convert ConcurrentDictionary to Dictionary with HashSet
var finalModDictionary = modDict.ToDictionary(
var finalModDictionary = mergedDictionaries.ToDictionary(
kvp => kvp.Key,
kvp => new HashSet<Tuple<int, Modification>>(kvp.Value)
);
Expand Down Expand Up @@ -241,4 +252,4 @@ private static IEnumerable<Modification> GetPossibleMods(double totalMassToGetTo
}
}
}
}
}