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enable subtomogram alignment on multiple gpus #69

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Merged
sroet merged 1 commit into from
Apr 16, 2025
Merged

enable subtomogram alignment on multiple gpus #69

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11 changes: 6 additions & 5 deletions pytom/alignment/GLocalSampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,7 +317,7 @@ def mainAlignmentLoop(alignmentJob, verbose=False):
else:
from pytom.gpu.gpuFunctions import applyFourierFilter
from pytom.agnostic.io import read
print(">>>>>>>>> Aligning Even ....")
print(">>>>>>>>> Aligning Even {len(evenSplitList)} processes on {alignmentJob.gpu}....")
resultsEven = mpi.parfor(alignParticleListGPU, list(zip(evenSplitList,
[currentReferenceEven] * len(evenSplitList),
[evenCompoundWedgeFile] * len(evenSplitList),
Expand All @@ -327,8 +327,8 @@ def mainAlignmentLoop(alignmentJob, verbose=False):
[alignmentJob.scoringParameters.preprocessing] * len(evenSplitList),
[progressBar] * neven,
[alignmentJob.samplingParameters.binning] * len(evenSplitList),
[verbose] * len(evenSplitList),alignmentJob.gpu)))
print(">>>>>>>>> Aligning Odd ....")
[verbose] * len(evenSplitList), [alignmentJob.gpu[p % len(alignmentJob.gpu)] for p in range(len(evenSplitList))])))
print(">>>>>>>>> Aligning Odd {len(oddSplitList)} processes on {alignmentJob.gpu}....")
resultsOdd = mpi.parfor(alignParticleListGPU, list(zip(oddSplitList,
[currentReferenceOdd]*len(oddSplitList),
[oddCompoundWedgeFile]*len(oddSplitList),
Expand All @@ -337,7 +337,7 @@ def mainAlignmentLoop(alignmentJob, verbose=False):
[alignmentJob.destination+"/"+'CurrentMask.xml']*len(oddSplitList),
[alignmentJob.scoringParameters.preprocessing]*len(oddSplitList),
[progressBar]*nodd, [alignmentJob.samplingParameters.binning]*len(oddSplitList),
[verbose]*len(oddSplitList), alignmentJob.gpu)))
[verbose]*len(oddSplitList), [alignmentJob.gpu[p % len(alignmentJob.gpu)] for p in range(len(oddSplitList))])))

xp.cuda.Device(alignmentJob.gpu[0]).use()
bestPeaksEvenSplit, plansEven = zip(*resultsEven)
Expand Down Expand Up @@ -829,10 +829,11 @@ def averageParallel(particleList,averageName, showProgressBar=False, verbose=Fal

#reference = average(particleList=plist, averageName=xxx, showProgressBar=True, verbose=False,
# createInfoVolumes=False, weighting=weighting, norm=False)
print(f"{splitFactor} averaging processes on {gpuIDs}")

averageList = mpi.parfor( average, list(zip(splitLists, avgNameList, [showProgressBar]*splitFactor,
[verbose]*splitFactor, [createInfoVolumes]*splitFactor,
[weighting]*splitFactor, [norm]*splitFactor, gpuIDs)))
[weighting]*splitFactor, [norm]*splitFactor, [gpuIDs[p % len(gpuIDs)] for p in range(len(splitLists))])))
if 'gpu' in device:
xp.cuda.Device(gpuIDs[0]).use()

Expand Down
2 changes: 2 additions & 0 deletions pytom/gpu/gpuStructures.py
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Expand Up @@ -435,6 +435,8 @@ def subPixelMaxSpline(self):

# get the shift
peak_shift = [ip - s // 2 for ip, s in zip(interpolated_peak, self.ccc_map.shape)]
# get the shift without binning
peak_shift = [ip*self.binning for ip in peak_shift]

# compared to cpu there is always a shift of 2 here... likely goes wrong before this function
# print([ip - s // 2 for ip, s in zip(peak, self.ccc_map.shape)])
Expand Down