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Got wrong dimensions (too big) #10

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DStrelak opened this issue Aug 2, 2019 · 0 comments
Open

Got wrong dimensions (too big) #10

DStrelak opened this issue Aug 2, 2019 · 0 comments

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@DStrelak
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DStrelak commented Aug 2, 2019

00001: RUNNING PROTOCOL -----------------
00002: HostName: einstein
00003: PID: 2588
00004: Scipion: v2.0 (2019-04-23) Diocletian
00005: currentDir: /home/buildbot/scipionBot/devel/ScipionUserData/projects/TestMixedMovies
00006: workingDir: Runs/000182_XmippProtMovieCorr
00007: runMode: Continue
00008: MPI: 1
00009: threads: 1
00010: len(steps) 5 len(prevSteps) 0
00011: Starting at step: 1
00012: Running steps
00013: STARTED: _convertInputStep, step 1
00014: 2019-08-01 10:13:26.276986
00015: FINISHED: _convertInputStep, step 1
00016: 2019-08-01 10:13:26.286114
00017: STARTED: processMovieStep, step 2
00018: 2019-08-01 10:13:26.306540
00019: Processing movie: Runs/000182_XmippProtMovieCorr/tmp/movie_000001/Falcon_2012_06_12-14_33_35_0_movie.mrcs
00020: xmipp_cuda_movie_alignment_correlation -i "Runs/000182_XmippProtMovieCorr/tmp/movie_000001/input_movie.xmd" -o "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_shifts.xmd" --sampling 3.540000 --max_freq 4.000000 --Bspline 3 --cropULCorner 0 0 --cropDRCorner 1949 1949 --outside wrap --frameRange 0 8 --frameRangeSum 0 8 --max_shift 30 --oavg "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_mic.mrc" --oavgInitial Runs/000182_XmippProtMovieCorr/tmp/movie_000001/initialMic.mrc --oaligned Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_movie.mrcs --device 0 --storage Runs/000182_XmippProtMovieCorr/extra/fftBenchmark.txt --controlPoints 5 5 5 --patches 10 10 --locCorrDownscale 4 4 --patchesAvg 3
00021: Input movie: Runs/000182_XmippProtMovieCorr/tmp/movie_000001/input_movie.xmd
00022: Output metadata: Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_shifts.xmd
00023: Dark image:
00024: Gain image:
00025: Max. Shift: 30
00026: Max. Scale: 4
00027: Sampling: 3.54
00028: Solver iterations: 2
00029: Aligned movie: Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_movie.mrcs
00030: Aligned micrograph: Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_mic.mrc
00031: Unaligned micrograph: Runs/000182_XmippProtMovieCorr/tmp/movie_000001/initialMic.mrc
00032: Frame range alignment: 0 8
00033: Frame range sum: 0 8
00034: Crop corners (0, 0) (1949, 1949)
00035: Use input shifts: 0
00036: Binning factor: -1
00037: Bspline: 3
00038: Local shift correction: no
00039: Control points: 5 * 5 * 1 * 5
00040: Patches: 10 x 10
00041: Device: 0 (GPU-bcc22c91-f852-50f3-1188-54cfe3cea079)
00042: Benchmark storage Runs/000182_XmippProtMovieCorr/extra/fftBenchmark.txt
00043: Patches avg: 3
00044: File Runs/000182_XmippProtMovieCorr/extra/fftBenchmark.txt does NOT exist yet or cannot be read.
00045: Benchmarking cuFFT ...
00046: rank|placeness|type|data|X|Y|Z|batch|plan size estimate (MB)|plan size estimate 2 (MB)|plan size actual (MB)|data size (MB)|plan time (ms)|exec time (ms/signal)|exec time of batch (ms)|elements|performance (1k elem of signal/ms)|error message
00047: many|out-of-place|R2R forward|float|1944|1944|1|8|115.4487228394|115.4487228394|115.4487228394|230.7788085938|0.9869999886|0.2725250125|2.1802000999|30233088|13867.1162109375|
00048: Estimated binning factor = 1
00049: Settings for the movie: 1944(973) * 1944 * 1 * 9, batch: 8, inPlace: no
00050: Benchmarking cuFFT ...
00051: rank|placeness|type|data|X|Y|Z|batch|plan size estimate (MB)|plan size estimate 2 (MB)|plan size actual (MB)|data size (MB)|plan time (ms)|exec time (ms/signal)|exec time of batch (ms)|elements|performance (1k elem of signal/ms)|error message
00052: many|out-of-place|R2R forward|float|2000|2000|1|4|61.0961837769|61.0961837769|61.0961837769|122.1313476562|0.9869999886|0.2674749792|1.0698999166|16000000|14954.6699218750|
00053: Settings for the correlation: 2000(1001) * 2000 * 1 * 36, batch: 4, inPlace: no
00054: xmipp_cuda_movie_alignment_correlation: libraries/reconstruction_cuda/cuda_gpu_movie_alignment_correlation.cpp:37: void performFFTAndScale(T*, int, int, int, int, int, int, MultidimArray&) [with T = float]: Assertion `(inX / 2 + 1) >= outFFTX' failed.
00055: Aborted (core dumped)
00056: Traceback (most recent call last):
00057: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/protocol/protocol.py", line 186, in run
00058: self._run()
00059: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/protocol/protocol.py", line 237, in _run
00060: resultFiles = self._runFunc()
00061: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/protocol/protocol.py", line 233, in _runFunc
00062: return self._func(*self._args)
00063: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/em/protocol/protocol_movies.py", line 375, in processMovieStep
00064: self._processMovie(movie)
00065: File "/home/buildbot/scipionBot/devel/scipion/software/lib/python2.7/site-packages/xmipp3/protocols/protocol_movie_correlation.py", line 237, in _processMovie
00066: self.runJob('xmipp_cuda_movie_alignment_correlation', args, numberOfMpi=1)
00067: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/protocol/protocol.py", line 1311, in runJob
00068: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00069: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/protocol/executor.py", line 70, in runJob
00070: env=env, cwd=cwd, gpuList=self.getGpuList())
00071: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/utils/process.py", line 52, in runJob
00072: return runCommand(command, env, cwd)
00073: File "/home/buildbot/scipionBot/devel/scipion/pyworkflow/utils/process.py", line 67, in runCommand
00074: env=env, cwd=cwd)
00075: File "/home/buildbot/scipionBot/devel/scipion/software/lib/python2.7/subprocess.py", line 190, in check_call
00076: raise CalledProcessError(retcode, cmd)
00077: CalledProcessError: Command 'xmipp_cuda_movie_alignment_correlation -i "Runs/000182_XmippProtMovieCorr/tmp/movie_000001/input_movie.xmd" -o "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_shifts.xmd" --sampling 3.540000 --max_freq 4.000000 --Bspline 3 --cropULCorner 0 0 --cropDRCorner 1949 1949 --outside wrap --frameRange 0 8 --frameRangeSum 0 8 --max_shift 30 --oavg "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_mic.mrc" --oavgInitial Runs/000182_XmippProtMovieCorr/tmp/movie_000001/initialMic.mrc --oaligned Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_movie.mrcs --device 0 --storage Runs/000182_XmippProtMovieCorr/extra/fftBenchmark.txt --controlPoints 5 5 5 --patches 10 10 --locCorrDownscale 4 4 --patchesAvg 3' returned non-zero exit status 134
00078: Protocol failed: Command 'xmipp_cuda_movie_alignment_correlation -i "Runs/000182_XmippProtMovieCorr/tmp/movie_000001/input_movie.xmd" -o "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_shifts.xmd" --sampling 3.540000 --max_freq 4.000000 --Bspline 3 --cropULCorner 0 0 --cropDRCorner 1949 1949 --outside wrap --frameRange 0 8 --frameRangeSum 0 8 --max_shift 30 --oavg "Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_mic.mrc" --oavgInitial Runs/000182_XmippProtMovieCorr/tmp/movie_000001/initialMic.mrc --oaligned Runs/000182_XmippProtMovieCorr/extra/Falcon_2012_06_12-14_33_35_0_movie_aligned_movie.mrcs --device 0 --storage Runs/000182_XmippProtMovieCorr/extra/fftBenchmark.txt --controlPoints 5 5 5 --patches 10 10 --locCorrDownscale 4 4 --patchesAvg 3' returned non-zero exit status 134
00079: FAILED: processMovieStep, step 2
00080: 2019-08-01 10:14:11.461104
00081: ------------------- PROTOCOL FAILED (DONE 2/5)
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