From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2023-01-31 17:30:12
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Hi, We're trying to use the deepLearning toolkit package as part of xmipp, and have run into problems. The latest gives this error message: 00001: === XMIPP_WARNING === 00002: Do not apply large scale factor using B-splines choose fourier option. 00003: === XMIPP_WARNING === 00004: Do not apply large scale factor using B-splines choose fourier option. 00005: Using TensorFlow backend. 00006: Traceback (most recent call last): 00007: File "/usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/bin/xmipp_deepRes_resolution", line 35, in <module> 00008: import xmippLib 00009: ModuleNotFoundError: No module named 'xmippLib' 00010: Traceback (most recent call last): 00011: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run 00012: self._run() 00013: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run 00014: resultFiles = self._runFunc() 00015: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc 00016: return self._func(*self._args) 00017: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_deepres.py", line 236, in resolutionStep 00018: self.runJob("xmipp_deepRes_resolution", params, numberOfMpi=1, 00019: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1480, in runJob 00020: self._stepsExecutor.runJob(self._log, program, arguments, **kwargs) 00021: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob 00022: process.runJob(log, programName, params, 00023: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 55, in runJob 00024: return runCommand(command, env, cwd) 00025: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 70, in runCommand 00026: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, 00027: File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call 00028: raise CalledProcessError(retcode, cmd) 00029: subprocess.CalledProcessError: Command ' xmipp_deepRes_resolution -dl /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 -i Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s 1.660000 -o Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned non-zero exit status 1. 00030: Protocol failed: Command ' xmipp_deepRes_resolution -dl /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 -i Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s 1.660000 -o Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned non-zero exit status 1. Is there an xmippLib package that needs to be installed? I can find an xmippLib.so file, but python will not accept this as a package. Any insight would be helpful. David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp... |