Problems with tutorial: "calibrating single frames with processCcd.py"

Paula · April 8, 2021, 10:49pm

Hi everyone
I’m currently starting to use the lsst pipeline, and I’ve been following the Getting started tutorial (Getting started with the LSST Science Pipelines — LSST Science Pipelines). In part 2 to calibrate the data, the command processCcd.py is used; I can do the ‘dry-run’ to see what data will be processed in the Butler repository:

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ processCcd.py DATA --rerun processCcdOutputs --id --show data

root INFO: Loading config overrride file '/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/config/processCcd.py'

Cannot import lsst.meas.extensions.convolved (No module named convolved): disabling convolved flux measurements

root INFO: Loading config overrride file '/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/config/hsc/processCcd.py'

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 22, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 16, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 100, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903336, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 24, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903336, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 17, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903338, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 25, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903338, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 18, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903342, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 100, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903342, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 10, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903342, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 4, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903344, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 11, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903344, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 5, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903344, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 0, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903346, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 12, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903346, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 6, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903346, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 1, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903986, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903986, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 22, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903986, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 16, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903986, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 100, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903988, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 24, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903988, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903988, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 17, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903988, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 16, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903990, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 25, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 903990, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 18, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904010, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 100, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904010, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 10, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904010, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 4, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904014, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 12, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904014, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 6, 'expTime': 30.0}

id dataRef.dataId = {'taiObs': '2013-11-02', 'pointing': 671, 'visit': 904014, 'dateObs': '2013-11-02', 'filter': 'HSC-I', 'field': 'STRIPE82L', 'ccd': 1, 'expTime': 30.0}

But once I try to actually run it, I get the following error:

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ processCcd.py DATA --rerun processCcdOutputs --id
root INFO: Loading config overrride file '/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/config/processCcd.py'
Cannot import lsst.meas.extensions.convolved (No module named convolved): disabling convolved flux measurements
root INFO: Loading config overrride file '/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/config/hsc/processCcd.py'
root INFO: Running: /home/jahumada/.conda/envs/lsst/opt/lsst/pipe_tasks/bin/processCcd.py DATA --rerun processCcdOutputs --id
processCcd INFO: Processing {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}
processCcd.isr INFO: Performing ISR on sensor {'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}
processCcd FATAL: Failed on dataId={'taiObs': '2013-06-17', 'pointing': 533, 'visit': 903334, 'dateObs': '2013-06-17', 'filter': 'HSC-R', 'field': 'STRIPE82L', 'ccd': 23, 'expTime': 30.0}: disk I/O error
Traceback (most recent call last):
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/pipe_base/python/lsst/pipe/base/cmdLineTask.py", line 347, in __call__
    result = task.run(dataRef, **kwargs)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/pipe_base/python/lsst/pipe/base/timer.py", line 121, in wrapper
    res = func(self, *args, **keyArgs)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/pipe_tasks/python/lsst/pipe/tasks/processCcd.py", line 181, in run
    exposure = self.isr.runDataRef(sensorRef).exposure
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/python/lsst/obs/subaru/isr.py", line 230, in runDataRef
    defects = sensorRef.get("defects", immediate=True)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/butlerSubset.py", line 198, in get
    return self.butlerSubset.butler.get(datasetType, self.dataId, **rest)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/butler.py", line 699, in get
    location = self._locate(datasetType, dataId, write=False)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/butler.py", line 649, in _locate
    location = repoData.repo.map(datasetType, dataId, write=write)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/repository.py", line 183, in map
    loc = self._mapper.map(*args, **kwargs)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/obs_subaru/python/lsst/obs/hsc/hscMapper.py", line 156, in map
    location = super(HscMapper, self).map(datasetType, copyId, write=write)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/mapper.py", line 144, in map
    return func(self.validate(dataId), write)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/obs_base/python/lsst/obs/base/cameraMapper.py", line 688, in map_defects
    defectFitsPath = self._defectLookup(dataId=dataId)
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/obs_base/python/lsst/obs/base/cameraMapper.py", line 985, in _defectLookup
    (ccdVal, taiObs))
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/daf_persistence/python/lsst/daf/persistence/registries.py", line 365, in executeQuery
    c = self.conn.execute(cmd, values)
OperationalError: disk I/O error

Its an Input/Output error, but I have no idea why is wrong or how it could be solved, maybe there is something that I missed along the way!

Just in case, these are the commands I use to get to the point of using processccd.py

jahumada@leftraru2:/mnt/flock/jahumada/Paula$ source activate lsst

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ source eups-setups.sh

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ setup lsst_distrib

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ ml git-lfs

(lsst) jahumada@leftraru2:/mnt/flock/jahumada/Paula$ git lfs install

Git LFS initialized.

I apply the git-lfs related commands every time I log in since I’m using the lsst pipeline in a cluster called ‘leftraru’ from NLHPC.
Thanks a lot!

ktl · April 8, 2021, 11:42pm

What version of the Science Pipelines are you using? It looks like the problem is occurring when trying to access the defectRegistry.sqlite3 file, which went away a number of releases ago.

Paula · April 9, 2021, 2:15pm

Hi
The Science Pipelines were installed following the instructions of Installing and Using LSST Science Pipelines as a Conda Package — LSST Science Pipelines DM-10013 documentation, which ultimately uses the link http://conda.lsst.codes/stack/0.13.0
I imagine 0.13.0 to be the version?

ktl · April 10, 2021, 12:49am

Wow, that’s old (2017, I think). Thanks for pointing it out, but in general you should not be using development versions of the documentation (indicated by “Edition: DM-NNNNN” in the sidebar) as a reference.

If you would like to use a conda installation of the Science Pipelines rather than one of our other mechanisms documented at The LSST Science Pipelines — LSST Science Pipelines, I would suggest installing stackvana from conda-forge (courtesy of @beckermr ). I believe it will give you a recent weekly release, rather than a stable official release, however.

Paula · April 12, 2021, 7:14pm

Thanks a lot for the suggestion . I will try installing stackvana and see how it goes.

Paula · April 12, 2021, 11:42pm

Hi
I installed stackvana from conda-forge and now obtain the following:

(lsst) jahumada@leftraru3:/mnt/flock/jahumada/Paula$ processCcd.py DATA --rerun processCcdOutputs --id
Could not import lsstcppimport; please ensure the base package has been built (not just setup).

Traceback (most recent call last):
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/ip_isr/python/lsst/ip/isr/isrLib.py", line 24, in swig_import_helper
    return importlib.import_module(mname)
  File "/home/lmod/software/Anaconda3/2020.02/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 670, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 583, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 1043, in create_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
ImportError: dynamic module does not define module export function (PyInit__isrLib)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/pipe_tasks/bin/processCcd.py", line 23, in <module>
    from lsst.pipe.tasks.processCcd import ProcessCcdTask
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/pipe_tasks/python/lsst/pipe/tasks/processCcd.py", line 22, in <module>
    from lsst.ip.isr import IsrTask
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/ip_isr/python/lsst/ip/isr/__init__.py", line 24, in <module>
    from .isrLib import *
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/ip_isr/python/lsst/ip/isr/isrLib.py", line 27, in <module>
    _isrLib = swig_import_helper()
  File "/home/jahumada/.conda/envs/lsst/opt/lsst/ip_isr/python/lsst/ip/isr/isrLib.py", line 26, in swig_import_helper
    return importlib.import_module('_isrLib')
  File "/home/lmod/software/Anaconda3/2020.02/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
ModuleNotFoundError: No module named '_isrLib'

I suspect this is most probably because it’s not a stable release… considering that the ‘base’ version of the lsst pipeline that I have is from 2017. Do you think there is any way to complete the tutorials without updating the lsst pipeline?.

ktl · April 13, 2021, 4:59am

Stackvana (which we do not officially support) comes with all the software necessary; there’s no need for any “base” version.

I did the following successfully, following the instructions in Getting started with the LSST Science Pipelines — LSST Science Pipelines exactly, after the first two commands and making sure to start in a clean shell with no LSST-related environment variables set:

$ conda create -n sv stackvana
$ conda activate sv
$ git clone https://github.com/lsst/testdata_ci_hsc
$ mkdir DATA
$ setup -j -r testdata_ci_hsc
$ echo "lsst.obs.hsc.HscMapper" > DATA/_mapper
$ ingestImages.py DATA $TESTDATA_CI_HSC_DIR/raw/*.fits --mode=link
$ installTransmissionCurves.py DATA
$ ln -s $TESTDATA_CI_HSC_DIR/CALIB/ DATA/CALIB
$ mkdir -p DATA/ref_cats
$ ln -s $TESTDATA_CI_HSC_DIR/ps1_pv3_3pi_20170110 DATA/ref_cats/ps1_pv3_3pi_20170110
$ processCcd.py DATA --rerun processCcdOutputs --id --show data
$ processCcd.py DATA --rerun processCcdOutputs --id

Paula · April 19, 2021, 9:59pm

Hi thanks a lot for your help. I’m still unable to install stackvana completely, but parallel to this I could ultimately get the version 21 of the lsst pipeline installed. Now re-doing the tutorial, the processCcd.py command line gives me the following:

(lsst-scipipe-cb4e2dc) jahumada@leftraru4:/mnt/flock/jahumada/Paula$ processCcd.py DATA --rerun processCcdOutputs --id

root INFO: Loading config overrride file '/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/obs_subaru/21.0.0+d401af1dcd/config/processCcd.py'

root INFO: Loading config overrride file '/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/obs_subaru/21.0.0+d401af1dcd/config/hsc/processCcd.py'

CameraMapper INFO: Loading exposure registry from /mnt/flock/jahumada/Paula/DATA/registry.sqlite3

CameraMapper INFO: Loading calib registry from /mnt/flock/jahumada/Paula/DATA/CALIB/calibRegistry.sqlite3

CameraMapper INFO: Loading calib registry from /mnt/flock/jahumada/Paula/DATA/CALIB/calibRegistry.sqlite3

root INFO: Running: /home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/pipe_tasks/21.0.0+44ca056b81/bin/processCcd.py DATA --rerun processCcdOutputs --id

Caught signal 11, backtrace follows:

/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/utils/21.0.0+e0676b0dc8/lib/libutils.so(+0x17364) [0x2ad1ac1ec364]

/lib64/libc.so.6(+0x36280) [0x2ad1a1ae4280]

/home/lmod/software/MPI/intel/2019.2.187-GCC-8.2.0-2.31.1/impi/2019.2.187/imkl/2019.2.187/lib/intel64/libiomp5.so(+0x96c09) [0x2ad1b419bc09]

/home/lmod/software/MPI/intel/2019.2.187-GCC-8.2.0-2.31.1/impi/2019.2.187/imkl/2019.2.187/lib/intel64/libiomp5.so(+0xcde9a) [0x2ad1b41d2e9a]

/home/lmod/software/MPI/intel/2019.2.187-GCC-8.2.0-2.31.1/impi/2019.2.187/imkl/2019.2.187/lib/intel64/libiomp5.so(+0xb6c8d) [0x2ad1b41bbc8d]

/home/lmod/software/MPI/intel/2019.2.187-GCC-8.2.0-2.31.1/impi/2019.2.187/imkl/2019.2.187/lib/intel64/libiomp5.so(omp_get_max_threads+0x35) [0x2ad1b419ce45]

/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/base/21.0.0+d529cf1a41/lib/libbase.so(+0x4fb3) [0x2ad1ac226fb3]

/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/base/21.0.0+d529cf1a41/lib/libbase.so(lsst::base::disableImplicitThreading()+0x170) [0x2ad1ac227400]

/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/base/21.0.0+d529cf1a41/python/lsst/base/threads.so(+0x62ea) [0x2ad24fc662ea]

/home/jahumada/lsst_stack-v21/stack/miniconda3-py37_4.8.2-cb4e2dc/Linux64/base/21.0.0+d529cf1a41/python/lsst/base/threads.so(+0xeffd) [0x2ad24fc6effd]

python((null)+0x264) [0x5583eac3e9a4]

python(_PyMethodDef_RawFastCallKeywords+0x264) [0x5583eac3e9a4]

python((null)+0x4509) [0x5583eacbc639]

python(_PyEval_EvalFrameDefault+0x4509) [0x5583eacbc639]

python((null)+0x187) [0x5583eac2dfa7]

python(_PyFunction_FastCallKeywords+0x187) [0x5583eac2dfa7]

python(+0x17f995) [0x5583eac74995]

python((null)+0x681) [0x5583eacb87b1]

python(_PyEval_EvalFrameDefault+0x681) [0x5583eacb87b1]

python((null)+0x255) [0x5583eac0e735]

python(_PyEval_EvalCodeWithName+0x255) [0x5583eac0e735]

python((null)+0x521) [0x5583eac2e341]

python(_PyFunction_FastCallKeywords+0x521) [0x5583eac2e341]

python(+0x17f995) [0x5583eac74995]

python((null)+0x48b2) [0x5583eacbc9e2]

python(_PyEval_EvalFrameDefault+0x48b2) [0x5583eacbc9e2]

python((null)+0x255) [0x5583eac0e735]

python(_PyEval_EvalCodeWithName+0x255) [0x5583eac0e735]

python(PyEval_EvalCode+0x23) [0x5583eac0fb33]

python(+0x227962) [0x5583ead1c962]

python(PyRun_FileExFlags+0x9e) [0x5583ead26a1e]

python(PyRun_SimpleFileExFlags+0x1bb) [0x5583ead26c0b]

python(+0x232cf1) [0x5583ead27cf1]

python((null)+0x3c) [0x5583ead27d7c]

python(_Py_UnixMain+0x3c) [0x5583ead27d7c]

/lib64/libc.so.6((null)+0xf5) [0x2ad1a1ad03d5]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x2ad1a1ad03d5]

python(+0x1d7a25) [0x5583eaccca25]

Segmentation fault

I’m not sure if this is okay?, it seems that the objects couldn’t be processed for some reason, and I not sure why.

Thanks!

ktl · April 19, 2021, 10:05pm

I think you will have to disable your use of the Intel MPI/MKL library that seems to be inserted in place of the conda-installed libraries.

It’s possible you could build from source with that library in place, but I’m not sure how easy it would be, and the configuration would be unsupported.

Paula · April 21, 2021, 10:57pm

Thanks a lot!!! disabling the intel MPI/MKL library made it work