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metaspace2020 / sm-engine-ansible

Setting up cloud infrastructure for the engine using Ansible
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ImportError: libgfortran.so.1 #12

Closed sean-ocall closed 8 years ago

sean-ocall commented 8 years ago

Hi guys, I'm getting an error when I try to run the spheroid test. Full error message here:

(sm)ubuntu@vagrant-ubuntu-trusty-64:/opt/dev/sm$ scripts/run.sh scripts/run_molecule_search.py spheroid /opt/dev/sm/tests/data/sci_test_search_job_spheroid_dataset/ /opt/dev/sm/tests/data/sci_test_search_job_spheroid_dataset/config.json ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. Traceback (most recent call last): File "scripts/run_molecule_search.py", line 10, in from sm.engine.search_job import SearchJob File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/search_job.py", line 15, in from sm.engine.msm_basic.msm_basic_search import MSMBasicSearch File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/msm_basic/msm_basic_search.py", line 2, in from sm.engine.msm_basic.formula_img_validator import sf_image_metrics, sf_image_metrics_est_fdr File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/msm_basic/formula_img_validator.py", line 8, in from pyImagingMSpec.image_measures import isotope_image_correlation, isotope_pattern_match File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/pyImagingMSpec/image_measures.py", line 2, in import scipy.stats File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/stats/init.py", line 321, in from .stats import File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/stats/stats.py", line 180, in import scipy.special as special File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/special/init.py", line 601, in from ._ufuncs import ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory

Looks like it's some sort of scipy issue from a quick google search.

lomereiter commented 8 years ago

Hi, I googled a bit and it looks like https://github.com/ContinuumIO/anaconda-issues/issues/686

The suggested workaround is to run conda install -f libgfortran==1

sean-ocall commented 8 years ago

Hi,

I should have said - I did try that (and have done so again), unfortunately it doesn't fix it, and the error message is the same. Thanks, Sean

lomereiter commented 8 years ago

Hi, Apparently some nasty package sets LD_PRELOAD to point to system-wide installation of libgfortran3, and it is not installed. Please try running apt-get install libgfortran3, hopefully it'll help.

sean-ocall commented 8 years ago

Yes, that did it!