itom crashing with PGRFlyCapture plugin and numpy-1.17-mkl

Create issue
Issue #91 new
Former user created an issue

Hi! Updating matplotlib (and consequently numpy) I ran into another issue. itom (latest Head) reproducibly crashes when opening when the PGRFlyCapture plugin is present with the message shown in image (numpy error). Regards Chris

Official response

  • M. Gronle

    The issue is known: Both Numpy+MKL and the FlyCapture driver use libiomp5 for OpenMP parallelization. Older numpy versions had the same version of libiomp5 than the FlyCapture SDK. Now, both versions are different, hence, numpy or PGRFlyCapture tend to load the wrong version of libiomp5.

    One possible solution is to not use Numpy+MKL but the official Numpy from pypi.python.org without MKL support (Vanilla) or to modify some FlyCapture DLLs as described in the https://bitbucket.org/itom/plugins/src/master/PGRFlyCapture/docs/pgrFlyCapture.rst file (section Compilation). This hack worked when we were compiling the official itom setup 3.2.1 and is applied there. Currently we did not find any better solution for this.

    Cheers

    Marc

Comments (3)

  1. M. Gronle

    The issue is known: Both Numpy+MKL and the FlyCapture driver use libiomp5 for OpenMP parallelization. Older numpy versions had the same version of libiomp5 than the FlyCapture SDK. Now, both versions are different, hence, numpy or PGRFlyCapture tend to load the wrong version of libiomp5.

    One possible solution is to not use Numpy+MKL but the official Numpy from pypi.python.org without MKL support (Vanilla) or to modify some FlyCapture DLLs as described in the https://bitbucket.org/itom/plugins/src/master/PGRFlyCapture/docs/pgrFlyCapture.rst file (section Compilation). This hack worked when we were compiling the official itom setup 3.2.1 and is applied there. Currently we did not find any better solution for this.

    Cheers

    Marc

  2. M. Gronle

    Further hint: This crash can occur if one installs itom 3.2.1 under Windows in the same location of a previously installed version of itom. If so, check if the file libiomp5md.dll exists in the lib subdirectory of the itom installation. If so, delete it (since it comes from the previous version of itom).

  3. M. Gronle

    Upcoming official itom setups will be shipped with the Vanilla versions of Numpy (from pypi.org), such that this problem should not occur in the future. Else the fix, mentioned in my comment above, has to be applied.

  4. Log in to comment