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Segmentation fault (Ubuntu 18.04, Trelis 17.1) #94

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zxkjack123 opened this issue Mar 31, 2021 · 8 comments
Open

Segmentation fault (Ubuntu 18.04, Trelis 17.1) #94

zxkjack123 opened this issue Mar 31, 2021 · 8 comments

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@zxkjack123
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A "Segmentation fault (core dumped)" error happened when Trelis-plugin installed.

Environment

  • OS: Ubuntu 18.04
  • Trelis: Trelis 17.1
  • Trelis SDK: Installed SDK for Trelis 17.1
  • Submodules:
    • pyne: develop (failed to clone it during the default installation, it is manually linked to pyne develop)
    • mcnp2cad: default
  • Others: A fresh new account created for Trelis-plugin installation and test. Therefore, empty LD_LIBRARY_PATH.

Installation

  • Following the install procedure in instruction. (Copy and paste)

Behaviour

  • Without Trelis-plugin: Trelis 17.1 can be launched.
  • With Trelis-plugin: Segmentation fault (core dumped)

Status of the Trelis-plugin files

Files under /opt/Trelis-17.1/bin/plugins/svalinn:

/opt/Trelis-17.1/bin/plugins/svalinn$ ll -lh
total 11M
drwxrwxr-x  2 trelis trelis 4.0K 3月  31 10:40 ./
drwxrwxr-x 18 trelis trelis 4.0K 3月  31 10:41 ../
-rw-r--r--  1 trelis trelis 175K 3月  31 10:41 libdagmc.so
lrwxrwxrwx  1 trelis trelis   25 8月  14  2017 libhdf5_serial.so.100 -> libhdf5_serial.so.100.0.1
-rw-r--r--  1 trelis trelis 3.4M 8月  14  2017 libhdf5_serial.so.100.0.1
-rw-r--r--  1 trelis trelis 121K 3月  31 10:40 libiGeom.so
-rw-r--r--  1 trelis trelis 304K 3月  31 10:41 libmakeWatertight.so
-rw-r--r--  1 trelis trelis 416K 3月  31 10:40 libmcnp2cad.so
lrwxrwxrwx  1 trelis trelis   16 3月  31 10:20 libMOAB.so -> libMOAB.so.0.0.0
lrwxrwxrwx  1 trelis trelis   16 3月  31 10:20 libMOAB.so.0 -> libMOAB.so.0.0.0
-rw-r--r--  1 trelis trelis 4.6M 3月  31 10:41 libMOAB.so.0.0.0
-rw-r--r--  1 trelis trelis 1.2M 3月  31 10:41 libpyne_dagmc.so
-rw-r--r--  1 trelis trelis 122K 3月  31 10:40 libsvalinn_plugin.so
-rw-r--r--  1 trelis trelis 151K 3月  31 10:41 libuwuw.so

ldd info of libsvalinn_plugin.so:

	linux-vdso.so.1 (0x00007ffd5edd6000)
	libcubiti19.so => /opt/Trelis-17.1/bin/libcubiti19.so (0x00007f9424ef4000)
	libMOAB.so.0 => /opt/Trelis-17.1/bin/plugins/svalinn/libMOAB.so.0 (0x00007f94248b6000)
	libmakeWatertight.so => /opt/Trelis-17.1/bin/plugins/svalinn/libmakeWatertight.so (0x00007f9424670000)
	libmcnp2cad.so => /opt/Trelis-17.1/bin/plugins/svalinn/libmcnp2cad.so (0x00007f9424412000)
	libiGeom.so => /opt/Trelis-17.1/bin/plugins/svalinn/libiGeom.so (0x00007f94241f9000)
	libcubit_geom.so => /opt/Trelis-17.1/bin/libcubit_geom.so (0x00007f9423d04000)
	libcubit_util.so => /opt/Trelis-17.1/bin/libcubit_util.so (0x00007f9423a37000)
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f94236ae000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9423310000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f94230f8000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9422d07000)
	libgtcAttrib.so => /opt/Trelis-17.1/bin/libgtcAttrib.so (0x00007f9422af7000)
	libSpaACIS.so => /opt/Trelis-17.1/bin/libSpaACIS.so (0x00007f941f9aa000)
	libmg-tetra_hpc.so => /opt/Trelis-17.1/bin/libmg-tetra_hpc.so (0x00007f941f6a3000)
	libmg-adapt.so => /opt/Trelis-17.1/bin/libmg-adapt.so (0x00007f9428845000)
	libmg-tetra.so => /opt/Trelis-17.1/bin/libmg-tetra.so (0x00007f941f15e000)
	libmg-surfopt.so => /opt/Trelis-17.1/bin/libmg-surfopt.so (0x00007f941ef1c000)
	libmg-cadsurf.so => /opt/Trelis-17.1/bin/libmg-cadsurf.so (0x00007f941e97e000)
	libmeshgems_stubs.so => /opt/Trelis-17.1/bin/libmeshgems_stubs.so (0x00007f941e87d000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f941e65e000)
	libmeshgems.so => /opt/Trelis-17.1/bin/libmeshgems.so (0x00007f941e3f9000)
	libcubit_sizing_source.so => /opt/Trelis-17.1/bin/libcubit_sizing_source.so (0x00007f941e1f3000)
	libshowviz_cubit.so => /opt/Trelis-17.1/bin/libshowviz_cubit.so (0x00007f941df78000)
	libshowviz_sim.so => /opt/Trelis-17.1/bin/libshowviz_sim.so (0x00007f941dd2e000)
	libshowviz_mesh.so => /opt/Trelis-17.1/bin/libshowviz_mesh.so (0x00007f941dae7000)
	libshowviz_base.so => /opt/Trelis-17.1/bin/libshowviz_base.so (0x00007f941d859000)
	libshowviz_geom.so => /opt/Trelis-17.1/bin/libshowviz_geom.so (0x00007f941d619000)
	libvtkCommonCore-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonCore-8.2.so.1 (0x00007f941d005000)
	libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f941cccd000)
	libmesquite.so => /opt/Trelis-17.1/bin/libmesquite.so (0x00007f941c91c000)
	libSPAIInterop.so => /opt/Trelis-17.1/bin/libSPAIInterop.so (0x00007f941c6fb000)
	libSPAIAcis.so => /opt/Trelis-17.1/bin/libSPAIAcis.so (0x00007f941c4f0000)
	libSPAIop.so => /opt/Trelis-17.1/bin/libSPAIop.so (0x00007f941c1ad000)
	libcubit_smd.so => /opt/Trelis-17.1/bin/libcubit_smd.so (0x00007f941bf65000)
	libtrelis_lm.so => /opt/Trelis-17.1/bin/libtrelis_lm.so (0x00007f941be9c000)
	libQt5Core.so.5 => /opt/Trelis-17.1/bin/libQt5Core.so.5 (0x00007f941b8c3000)
	libverdict.so.1.3 => /opt/Trelis-17.1/bin/libverdict.so.1.3 (0x00007f941b692000)
	liblpsolve55.so => /opt/Trelis-17.1/bin/liblpsolve55.so (0x00007f941b3d4000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f941b1d0000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f941afc8000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f941adab000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f94287ef000)
	libhdf5_serial.so.100 => /opt/Trelis-17.1/bin/plugins/svalinn/libhdf5_serial.so.100 (0x00007f941a853000)
	libvtkRenderingOpenGL2-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingOpenGL2-8.2.so.1 (0x00007f941a42a000)
	libvtkglew-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkglew-8.2.so.1 (0x00007f941a17e000)
	libvtkInteractionWidgets-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkInteractionWidgets-8.2.so.1 (0x00007f9419ce8000)
	libvtkFiltersVerdict-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersVerdict-8.2.so.1 (0x00007f9419ac4000)
	libXt.so.6 => /usr/lib/x86_64-linux-gnu/libXt.so.6 (0x00007f941985b000)
	libSM.so.6 => /usr/lib/x86_64-linux-gnu/libSM.so.6 (0x00007f9419653000)
	libICE.so.6 => /usr/lib/x86_64-linux-gnu/libICE.so.6 (0x00007f9419438000)
	libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f9419226000)
	libvtkRenderingCore-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingCore-8.2.so.1 (0x00007f9418e12000)
	libvtkFiltersSources-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersSources-8.2.so.1 (0x00007f9418b68000)
	libvtkFiltersGeneral-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersGeneral-8.2.so.1 (0x00007f9418645000)
	libvtkFiltersCore-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersCore-8.2.so.1 (0x00007f9417ece000)
	libvtkCommonExecutionModel-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonExecutionModel-8.2.so.1 (0x00007f9417c13000)
	libvtkCommonDataModel-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonDataModel-8.2.so.1 (0x00007f94175ed000)
	libvtkCommonTransforms-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonTransforms-8.2.so.1 (0x00007f94173bc000)
	libvtkCommonMisc-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonMisc-8.2.so.1 (0x00007f94171a0000)
	libvtkCommonMath-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonMath-8.2.so.1 (0x00007f9416f6b000)
	libvtkverdict-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkverdict-8.2.so.1 (0x00007f9416d37000)
	libvtkRenderingLabel-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingLabel-8.2.so.1 (0x00007f9416aaa000)
	libvtkFiltersModeling-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersModeling-8.2.so.1 (0x00007f9416817000)
	libvtkFiltersExtraction-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersExtraction-8.2.so.1 (0x00007f9416518000)
	libvtkRenderingFreeType-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingFreeType-8.2.so.1 (0x00007f941626d000)
	libvtkfreetype-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkfreetype-8.2.so.1 (0x00007f9415fdf000)
	libvtkzlib-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkzlib-8.2.so.1 (0x00007f9415dc3000)
	libvtkRenderingAnnotation-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingAnnotation-8.2.so.1 (0x00007f9415a99000)
	libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f941582a000)
	libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007f941559e000)
	libvtkInteractionStyle-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkInteractionStyle-8.2.so.1 (0x00007f941534d000)
	libvtkIOImage-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkIOImage-8.2.so.1 (0x00007f9414fa9000)
	libvtkFiltersGeometry-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersGeometry-8.2.so.1 (0x00007f9414d23000)
	libvtkCommonSystem-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonSystem-8.2.so.1 (0x00007f9414b0e000)
	libvtksys-8.2.so.1 => /opt/Trelis-17.1/bin/libvtksys-8.2.so.1 (0x00007f94148b1000)
	libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f9414689000)
	libSPAIInteropC.so => /opt/Trelis-17.1/bin/libSPAIInteropC.so (0x00007f9414451000)
	libSPAIopC.so => /opt/Trelis-17.1/bin/libSPAIopC.so (0x00007f94140fb000)
	libSPAIopAcisC.so => /opt/Trelis-17.1/bin/libSPAIopAcisC.so (0x00007f9413eef000)
	libQt5Network.so.5 => /opt/Trelis-17.1/bin/libQt5Network.so.5 (0x00007f9413d5e000)
	libQt5Widgets.so.5 => /opt/Trelis-17.1/bin/libQt5Widgets.so.5 (0x00007f94136ee000)
	libQt5Gui.so.5 => /opt/Trelis-17.1/bin/libQt5Gui.so.5 (0x00007f94130d4000)
	libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007f9412ed1000)
	libvtkFiltersHybrid-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersHybrid-8.2.so.1 (0x00007f9412be5000)
	libvtkImagingGeneral-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingGeneral-8.2.so.1 (0x00007f94128f2000)
	libvtkImagingHybrid-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingHybrid-8.2.so.1 (0x00007f941267a000)
	libvtkRenderingVolume-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkRenderingVolume-8.2.so.1 (0x00007f9411f21000)
	libvtkImagingColor-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingColor-8.2.so.1 (0x00007f9411ccb000)
	libvtkCommonComputationalGeometry-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonComputationalGeometry-8.2.so.1 (0x00007f9411a95000)
	libvtkImagingCore-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingCore-8.2.so.1 (0x00007f94115d5000)
	libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f94113ce000)
	libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f94111b9000)
	libvtkCommonColor-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkCommonColor-8.2.so.1 (0x00007f9410f9c000)
	libvtkFiltersStatistics-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkFiltersStatistics-8.2.so.1 (0x00007f9410cde000)
	libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f9410aad000)
	libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f94107f7000)
	libvtkDICOMParser-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkDICOMParser-8.2.so.1 (0x00007f94105dd000)
	libvtkmetaio-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkmetaio-8.2.so.1 (0x00007f941032f000)
	libvtkjpeg-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkjpeg-8.2.so.1 (0x00007f94100c9000)
	libvtkpng-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkpng-8.2.so.1 (0x00007f940fe85000)
	libvtktiff-8.2.so.1 => /opt/Trelis-17.1/bin/libvtktiff-8.2.so.1 (0x00007f940fc09000)
	libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f940fa05000)
	libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f940f7ff000)
	libSPAXCommon.so => /opt/Trelis-17.1/bin/libSPAXCommon.so (0x00007f940f5f5000)
	libSPAXBase.so => /opt/Trelis-17.1/bin/libSPAXBase.so (0x00007f940f2a7000)
	libSPAXInterop.so => /opt/Trelis-17.1/bin/libSPAXInterop.so (0x00007f940f00d000)
	libSPAXBoundaryRep.so => /opt/Trelis-17.1/bin/libSPAXBoundaryRep.so (0x00007f940edb1000)
	libSPAXIop.so => /opt/Trelis-17.1/bin/libSPAXIop.so (0x00007f940ea34000)
	libSPAXIopAcis.so => /opt/Trelis-17.1/bin/libSPAXIopAcis.so (0x00007f940e811000)
	libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x00007f940e609000)
	libvtkImagingSources-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingSources-8.2.so.1 (0x00007f940e3bb000)
	libvtkIOXML-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkIOXML-8.2.so.1 (0x00007f940e0c4000)
	libvtkIOXMLParser-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkIOXMLParser-8.2.so.1 (0x00007f940dead000)
	libvtkImagingFourier-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkImagingFourier-8.2.so.1 (0x00007f940dc87000)
	libSPAXicuC.so => /opt/Trelis-17.1/bin/libSPAXicuC.so (0x00007f940da82000)
	libSPAXGeometryRepresentation.so => /opt/Trelis-17.1/bin/libSPAXGeometryRepresentation.so (0x00007f940d73f000)
	libSPAXAssemblyRep.so => /opt/Trelis-17.1/bin/libSPAXAssemblyRep.so (0x00007f940d520000)
	libSPAXVisualizationRep.so => /opt/Trelis-17.1/bin/libSPAXVisualizationRep.so (0x00007f940d2a5000)
	libSPAXVisualizationAsm.so => /opt/Trelis-17.1/bin/libSPAXVisualizationAsm.so (0x00007f940d093000)
	libSPAXPMIRep.so => /opt/Trelis-17.1/bin/libSPAXPMIRep.so (0x00007f940ce7f000)
	libSPAXManufacturingRep.so => /opt/Trelis-17.1/bin/libSPAXManufacturingRep.so (0x00007f940cc77000)
	libSPAXAcis.so => /opt/Trelis-17.1/bin/libSPAXAcis.so (0x00007f940c865000)
	libSPAXAcisBase.so => /opt/Trelis-17.1/bin/libSPAXAcisBase.so (0x00007f940c611000)
	libSPAXAcisManufacturingImporter.so => /opt/Trelis-17.1/bin/libSPAXAcisManufacturingImporter.so (0x00007f940c3fe000)
	libSPAXAcisPMIImporter.so => /opt/Trelis-17.1/bin/libSPAXAcisPMIImporter.so (0x00007f940c1d0000)
	libvtkIOCore-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkIOCore-8.2.so.1 (0x00007f940bf62000)
	libvtkexpat-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkexpat-8.2.so.1 (0x00007f940bd33000)
	libSPAXicuuc54.so => /opt/Trelis-17.1/bin/libSPAXicuuc54.so (0x00007f940b993000)
	libSPAXicuin54.so => /opt/Trelis-17.1/bin/libSPAXicuin54.so (0x00007f940b505000)
	libSPAXicuio54.so => /opt/Trelis-17.1/bin/libSPAXicuio54.so (0x00007f940b2f8000)
	libSPAXAcisKernel.so => /opt/Trelis-17.1/bin/libSPAXAcisKernel.so (0x00007f940b0e6000)
	libSPAXAcisMesh.so => /opt/Trelis-17.1/bin/libSPAXAcisMesh.so (0x00007f940aedb000)
	libSPAXAcisPMIEntities.so => /opt/Trelis-17.1/bin/libSPAXAcisPMIEntities.so (0x00007f940ac91000)
	libvtklz4-8.2.so.1 => /opt/Trelis-17.1/bin/libvtklz4-8.2.so.1 (0x00007f940aa74000)
	libvtklzma-8.2.so.1 => /opt/Trelis-17.1/bin/libvtklzma-8.2.so.1 (0x00007f940a844000)
	libvtkdoubleconversion-8.2.so.1 => /opt/Trelis-17.1/bin/libvtkdoubleconversion-8.2.so.1 (0x00007f940a637000)
	libicudt54.so => /opt/Trelis-17.1/bin/libicudt54.so (0x00007f9408c0b000)
@zxkjack123
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Tried pyne @ 860d983, and rebuild dagmc, trelis-plugin again. But failed with Segmentation fault (core dumped) too.

@bam241
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bam241 commented Mar 31, 2021

have you try to unset you LD_LIBRARY_PATH before launching Trelis ?

@bam241
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bam241 commented Mar 31, 2021

if that still does not work you can always try the one built with our GitHub Action:
https://github.com/svalinn/Trelis-plugin/suites/2383066015/artifacts/50610701

@bam241
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bam241 commented Mar 31, 2021

also are you able to get a backtrace ?

also have you compiled the MOAB DAGMC and the plugin with the -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 flag ?

@zxkjack123
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have you try to unset you LD_LIBRARY_PATH before launching Trelis ?

Sure, but this error happens after unsetting LD_LIBRARY_PATH too. Actually, there is nothing in LD_LIBRARY_PATH when I use the new account.

@zxkjack123
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if that still does not work you can always try the one built with our GitHub Action:
https://github.com/svalinn/Trelis-plugin/suites/2383066015/artifacts/50610701

The package of GitHub Action works on my machine, the following info shows up when trelis launched:

Loaded Svalinn plugin.
-- DAGMC export command available.
-- iGeom_test command available.
-- MCNP import command available.
Finished Command: undo on

@zxkjack123
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also are you able to get a backtrace ?

also have you compiled the MOAB DAGMC and the plugin with the -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 flag ?

There isn't backtrace information printed.
As for the compile command, I followed the command provided in the README. Both of MOAB and DAGMC has the -D_GLIBCXX_USE_CXX11_ABI=0 flag.

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bam241 commented Mar 31, 2021

what you can try is run this in command line inside gdb (there is an example of a Trelis run using command line in https://github.com/svalinn/Trelis-plugin/blob/develop/test_plugin/test.sh

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