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./update_and_rebuild_libmesh.sh --with-vtk-include=$VTKINCLUDE_DIR --with-vtk-lib=$VTKLIB_DIR
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HPC Software Consultant
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Idaho National Laboratory
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I seem to have this problem every year for the past 3 years. I freshly cloned moose into my directory on the HPC.
I loaded the necessary modules (use.projects, moose-dev/5.6.0-gmvolf-5.5.4).
My goal is to use the Image Reader. I followed the instructions herebut those modules are not available on the HPC, so I then tried to follow the old instructions I was given 2 years ago (earlier in this post), so I executed module list, saw VTK/6.1.0-gmvolf-5.5.4-Python-2.7.8 in the module list, then executedmodule display VTK/6.1.0-gmvolf-5.5.4-Pyton-2.7.8which output/apps/local/easybuild/modules/vis/VTK/6.1.0-gmvolf-5.5.4-Python-2.7.8.So then I executed the following commands:export VTKINCLUDE_DIR=/apps/local/easybuild/software/VTK/6.1.0-gmvolf-5.5.4-Python-2.7.8/include/vtk-6.1export VTKLIB_DIR=/apps/local/easybuild/software/VTK/6.1.0-gmvolf-5.5.4-Python-2.7.8/lib./update_and_rebuild_libmesh.sh --with-vtk-include=$VTKINCLUDE_DIR --with-vtk-lib=$VTKLIB_DIR
When that finished, I went to moose/modules/phase_field and executed make -j8. Last year there was an image_function test in phase_field/tests, but there isn't anymore. So I went to my own app and executed make -j8 to compile it.
I must have broken something in the process above, because I received errors, including the following:Linking Library /home/harrwh/projects_2017/moose/modules/module_loader/lib/libmodule_loader_with-opt.la...In file included from /home/harrwh/projects_2017/moose/scripts/../libmesh/installed/include/libmesh/perf_log.h:25:0,from /home/harrwh/projects_2017/moose/framework/include/base/Moose.h:19,from /home/harrwh/projects_2017/moose/framework/include/base/MooseError.h:18,from /home/harrwh/projects_2017/moose/framework/include/utils/InputParameters.h:19,from /home/harrwh/projects_2017/moose/framework/include/base/MooseObject.h:19,from /home/harrwh/projects_2017/moose/framework/include/kernels/KernelBase.h:18,from /home/harrwh/projects_2017/moose/framework/include/kernels/Kernel.h:18,from /home/harrwh/projects_2017/liger/include/kernels/kernelA.h:18,from /home/harrwh/projects_2017/liger/src/kernels/kernelA.c:15:/home/harrwh/projects_2017/moose/scripts/../libmesh/installed/include/libmesh/libmesh_common.h:36:19: fatal error: cstdlib: No such file or directory#include <cstdlib>
^
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Stay tuned...
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Find the VTK module’s information using
module display VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9
For me, the output of this command was (among other things)
/apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua:
Then, execute the following commands to compile libMesh with VTK enabled so we can use the ImageFunction.
export VTKINCLUDE_DIR= /apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua/include/vtk-6.1
export VTKLIB_DIR= /apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua/lib
./update_and_rebuild_libmesh.sh --with-vtk-include=$VTKINCLUDE_DIR --with-vtk-lib=$VTKLIB_DIR
Does this require compiling libMesh with VTK enabled? If so, is the following procedure correct...
Find the VTK module’s information usingmodule display VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9
For me, the output of this command was (among other things)
/apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua:
Then, execute the following commands to compile libMesh with VTK enabled so we can use the ImageFunction.
export VTKINCLUDE_DIR= /apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua/include/vtk-6.1
export VTKLIB_DIR= /apps/local/easybuild/modules/vis/VTK/7.1.1-gmvolf-5.5.4-Python-2.7.9.lua/lib
./update_and_rebuild_libmesh.sh --with-vtk-include=$VTKINCLUDE_DIR --with-vtk-lib=$VTKLIB_DIR
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In both cases, when I go to moose/modules/phase_field/tests/boundary_intersecting_features and run this, I get the error*** ERROR ***libMesh must be configured with VTK enabled to utilize ImageSampler [39m
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I didn't change VTK_DIR, so I'm assuming that it is set correctly when I loaded the module, as suggested by Brian Alger in a previous reply.
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*** ERROR ***
libMesh must be configured with VTK enabled to utilize ImageSampler [39m
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