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Build fails linking nem_spread with undefined reference to 'H5get_libversion' #13320

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vk2diy opened this issue Aug 5, 2024 · 2 comments
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type: bug The primary issue is a bug in Trilinos code or tests type: new to Trilinos type: question

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@vk2diy
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vk2diy commented Aug 5, 2024

Bug Report

G'day from Sydney town down under.

Sorry no idea who to mention based on the page you link to.

image

Description

Build fails at ~30% with...

/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: ../../libraries/exodus/libexodus.a(ex_utils.c.o): undefined reference to symbol 'H5get_libversion'
/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: /usr/lib64/libhdf5.so.310: error adding symbols: DSO missing from command line

This suggests the linker failed to find libhdf5.

However, I am on gentoo and it's installed.

*  sci-libs/hdf5
      Latest version available: 1.14.3-r1
      Latest version installed: 1.14.3-r1
      Size of files: 15,938 KiB
      Homepage:      https://www.hdfgroup.org/HDF5/
      Description:   General purpose library and file format for storing scientific data
      License:       NCSA-HDF

My objective is to use xyce instead of ngspice just because I'd like to support some progress.

Steps to Reproduce

  1. Build with command: cmake -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran -DTrilinos_ENABLE_ALL_PACKAGES=ON -DCMAKE_INSTALL_PREFIX=~/trilinos-xyce/trilinos ../Trilinos && make -j16 install
  2. Shake fist angrily at computer.
  3. She'll be right mate, crack a tinny.

image

Logs

Attached.
build-cmake-log.txt
build-log.txt

@vk2diy vk2diy added the type: bug The primary issue is a bug in Trilinos code or tests label Aug 5, 2024
@vk2diy vk2diy changed the title Build fails linking nem_spread with undefined reference to 'H5get_libversion' (solved) Build fails linking nem_spread with undefined reference to 'H5get_libversion' Aug 5, 2024
@ccober6
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ccober6 commented Aug 5, 2024

@trilinos/seacas

@jhux2
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jhux2 commented Aug 5, 2024

@vk2diy When configuring Trilinos, you need to specify the 3rd party libraries desired. You might also need to specify their locations if in a non-standard location. If you want HDF, then use the following:

-DTPL_ENABLE_HDF5=ON
-DHDF5_LIBRARY_DIRS=${HDF5_ROOT}/lib
-DHDF5_INCLUDE_DIRS=${HDF5_ROOT}/include

I would also suggest enabling only the Trilinos packages that Xyce needs. @hkthorn Does Xyce have a list of packages/TPLs to enable, or better yet, an example Trilinos configure script?

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Labels
type: bug The primary issue is a bug in Trilinos code or tests type: new to Trilinos type: question
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