Building DealII fails at step-60. P4est. Linking error

[Oleg Kmechak]

Hello, 

DealII was configured with cxx 14, 17, cos previous build without cxx 17 flag was ok(but there was also another build of p4est). 

p4est was configured with next options --enable-mpi --enable-shared --disable-vtk-binary --without-blas. These options are recommended here.

And it returns:

[ 85%] Linking CXX executable ../bin/step-60.debug
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_fixed_end'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_custom_begin'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_fixed_begin'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_fixed'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_custom_end'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_fixed_end'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_custom_end'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_custom_begin'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p4est_transfer_custom'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_fixed_begin'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_custom'
../lib/libdeal_II.g.so.9.1.0-pre: undefined reference to `p8est_transfer_fixed'
collect2: error: ld returned 1 exit status
examples/CMakeFiles/step-60.debug.dir/build.make:220: recipe for target 'bin/step-60.debug' failed
make[3]: *** [bin/step-60.debug] Error 1
CMakeFiles/Makefile2:8632: recipe for target 'examples/CMakeFiles/step-60.debug.dir/all' failed
make[2]: *** [examples/CMakeFiles/step-60.debug.dir/all] Error 2
CMakeFiles/Makefile2:339: recipe for target 'CMakeFiles/examples.dir/rule' failed
make[1]: *** [CMakeFiles/examples.dir/rule] Error 2
Makefile:238: recipe for target 'examples' failed
make: *** [examples] Error 2

[Wolfgang Bangerth]

Oleg,
I have not seen this error before. In your build directory, can you do
make quick_test
and report back what that shows? It looks like either your libp4est.so is
missing a lot of symbols, or that we don't link with it.

Although, on second thought, it occurs to me that the functions you show here
are all functions that were only introduced in a recent version of p4est.
Since compiling deal.II worked, they must have been declared in the p4est.h
file. But apparently they are not present in libp4est.so. Are you sure that
the .h file and the .so file correspond to the same p4est version?

Best
W.

On 10/09/2018 12:09 AM, Oleg Kmechak wrote:
> Hello,
>
> DealII was configured with cxx 14, 17, cos previous build without cxx 17 flag
> was ok(but there was also another build of p4est).

> p4est was configured with next options--enable-mpi --enable-shared

> --disable-vtk-binary --without-blas. These options are recommended here.

> <https://www.dealii.org/developer/external-libs/p4est.html>

> **//___^
>
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--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[Oleg Kmechak]

Thanks for watching out, 

I already chanched setup of whole system and can't check how would behave make quick_test  in this situation.

Also I missed, while clonning p4est from git, that it has submodule "cl" and forget to call git submodule init & git submodule update.

DealII setup and it dependencies from scratch now works well, except two dependecies: hdf5 and netcdf(currently i just turned them off).

Triend to resolve this in different ways:

 - Installing libhdf5-dev and/or libnetcdf-dev, (not sure but probably libphdf5-dev, libhdf5-mpi-dev and/or libpnetcdf-dev tried too).

 - Building parallel version of hdf5 from git(used dependencie on the same mpi as dealii).

 - And/or building with or without dependencie on hdf5 - netcdf-c.

 - Also tried build netcdf and hdf5 from tar file from offitial websites(not sure about deatails of building it was some time ago).

With regards, 

Oleg Kmechak

[Wolfgang Bangerth]

On 10/10/2018 03:35 AM, Oleg Kmechak wrote:
> Triend to resolve this in different ways:
>
>  - Installing libhdf5-dev and/or libnetcdf-dev, (not sure but probably
> libphdf5-dev, libhdf5-mpi-dev and/or libpnetcdf-dev tried too).

>  - Building parallel version of *hdf5*
> <https://github.com/live-clones/hdf5> from git(used dependencie on the
> same mpi as dealii).
>  - And/or building with or without dependencie on hdf5 - *netcdf-c*.
> <https://github.com/Unidata/netcdf-c>

>  - Also tried build netcdf and hdf5 from tar file from offitial
> websites(not sure about deatails of building it was some time ago).

Neither of these are important dependencies. Unless you know that you
need one of these two, just turn off these dependencies.

Best
W.