On 01. sep. 2014 13:52, Matthew Knepley wrote: > On Mon, Sep 1, 2014 at 6:18 AM, Åsmund Ervik <[email protected]> wrote: > >> >> >> On 01. sep. 2014 12:51, Matthew Knepley wrote: >>> On Mon, Sep 1, 2014 at 3:22 AM, Åsmund Ervik <[email protected]> >> wrote: >>> >>>> >>>> Subsequently I installed HDF5 v. 1.8.12 using my OS package manager and >>>> then tried to configure with "--with-hdf5 >>>> --with-hdf5-dir=/path/to/system/hdf5" using PETSc 3.5.1. This time both >>>> configure and make were successful, but "make test" fails with loads of >>>> undefined references to PETSc HDF5 stuff (see below). configure.log and >>>> make.log attached also for this case (error-with-hdf5.tar.gz) >>>> >>> >>> It did not build src/sys/classes/viewer/impls/hdf5/, clearly from the >> log. >>> However, it >>> should have. We have been trying to understand why Make behaves in a bad >> way >>> after configuration failure. It should go away with make clean and >> another >>> make. >> >> Thanks Matt, make clean and then make did result in make test passing >> all tests. >> >> However, I am still unable to use HDF5 functionality. When I compile and >> run e.g. vec/vec/examples/tutorials/ex10.c it works fine with binary >> output, but with HDF5 I get the error message below. >> >> I'm guessing this is some incompatibility between the various MPI, HDF5 >> and PETSc versions, i.e. that the HDF5 from my OS is not using the same >> MPI as PETSc. Is it simple to edit something in PETSc and have >> "./configure --download-hdf5" get the most recent HDF5 library which >> compiles on my machine? >> > > Yes, I cannot reproduce, so it must be something like that. Can you > reconfigure > using the --download version?
No, I am not able to, that is why I switched to "--with-hdf5-dir=". Like I said in the first email, the version of HDF5 (1.8.10) that ships with PETSc 3.5.1 does not compile on my machine. This is apparently a known bug that was fixed upstream, cf. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777 This is the reason why I asked whether I can somehow tell "--download-hdf5" to download a more recent version. 1.8.11 should do it. Åsmund
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