[Users] x86_64 link-time errors on MacOS Mojave

[Bernard Kelly]

Hi Roland.

No, my locally set environment variables are few, and don't include
anything to do with HDF5.

Bernard

On Tue, 2 Jul 2019 at 17:46, Haas, Roland <rhaas at illinois.edu> wrote:
>
> Hello Bernard,
>
> thank you for the update. Glad that you could find a workaround.
>
> These should not be needed as the scripts in ExternalLibraries/HDF5 are
> supposed to figure these out based on just HDF5_DIR (and possible
> pkgconfig files though MacPorts does not always deliver those).
>
> We had issues in the past where there were environment variables
> HDF5_DIR (though never anything else really) defined in a user's
> environment (for example from a environment module on a cluster) and,
> due to the way make works, these take precedence over values in the
> optionlists.
>
> Can you check if you enter
>
> env | grep HDF5
>
> if anything shows up, please? In particular a HDF5_DIR would likely fool
> the automatic detection but as long as you *also* have the
> HDF5_INC/LIB/BLAH variables set, then HDF5_DIR is (almost, b/c it
> is used to find things like h5ls) not needed.
>
> Yours,
> Roland
>
> > Hi Roland, everyone:
> >
> > I just came back to this problem in the last day or two, and with some
> > experimentation, I fixed it by adding the following lines to my
> > config-info ---that is, to
> > simfactory/mdb/optionlists/osx-macports.cfg:
> >
> > HDF5_INC_DIRS=/opt/local/include
> > HDF5_LIBS=hdf5 hdf5_cpp hdf5_hl
> > HDF5_LIB_DIRS=/opt/local/lib
> >
> > That is, it wasn't enough to just say "HDF5_DIR=/opt/local"
> >
> > Hope this helps if someone else runs into problems (and thanks for the
> > help getting here),
> >
> > Bernard
> >
> > On Fri, 21 Jun 2019 at 14:20, Haas, Roland <rhaas at illinois.edu> wrote:
> > >
> > > Hello Bernard,
> > >
> > > unfortunately (or fortunately) it linked fine for me. No errors were
> > > reported.
> > >
> > > Looking at the installed ports I also cannot see anything strange.
> > >
> > > I am not sure what else I could now do to help debug this. Possibly
> > > some other package that you have installed is interfering or there is
> > > some environment variable set?
> > >
> > > Yours,
> > > Roland
> > >
> > > > Hi Roland.
> > > >
> > > > Here's the result of uname -a:
> > > >
> > > > Darwin gs66-dodder 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25
> > > > 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64
> > > >
> > > > Attached is the full list of installed ports (a bit longer than yours)
> > > >
> > > > Bernard
> > > >
> > > > On Thu, 20 Jun 2019 at 12:44, Haas, Roland <rhaas at illinois.edu> wrote:
> > > > >
> > > > > Hello Bernard,
> > > > >
> > > > > > I did a clean, from-scratch compilation after copying that 18.2.0
> > > > > > Darwin architecture file to 18.6.0.
> > > > > >
> > > > > > Sadly, no change. Still fails at link time with all the "Undefined
> > > > > > _H5xxxx" errors.
> > > > > Ok. Since it starts with at "_" I almost suspected it may be some
> > > > > Fortran binding but then it is being called from C++ code.
> > > > >
> > > > > My own test is still compiling (slow VM).
> > > > >
> > > > > Could you include the output of:
> > > > >
> > > > > * sudo port installed
> > > > > * uname -a
> > > > >
> > > > > I have included my own output to give you an idea of what I am looking
> > > > > for (note that I cannot tell yet if compiling in my VM will encounter
> > > > > the same error you see).
> > > > >
> > > > > Yours,
> > > > > Roland
> > > > >
> > > > > --
> > > > > My email is as private as my paper mail. I therefore support encrypting
> > > > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > --
> > > My email is as private as my paper mail. I therefore support encrypting
> > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >
> >
> >
>
>
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://keys.gnupg.net.



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Bernard Kelly -- CRESST Assistant Research Scientist, NASA/GSFC
Gravitational Astrophysics Laboratory --- Code 663

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Web: http://science.gsfc.nasa.gov/sed/bio/bernard.j.kelly
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