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@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@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
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