[ncl-install] HDF-EOS5 build issues

[Mary Haley]

[Before I address this issue, I would like to appeal to other people
subscribed to ncl-install to see if anybody has successfully built NCL
using the "clang" compiler on MacOS, paired with a fortran compiler like
"gfortran".]

Hi David,

The config.log file was very helpful, thanks.

I hate to deflect this, but this looks like an issue that perhaps the
HDF-EOS5 people need to address.

The problem is that "h5cc" is being used build HDF-EOS5, which is what it
should do, but apparently HDF5 was built with "clang", so this got put into
"h5cc", and HDF-EOS5 doesn't seem to work with "clang". Here's the place in
the "config.log" file that I think is the source of the problem:

configure:22754: checking for hdf5 szip encoding filter
configure:22796: /usr/local/hdf5-1.8.15/bin/h5cc -o conftest -g -O2
-I/usr/local/hdf5-1.8.15//include  -I/usr/local/zlib-1.2.8//include
-I/usr/local/szip-2.1//include -I/usr/local/hdf5-1.8.15//include
 -L/usr/local/zlib-1.2.8//lib -L/usr/local/szip-2.1//lib
-L/usr/local/hdf5-1.8.15//lib
conftest.c -lhdf5_hl -lhdf5 -lsz -lz -lm  >&5
clang: warning: argument unused during compilation:
'-L/usr/local/zlib-1.2.8//lib'
clang: warning: argument unused during compilation:
'-L/usr/local/szip-2.1//lib'
clang: warning: argument unused during compilation:
'-L/usr/local/hdf5-1.8.15//lib'
conftest.c:41:21: warning: implicitly declaring library function 'exit'
with type 'void (int) __attribute__((noreturn))'
              if (ret < 0) exit(1);
                           ^
conftest.c:41:21: note: please include the header <stdlib.h> or explicitly
provide a declaration for 'exit'
1 warning generated.
configure:22799: $? = 0
configure:22805: ./conftest
HDF5-DIAG: Error detected in HDF5 (1.8.15) thread 0:
  #000: H5Z.c line 1673 in H5Zget_filter_info(): Filter info not retrieved
    major: Data filters
    minor: Can't get value
  #001: H5Z.c line 1703 in H5Z_get_filter_info(): Filter not defined
    major: Data filters
    minor: Bad value
  #002: H5Z.c line 1247 in H5Z_find(): required filter is not registered
    major: Data filters
    minor: Object not found
configure:22808: $? = 1
configure: program exited with status 1

My general recommendation, as a work-around for now, is to try to build
things with gcc/gfortran, and not clang.  This means you would need to
rebuild HDF5, and potentially szip and zlib with gcc/gfortran.

Or, you can appeal to the HDF-EOS5 folks to see if they know how to get
this library built with clang.

I hope to attempt a clang build soon, which I believe will have to be
paired with gfortran because Apple hasn't provided a native Fortran
compiler that I know of.  Clang is supposed to work interchangeably with
gcc, but I haven't had a chance to verify this.

Let me know if you want to try the gcc/gfortran build solution, but are not
sure where to start.

--Mary


On Thu, May 28, 2015 at 3:02 PM, David Stanfel <dstanfel at ualberta.ca> wrote:

> Hello,
>
> I am trying to make the HDF-EOS5 software on my Macbook Pro (OS X 10.9.5)
> to build and install NCL but I am having some issues.
>
> I tried to use the 'make all install' command but that produced:
>
> make: *** No rule to make target `all'.  Stop.
>
>
> When trying to run the 'make' command:
>
> dstanfel:hdfeos5 ninjawarrior343$  make
>
> This file is for use by ECS Configuration Management processes only.
>
>
>  I have attached the config.log in case it is of some use.
>
>
> Thanks,
>
>
> David
>
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