[ncl-install] HDF-EOS5 build issues

[David Stanfel]

Hello,

Where can I find those precompiled binaries? Also, for the external
software packages, I would like to have a look at that script that you have.

Thanks,

David

On Fri, May 29, 2015 at 11:40 AM, Mary Haley <haley at ucar.edu> wrote:

> Hi David,
>
> First, though, would you be able to use one of our precompiled NCL
> binaries for LINUX, so you don't have to do the build yourself? We have
> Debian and RedHat binaries, and you should be able to use these on other
> flavors of Linux.
>
> If you still want to do the source build yourself, then here are the env
> vars I recommend setting:
>
> export CC=gcc
> export CXX=g++
> export FC=gfortran
> export F77=gfortran
> export F90=gfortran
>
> Using "f77" (lowercase) is probably not going to affect anything on your
> system.
>
> You may also want:
>
> export CFLAGS=-fPIC
> export FFLAGS=-fPIC
> export F90FLAGS=-fPIC
> export CXXFLAGS=-fPIC
>
> This is your chance to set any other particular flags you want, like
> optimization flags.  I usually try to keep it as "bare" as possible and let
> the compiler figure out the options it wants to use.
>
> Finally, as a precaution, I recommend setting LINUX_BRAND, depending on
> whether you have a 32-bit or 64-bit system:
>
> export LINUX_BRAND linux64
>
> or
>
> export LINUX_BRAND linux32
>
> If you are having to do a full blown build of all those external software
> packages that NCL depends on, let me know. I have a script that can help
> with this.
>
> --Mary
>
>
>
>
> On Fri, May 29, 2015 at 11:22 AM, David Stanfel <dstanfel at ualberta.ca>
> wrote:
>
>> Hello,
>>
>> Thanks for the reply. I would like to try that. How would I go about
>> specifying the use of gcc and gfortran? I set the environment variables:
>>
>> export CC=gcc
>> export f77=gfortran
>>
>> What more would be needed?
>>
>> Thanks,
>>
>> David
>>
>> On Fri, May 29, 2015 at 11:05 AM, Mary Haley <haley at ucar.edu> wrote:
>>
>>> [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
>>>>
>>>> _______________________________________________
>>>> ncl-install mailing list
>>>> List instructions, subscriber options, unsubscribe:
>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-install
>>>>
>>>>
>>>
>>
>
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