[ncl-install] HDF-EOS5 build issues

Fri May 29 14:40:08 MDT 2015

Sorry about the "Jerry" salutation, I cut-and-pasted a previous message and
didn't notice it!

I forgot to also mention that you can see a list of the external packages
required at:

http://www.ncl.ucar.edu/Download/build_from_src.shtml

I need to create a clean version of these packages so you can just see the
list without all the instructions.

--Mary

On Fri, May 29, 2015 at 2:38 PM, Mary Haley <haley at ucar.edu> wrote:

> https://www.earthsystemgrid.org/home.htm
>
> Click on "NCL : NCAR Command Language"
>
> and navigate your way to whichever version you want. This is the same
> place where you get the NCL source code.
>
> Download instructions are at:
>
> http://www.ncl.ucar.edu/Download/
>
> In the near future, we hope to offer NCL under the conda package manager,
> so you can type:
>
>   conda install ncl
>
> I believe enterprising folks have already put NCL under other linux
> package managers. You could try:
>
>   yum install ncl
>
> for example.
>
> Jerry,
>
> A few years ago, Carter Borst provided me with a build script he used to
> build all the external packagesNCL needs, and NCL itself, on various
> systems. I've attached this script in case it can be helpful. (Build-NCL.
> sh)
>
> I've also attached a shell script that I've used to build the external
> packages that NCL depends on.  This one doesn't build NCL itself.  I have
> separate scripts for this, as I tend to build NCL on a lot of different
> systems that don't necessarily share the same disk space.
> --Mary
>
>
> On Fri, May 29, 2015 at 2:24 PM, David Stanfel <dstanfel at ualberta.ca>
> wrote:
>
>> 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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