[ncl-install] HDF-EOS5 build issues

Mary Haley haley at ucar.edu
Fri May 29 14:38:09 MDT 2015 

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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