[FLASH-USERS] Fwd: Pb while using gmake on the Sedov example (fwd)

[Stratos Boutloukos]

Hello Beatrice, Klaus, Paul and other flash-users,

When compiling flash3.1 I had also encountered similar problems with  
the libraries. The latest version of HDF5 (1.8.1) apparently has some  
new build-in functions that are not recognized by flash's current  
makefile. For more info see the hdf software changes from version to  
version:
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
The latest version of HDF5 that works fine for me is 1.6.7 and that's  
what I use now.

Stratos

On Oct 21, 2008, at 8:26 PM, Beatrice Perret wrote:

> Hello flash-users
>
> Here is the exchange I had recently with Klaus Weide following the
> question about using gmake on the Sedov example for flash3.1. I
> unfortunately hit "reply" instead of "reply-to-all". I am posting this
> again in case other people have encountered the same kind of problem.
>
> Beatrice
>
>
> ---------- Forwarded message ----------
> From: Klaus Weide <klaus at flash.uchicago.edu>
> Date: Mon, Oct 20, 2008 at 8:21 AM
> Subject: Re: [FLASH-USERS] Pb while using gmake on the Sedov  
> example (fwd)
> To: "Paul M. Rich" <richp at flash.uchicago.edu>
> Cc: beatrice.perret at asu.edu
>
>
> Beatrice,
>
> Thank you for reporting back your findings.  If I understand you
> right, you are now able to use FLASH3.1, by using HDF5 version 1.6.5.
>
> I am forwarding your message to Paul Rich, who has a better  
> understanding
> of library versions.  I think such failures to build FLASH with  
> certain
> library versions have been reported before.
>
> You may also want to consider reporting your findings back to the
> flash-users list.
>
> Again thanks,
>
> Klaus
> ---------- Forwarded message ----------
> Date: Fri, 17 Oct 2008 13:52:47 -0700
> From: Beatrice Perret <bperret at asu.edu>
> Reply-To: beatrice.perret at asu.edu
> To: Klaus Weide <klaus at flash.uchicago.edu>
> Subject: Re: [FLASH-USERS] Pb while using gmake on the Sedov example
>
> Klaus
>
> I followed the same step as the ones above (previous email) for
> FLASH3.0 and got the same errors. I think this is expected.
>
> I tried the new Makefile.h with Flash2.5, but using the version
> hdf5-1.6.5, since this is the only version of hdf5 that works. The
> compilation was successful.
>
> Then I changed the version of hdf5 from 1.6.7 to 1.6.5 for Flash3.1
> and the compilation was successful.
>
> Here are the options I used to configure each hdf5 version:
> hdf5-1.6.5 and hdf5-1.6.7:
> ./configure --prefix=/...(whatever) --with-szlib=/usr/local/szip-2.1
> --disable-shared CPFLAGS=-fpic CPPFLAGS=-fPIC (both needed to use
> visit)
> hdf5-1.6.8:
> ./configure --prefix=/..(whatever) --with-szlib=/usr/local/szip-2.1
> --disable-shared --enable-cxx CPFLAGS=-fPIC CPPFLAGS=-fPIC
>
> Beatrice
>
> On Fri, Oct 17, 2008 at 1:21 PM, Beatrice Perret <bperret at asu.edu>  
> wrote:
>>
>> Klaus
>>
>> Thank you for fixing my Makefile.h. It works.
>>
>> Now I have a problem with the following:
>> io_h5read_bflags.c(76): errore #165: too few arguments in function  
>> call
>> dataset = H5Dopen(*file_identifier, "bflags");
>> compilation aborted for io_h5read_bflags.c (code 2)
>> (I was using hdf5-1.8.1)
>>
>> I switched to 1.6.7 and I am getting a lot of undefined reference to
>> SZ_encoder_enabled, H5Z_filter_deflate, H5Zdeflate,
>> H5Z_can_apply_szip, H5Z_filter_szip
>>
>> I don't know where the problem is coming from. Any idea would be  
>> great.
>>
>> Beatrice
>>
>> On Fri, Oct 17, 2008 at 8:57 AM, Klaus Weide  
>> <klaus at flash.uchicago.edu> wrote:
>>>
>>> On Thu, 16 Oct 2008, Beatrice Perret wrote:
>>>
>>>> I have attached the first 15 lines. But I have just noticed that  
>>>> line 10
>>>> is
>>>>
>>>> /usr/local/hdf5/hdf5-1.6.5:/usr/local/szip-2.1/include.o:
>>>>
>>>> I assumed that what is expected is:
>>>>
>>>> /usr/local/hdf5/hdf5-1.6.5/include.o
>>>> /usr/local/szip-2.1/include.o
>>>>
>>>> Right?
>>>
>>> Beatrice,
>>>
>>> Actually I think there isn't really any need for having this in the
>>> Makefile.Depend in any form.  You should be able to just delete the
>>> line
>>>  /usr/local/hdf5/hdf5-1.6.5:/usr/local/szip-2.1/include.o:
>>> and then make should work.
>>>
>>> The line in the Makefile.Depends is a result of this line in your
>>> Makefile.h:
>>>  HDF5_PATH = /usr/local/hdf5/hdf5-1.8.1:/usr/local/szip-2.1
>>>
>>> The setup_depends.py utility (which gets invoked automatically  
>>> from make)
>>> tries to analyze the command line flags used for invoking the  
>>> Fortran
>>> compiler, but it doesn't do a good job of it in this case;
>>> apparently it doesn't expect that any command line arguments,
>>> like -I /usr/local/hdf5/hdf5-1.8.1:/usr/local/szip-2.1/include,
>>> contain colons.
>>>
>>> I suppose the setup_depends.py should be fixed.
>>>
>>>> In flash2.5 I could not feed szip using a different way than  
>>>> this. If
>>>> this is the problem how should I do it for flash3.0 or 3.1? I have
>>>> also attached the Makefile.h for my machine.
>>>
>>> If you just need to pass
>>>  -I/usr/local/szip-2.1/include
>>> to the compiler invocations (and/or add something like
>>>  -L/usr/local/szip-2.1/lib
>>> for the linking step?), then you should modify your Makefile.h so  
>>> that
>>>
>>> 1) you have
>>>  HDF5_PATH = /usr/local/hdf5/hdf5-1.8.1
>>> 2) add -I/usr/local/szip-2.1/include explicitly in the line that  
>>> defines
>>>  CFLAGS_HDF5
>>> 3) add -L/usr/local/szip-2.1/lib explicitly in the line that defines
>>>  LIB_HDF5 (if needed).
>>>
>>> Hope this helps,
>>>
>>> Klaus
>>>
>>
>>
>>
>> --
>> Beatrice Perret
>> Department of Physics
>> Arizona State University
>> P.O. Box 871504
>> Tempe, AZ 85287-1504
>>
>
>
>
> --
> Beatrice Perret
> Department of Physics
> Arizona State University
> P.O. Box 871504
> Tempe, AZ 85287-1504
>
>
>
> -- 
> Beatrice Perret
> Department of Physics
> Arizona State University
> P.O. Box 871504
> Tempe, AZ 85287-1504