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

Wed Oct 22 15:48:08 EDT 2008

Hi Beatrice,

zlib was used to built the HDF5 source libraries into our system by  
Peter Teuben. That's actually the default, so just leave out the szip  
part (--with-szlib=..) when configuring .

Stratos

On Oct 22, 2008, at 2:55 PM, Beatrice Perret wrote:

> Stratos
>
> Are you also using szip for compression with 1.6.7? My problem seems
> to reside with this part.
>
> Beatrice
>
> On Wed, Oct 22, 2008 at 5:52 AM, Stratos Boutloukos  
> <stratos at uiuc.edu> wrote:
>> 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
>>
>>
>
>
>
> -- 
> Beatrice Perret
> Department of Physics
> Arizona State University
> P.O. Box 871504
> Tempe, AZ 85287-1504