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

Wed Oct 22 14:55:15 EDT 2008

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