[FLASH-USERS] Big Problem??

Wed Jul 30 05:48:44 EDT 2008

Ah thanks Nathan,

I see there is a good link to the api bindings. That answers the 
question I posted a minute ago I guess.
I think I just have to configure hdf5 with a certain flag. " 
|--with-default-api-version=v16 |"

Let me try that out.

Greetz,
Seyit

Nathan Hearn wrote:
> For everyone's information, the HDF Group has a nice page on the
> compatibility macros that are meant to bridge between the 1.6 and 1.8
> versions, as well as a discussion of the associated configuration
> options for HDF5:
>
> http://www.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html
>
> - Nathan
>
>
> On Tue, Jul 29, 2008 at 3:10 PM, Paul M. Rich <richp at flash.uchicago.edu> wrote:
>   
>> Seyit,
>>
>> I can clear up the HDF5 1.8 issue, I think.  I've experimented with HDF5
>> 1.8.1 in FLASH3 and that will only work if you have built the v1.8.x
>> implementation with support for the 1.6 api.  I believe that FLASH2.5's will
>> work in a similar fashion.  Is the version of HDF5 1.8.1 you are using built
>> with the 1.6 api bindings?
>>
>> Paul Rich
>>
>> Seyit Hocuk wrote:
>>     
>>> Hi,
>>>
>>> It has been some time now, but to continue the discussion, I have tested
>>> Jeans standard problem and Sedov standard problem including changing the
>>> refinement levels. The result is exactly same for all three different
>>> computers. Unfortunately my own setup shows differences and it seems the end
>>> result changes by the coice of computer/environment/compiler whatever. My
>>> own setup has a lot more physics than the simpe test problems.
>>>
>>> One thing I am thinking about is that I adjusted the refinement criteria
>>> to use a reference density instead of looking at the second order
>>> derivative. I don't know if this could be the problem, but dt_hydro should
>>> not depend on the refinement criteria so I guess there is more to it.
>>>
>>> Unfortunately it is not easy to change compilers and some other stuff
>>> (like cpu/kernel etc.) on the different computers because I have limited
>>> rights on those machines. I don't want to find out I have to choose one
>>> machine and stick with it. How do I know which machine is the best. Anyway,
>>> I am going to try at least to get the libraries the same (hdf5 / mpi) for
>>> all machines and see if that helps. Btw the latest hdf5 (1.8.1) doesn't seem
>>> to work with Flash2.5.
>>>
>>> I will also play with compiler options. Try to make them exactly the same
>>> and avoid aggressive optimizations. I hope this is where the solution lies.
>>>
>>> Thanks,
>>> Seyit
>>>
>>>
>>>
>>>
>>> Tomasz Plewa wrote:
>>>       
>>>> Although I prefer a low cost approach to debugging which avoids dealing
>>>> with setup/system/compiler information at first and attempts to eliminate
>>>> 99% of the source code, here are  quick comments on your systems.
>>>>
>>>> (1) pgi 6.0 is a quite antique compiler. It's so old that now I do not
>>>> even remember what problems we may have had with it. I suspect quite a few
>>>> and none of them might be relevant...
>>>>
>>>> (2) As you might noticed, intel has a newer compiler version. Your
>>>> CentOS5 system needs upgrades on both mpich2 and compiler sides.
>>>>
>>>> (3) Your Ubuntu system seems relatively up-to-date although HDF5 1.8.x is
>>>> out there and seems working fine.
>>>>
>>>> (4) Compilers are known to do strange things to perfect codes! So if you
>>>> run into a trouble on a new system, one of the first things to try is to
>>>> lower compiler optimization level. Avoiding -fast or -ip or -inline is
>>>> usually a good idea. Simple -O0 may suffice for a couple of steps. As a
>>>> bonus, the code compiles fast. Then the trick is to get it crashing
>>>> quickly...
>>>>
>>>> Again, I suggest to simplify your application, isolate the problem, fix
>>>> it, then find the best compiler, mpich, options, etc., to run your
>>>> production code.
>>>>
>>>> Enjoy your weekend!
>>>>
>>>> Tomek
>>>> --
>>>> Seyit Hocuk wrote:
>>>>         
>>>>> Hi Nathan,
>>>>>
>>>>> Thats a good Idea, I'll start simple and test those first thing monday.
>>>>> It's too late for me now.
>>>>>
>>>>> To answer your questions:
>>>>>
>>>>> The problem I am running is my own home made, actually it's a modified
>>>>> version of Jeans. Basically including heat, cool, eos gamma, compositions,
>>>>> adjusted refinement criteria similar to one of the other problems (with
>>>>> delta_ref and delta_deref) and a scala of other small things.
>>>>>
>>>>> 1)
>>>>> Centos5
>>>>> Linux celsius 2.6.18-53.1.19.el5 #1 SMP Wed May 7 08:20:19 EDT 2008 i686
>>>>> i686 i386 GNU/Linux
>>>>> ifort intel compiler version 8.0
>>>>> hdf5 1.6.6 (serial)
>>>>> mpich2 Version:  1.0.3
>>>>> gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)
>>>>> FFLAGS_OPT   =  -c -r8 -i4 -fast -ipo -ipo_obj  -I $(MPI_PATH)/include
>>>>>
>>>>> 2)
>>>>> Debian (??)
>>>>> Linux hpcibm1 2.6.8-11-amd64-k8-smp #1 SMP Sun Oct 2 20:03:22 UTC 2005
>>>>> x86_64 GNU/Linux
>>>>> pgf90 6.0-5 32-bit target on x86-64 Linux
>>>>> hdf5 1.4.5 (serial)
>>>>> mpich2 version 1.0.5
>>>>> gcc version 3.3.5 (Debian 1:3.3.5-13)
>>>>> FFLAGS_OPT = -c -fast -r8 -i4
>>>>>
>>>>> 3)
>>>>> Ubuntu
>>>>> Linux si01 2.6.24.3 #1 SMP Fri Jul 4 11:02:09 CEST 2008 x86_64 GNU/Linux
>>>>> ifort intel compiler version 10.1.012
>>>>> hdf5 1.6.7 (serial)
>>>>> mpich2 Version: 1.0.6
>>>>> gcc version 4.2.3 (Ubuntu 4.2.3-2ubuntu7)
>>>>> FFLAGS_OPT   = -c -r8 -i4  -xT -O3 -no-prec-div -static -I
>>>>> $(MPI_PATH)/include
>>>>> or (only -ipo difference, result seemingly doesn't change)
>>>>> FFLAGS_OPT   = -c -r8 -i4  -fast -I $(MPI_PATH)/include
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Nathan Hearn wrote:
>>>>>           
>>>>>> Hi Seyit,
>>>>>>
>>>>>>    Are you seeing these differences in the standard test problems
>>>>>> included in Flash (e.g., Noh, Sod, Sedov), or are they specific to the
>>>>>> problem that you are running.  (Really, this follows from Tomek's
>>>>>> advice to look at the simplest configurations where the differences
>>>>>> are seen.)
>>>>>>
>>>>>>    Also, it would be good to include some more information in your
>>>>>> messages, for instance: the problem that you are running, the specific
>>>>>> architectures and compilers, the optimization flags, and the library
>>>>>> versions for HDF5 and MPI that you are using.  Details like these can
>>>>>> be really helpful in evaluating and fixing the issues you are seeing.
>>>>>>
>>>>>>
>>>>>> - Nathan
>>>>>>
>>>>>>
>>>>>> On Fri, Jul 18, 2008 at 11:32 AM, Seyit Hocuk <seyit at astro.rug.nl>
>>>>>> wrote:
>>>>>>
>>>>>>             
>>>>>>> Oh man,
>>>>>>>
>>>>>>> I am using 3 different computers (with different architectures,
>>>>>>> compilers,
>>>>>>> optimizations, environments). All three start differently immediately
>>>>>>> from
>>>>>>> the beginning (difference in dt_hydro and refinement).
>>>>>>> Should I worry very very very much?
>>>>>>> I'm now doing a complete simulation and am going to check if my end
>>>>>>> results
>>>>>>> also change.
>>>>>>>
>>>>>>> I'm trembling by the thought.....
>>>>>>>
>>>>>>>               
>>>>>           
>>     
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