[FLASH-USERS] Big Problem??

[Seyit Hocuk]

Hi Paul and good morning,

Thanks for your reply. To answer your question " Is the version of HDF5 
1.8.1 you are using built with the 1.6 api bindings? ", I don't know. I 
didn't check that. I will try that, when I know how to do that. I just 
downloaded the source file and did configure-make-make install. Where 
does the bindings come in? I will try to find it out.

Greetz,
Seyit




Paul M. Rich 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.....
>>>>>>     
>>>>
>>>>
>>>
>