[FLASH-USERS] Big Problem??

[Paul M. Rich]

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.....
>>>>>     
>>>
>>>
>>