[FLASH-USERS] Big Problem??

[Paul M. Rich]

Seyit,

These bindings are disabled by default and can be enabled by passing
--with-default-api-version=v16 to configure, according to the
documentation at
http://hdf.ncsa.uiuc.edu/HDF5/doc/RM/APICompatMacros.html.

Good luck,
Paul

Seyit Hocuk wrote:
> 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.....
>>>>>>>     
>>>>>
>>>>>
>>>>
>>