[FLASH-USERS] Big Problem??

Tue Jul 29 16:24:44 EDT 2008

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


-- 
Nathan C. Hearn
nhearn at uchicago.edu

ASC Flash Center
Computational Physics Group
University of Chicago