[Nek5000-users] Reading binary data

Thu Aug 12 10:20:46 CDT 2010

Hi Mike,

I guess the name nfields is a little bit misleading. It actually the number of variables to dump (the mesh counts as ndim variables, same thing for the velocity) e.g. XUPTS03 => nfields = ndim + ndim + 5.
The variable encoder (here: XUPTS03) has a fixed order and represents the order of the variables in the file.

File Layout:

header: 132 bytes
endian test tag: 4 bytes
element mapping: nel* 4 bytes
data: nfields*nxyz*nel* wdsizo
metadata (min/max values): nfields*2*nel * 4 bytes

Does that make sense?

Stefan

On Aug 12, 2010, at 3:58 PM, <nek5000-users at lists.mcs.anl.gov> wrote:

> Stefan,
> 
> Ok, I see all the contributions to the field file when mesh data is included.  The only thing I am still unsure of is the order of the components.  Can you please check the order in my list below and tell me what should be moved?
> 
> Field File with mesh data
> ============================
> 1) header: 132 bytes
> 2) endian test tag: 4 bytes
> 3) element mapping: nel* 4 bytes
> 4) mesh data:  nel * nx*ny*nz * ndim * wdsizo
> 5) field data: nfields*nxyz*nel* wdsizo (where wdsizo is 4 or 8 bytes)
> 6) field metadata (min/max values): nfields*2*nel * 4 bytes
> 7) mesh metadata: ndim*ne*2*4
> 
> Thanks again for all your help.
> 
> --Mike
> 
> ________________________________________
> From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> Sent: Thursday, August 12, 2010 1:06 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Reading binary data
> 
> The 12288 bytes is the metadata for all 3 mesh coordinates:
> ndim * nel * 2 * 4 bytes
> 
> Stefan
> 
> On Aug 12, 2010, at 12:21 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 
>> Sorry -- I'm still not getting it.
>> 
>> The first file had mesh coordinates and field information in it; here is what the header shows:
>> 
>> #std 4  8  8  8        512        512  0.2000000000000E+02      1000      0      1 XUPS02
>> 
>> The size of this file is  9476232, but I can't figure out what is contributing to that size.  For the next field file, the header shows:
>> 
>> #std 4  8  8  8        512        512  0.1200000000000E+03      6000      0      1 UPS02
>> 
>> The size of this file is 6318216, which is exactly predicted by the expression below -- all is well.
>> 
>> What is the makeup of the 3158016 bytes difference between these files?  The mesh coordinates alone are only
>> 
>> 512 * 8^3 * 4 * 3 (ndim) = 3145728 bytes
>> 
>> Where and what are the remaining 12288 bytes?
>> 
>> Thanks.
>> 
>> 
>> 
>> On Aug 11, 2010, at 4:09 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>> 
>>> No, if a field file only contains the geometry (mesh coordinates) nfields is equal to ndim (2 or 3).
>>> Stefan
>>> 
>>> 
>>> On Aug 12, 2010, at 12:01 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
>>> 
>>>> Stefan,
>>>> 
>>>> Thanks.  I figured that, but the binary file size doesn't seem to be adding up.    For example,  a field file that doesn't have geometry data is the size described by the initial thread, i.e.
>>>> 
>>>> 132 bytes + 4 bytes + nel* 4 bytes + nfields*nxyz*nel* wdsizo  +  nfields*2*nel * 4 bytes
>>>> 
>>>> My naive assumption was that a field file with xyz data would then have the additional space requirement of
>>>> 
>>>> nx*ny*nz*nel*wdsizo
>>>> 
>>>> but the file's bigger than that.  What info am I missing?
>>>> 
>>>> --Mike
>>>> 
>>>> On Aug 11, 2010, at 3:50 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>>>> 
>>>>> Hi Mike,
>>>>> 
>>>>> vector fields (e.g. mesh coordinates) are stored in the following way:
>>>>> 
>>>>> LOOP over all elements
>>>>>   LOOP i = {x,y,z}
>>>>>            i for all GLL points (internal element points)
>>>>>   ENDLOOP
>>>>> ENDLOOP
>>>>> 
>>>>> 2D example with (E=2,N=2):
>>>>> x1_1 x2_1 x3_1 y1_1 y2_1 y3_1 x1_1 x2_2 x3_2 y1_2 y2_2 y3_2
>>>>> 
>>>>> where x2_1 means the x-coordinate of the 2nd GLL point of element 1.
>>>>> 
>>>>> hth,
>>>>> Stefan
>>>>> 
>>>>> On Aug 11, 2010, at 11:34 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>> 
>>>>>> 
>>>>>> Hello All.  I found this helpful message from Stefan regarding the structure of a binary field file.   Could someone please tell me what the structure is when the geometry info is also contained?
>>>>>> 
>>>>>> Thanks!
>>>>>> --Mike
>>>>>> 
>>>>>> nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
>>>>>>> Thu May 6 07:18:03 CDT 2010
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>>>>>>> Hi Fred,
>>>>>>> 
>>>>>>> header: 132 bytes
>>>>>>> endian test tag: 4 bytes
>>>>>>> element mapping: nel* 4 bytes
>>>>>>> data: nfields*nxyz*nel* wdsizo (where wdsizo is 4 or 8 bytes)
>>>>>>> metadata (min/max values): nfields*2*nel * 4 bytes
>>>>>>> 
>>>>>>> Stefan
>>>>>>> 
>>>>>> 
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