H5Part development and discussion

[Kurt Stockinger <KStockinger AT lbl.gov>]

One correction below:
> Hi Thomas,
>
> Thanks for the detailed code description. It's an excellent way for me
> to see how H5Part is currently being used. I have a few comments below.
>
> Thomas Schietinger wrote:
>   
>> Dear all,
>>
>> let me add some more info on the performance problem reported
>> at yesterday's phone meeting.
>>
>> The routines I use for reading in an HDF5 file in H5root are:
>> (see file TH5Dataset.cc)
>>
>> get the file handle:
>>
>>    fH5File = H5PartOpenFile(fFullFilename.Data(),H5PART_READ);
>>
>> (fFullFilename.Data() evaluates to a char string)
>>
>> get the number of datasets:
>>
>>   H5PartSetStep(fH5File,0);
>>   Int_t nDataset = H5PartGetNumDatasets(fH5File);
>>
>> get the dataset names:
>>
>>   for(Int_t i=0;i<nDataset;i++){
>>     H5PartGetDatasetName(fH5File,i,name,maxLength);
>>     ...
>>   }
>>
>> get the number of steps, step attributes and file attributes:
>>
>>   fNStep = H5PartGetNumSteps(fH5File);
>>   fNStepAttr = H5PartGetNumStepAttribs(fH5File);
>>   fNFileAttr = H5PartGetNumFileAttribs(fH5File);
>>
>> get file attribute info:
>>
>>   for (Int_t n = 0; n < fNFileAttr; n++) {
>>     H5PartGetFileAttribInfo(fH5File,n,an,32,0,nElem);
>>     
> Is it intended that you don't return the type of the attribute (the 5th
> parameter) or do you assume that you know the type, i.e. all are of type
> char?
>   
>>     ...
>>   }
>>
>> get step attribute info for step 0 - ASSUME THEY WILL BE THE SAME
>> FOR ALL STEPS!
>>
>>   H5PartSetStep(fH5File,0);
>>
>>   for (Int_t n=0; n<fNStepAttr; ++n) {
>>     H5PartGetStepAttribInfo(fH5File,n,an,32,0,nElem);
>>     
> Same comment about type as above.
>   
>>     ...
>>   // distinguish scalar and vector attributes, ignore others:
>>     TString type("?");
>>     if  (*nElem==1 )  { // scalar variable
>>       fScalarName.AddLast(new TObjString(attrName));
>>       fNScalarAttr++;
>>       type = TString(" (scalar)");
>>     } else if (*nElem==3 )  { // vector variable
>>       fVectorName.AddLast(new TObjString(attrName));
>>       fNVectorAttr++;
>>       type = TString(" (vector)");
>>     } else {
>>     ...
>>   }
>>
>> Read in the unit strings for the attributes found:
>>
>>   for (Int_t i = 0; i < 9; i++) fPartVarUnit[i] =
>> GetUnit(fPartVarName[i]);
>>   for (Int_t i = 0; i < fNScalarAttr; i++)
>>     fScalarUnit.AddLast(new TObjString(GetUnit(static_cast<TObjString*>
>>                            (fScalarName.At(i))->GetString())));
>>   for (Int_t i = 0; i < fNVectorAttr; i++)
>>     fVectorUnit.AddLast(new TObjString(GetUnit(static_cast<TObjString*>
>>                            (fVectorName.At(i))->GetString())));
>>
>> where GetUnit(...) is a method that contains a loop over the file
>> attributes to
>> find the associated unit name:
>>     
> In the H5Part doc I didn't find anything specific about unit names. Can
> you explain this a bit? Do you assume that the attribute name is unified
> to char[32]?
>   
>>   for (Int_t i = 0; i < fNFileAttr; i++) {
>>
>>     TObjString* s = static_cast<TObjString*>(fFileAttr.At(i));
>>     if (s->GetString() == varNameU) {
>>       char u[32];
>>      
>> H5PartReadFileAttrib(fH5File,const_cast<char*>(s->GetString().Data()),
>> &u);
>>       unit = TString(u);
>>     }
>>     ...
>>   }
>>
>> Now loop over steps and retrieve attribute and particle data for each
>> step:
>>
>>   for (Int_t step=0; step<fNStep; step++) {
>>     H5PartSetStep(fH5File,step);
>>     unsigned long n = H5PartGetNumParticles(fH5File);
>>
>>     // read in scalar attributes
>>     for (int i=0; i<fNScalarAttr; ++i) {
>>       TObjString* s = static_cast<TObjString*>(fScalarName.At(i));
>>      
>> H5PartReadStepAttrib(fH5File,const_cast<char*>(s->GetString().Data()),
>> &val);
>>       ...
>>     }
>>
>>     // read in vector attributes
>>     for (int i=0; i<fNVectorAttr; ++i) {
>>       TObjString* s = static_cast<TObjString*>(fVectorName.At(i));
>>      
>> H5PartReadStepAttrib(fH5File,const_cast<char*>(s->GetString().Data()),
>> arr);
>>       ...
>>     }
>>
>> Sorry if this is too much information, I just wanted to let you know
>> what routines
>> I am using, so you can see if I am doing something very inefficient. I
>> have not
>> given much thought to the choice of routines, I just looked for what I
>> needed,
>> typically found it rather quickly and then only made sure it does what
>> I want it
>> to do without measuring performance or anything. The files I look at
>> load very
>> quickly anyway, it is only when Andreas tries to simulate the whole
>> world that
>> he ends up waiting a couple of minutes ;-)
>>
>> Now some numbers: a 3 Giga file with some 500 time steps (21 file
>> attr., 12 step
>> attr.) takes 19.1 s to read in (the second time only 0.5 s since the
>> file is
>> buffered). 
>>     
> This the time for reading the attributes only, right? If yes, then the
> whole 3GB is not read entirely but only the 21*12 (char) attributes, right?
>   
Just looked at your code again: In total, you read ~500 * (21+12) =
16500 attributes, right?

Kurt
> Can you send me a pointer to the file to download so that we can look at
> this together? This would also help me understand your performance a bit
> better.
>
> Thanks,
> Kurt
>   
>> A 85 Giga file with 18263 time steps (same number of attributes)
>> takes 29:38.52 to read in (half an hour). That's where it starts to hurt!
>> It should be noted that a simple h5dump also groans under that file
>> and won't
>> produce anything before several minutes (I am still waiting in fact).
>> (These figures are for our merlin00 machine at PSI.)
>>
>> Achim suggested to use H5PartGetStepAttribInfo instead of
>> H5PartReadStepAttrib,
>> but I don't see how I can replace the functionality of ReadStepAttrib
>> with
>> GetStepAttribInfo ,i.e. read a value...
>>
>> Regards,
>>
>> Thomas
>>
>> _______________________________________________
>> H5Part mailing list
>> H5Part AT lists.psi.ch
>> https://lists.web.psi.ch/mailman/listinfo/h5part
>>     
>
>
>   


-- 
Kurt Stockinger
Computational Research Division
Lawrence Berkeley National Laboratory
Mail Stop 50B-3238, 1 Cyclotron Road
Berkeley, California 94720, USA

Tel: +1 (510) 486 5208, Fax: +1 (510) 486 4004
email: KStockinger AT lbl.gov
http://sdm.lbl.gov/kurts/