Issue with "integer" arguments in Fortran API for PNetCDF

Wed Oct 25 13:10:07 CDT 2006

Well, its probably too late for that, as the Fortran version of the  
parallel interface has been out for some time and is already in use.   
The real issue is the one that I mentioned - even for 32 bit systems,  
MPI_Offset is often 64 bits, and this is a more natural (and  
necessary) size when using parallel computing, as the files can  
easily exceed 2GB.  Also, given the MPI flavor of the interface, it  
seemed natural to use MPI file offsets for these values, particularly  
as that's supported in the MPI Fortran binding.

An alternative prefix might be nfo32mpi where the "o32" means "32-bit  
for file offset, even if MPI_Offset is 64 bits".  Redefining the  
current names (and breaking currently running code) is something I'd  
like to avoid :)

Bill

On Oct 25, 2006, at 12:42 PM, John Michalakes wrote:

> Not to be too facetious, but how about "api compliant"?
>
> Seriously, the NetCDF Fortran API defines these as INTEGER so if an
> interface needs to have a name that sets it off, it should probably  
> be the
> current Fortran interface to pNetCDF.
>
> -John
>
>> -----Original Message-----
>> From: owner-parallel-netcdf at mcs.anl.gov
>> [mailto:owner-parallel-netcdf at mcs.anl.gov]On Behalf Of William Gropp
>> Sent: Wednesday, October 25, 2006 10:21 AM
>> To: john at michalakes.us
>> Cc: parallel-netcdf at mcs.anl.gov
>> Subject: Re: Issue with "integer" arguments in Fortran API for  
>> PNetCDF
>>
>>
>> Actually, MPI_Offset can be 64 bits, even on 32-bit platforms, if the
>> file system accepts 64 bit offsets (e.g., has something like  
>> lseek64).
>>
>> What would you suggest as a name that indicated that the offset value
>> was a Fortran integer rather than an MPI_Offset-sized integer?
>>
>> Bill
>>
>> On Oct 25, 2006, at 11:05 AM, John Michalakes wrote:
>>
>>> That would be helpful. But I think putting 32 in the name would be
>>> misleading, since this is only an issue on 64 bit compiles.  (On 32
>>> bit
>>> compiles, MPI_Offset is the same length as a Fortran INTEGER).
>>>
>>> John
>>>
>>>> -----Original Message-----
>>>> From: William Gropp [mailto:gropp at mcs.anl.gov]
>>>> Sent: Wednesday, October 25, 2006 9:51 AM
>>>> To: john at michalakes.us
>>>> Cc: parallel-netcdf at mcs.anl.gov
>>>> Subject: Re: Issue with "integer" arguments in Fortran API for
>>>> PNetCDF
>>>>
>>>>
>>>> As the Fortran interfaces are generated with a script, we could
>>>> create an alternate version that was closer to the serial NetCDF
>>>> interface, using a different prefix to avoid confusion (e.g., maybe
>>>> nf32mpi_xxx).  Would that help?  What do others think of that
>>>> approach?
>>>>
>>>> Bill
>>>>
>>>> On Oct 25, 2006, at 2:06 AM, John Michalakes wrote:
>>>>
>>>>> PS... There is a problem with the pnetcdf.inc file itself.  This
>>>>> file
>>>>> defines INTEGER parameters such as NF_UNLIMITED which may be  
>>>>> used as
>>>>> arguments to NFMPI_* routines that are defined as
>>>>> INTEGER(KIND=MPI_OFFSET_KIND). An example is the 3rd argument of:
>>>>>
>>>>> FORTRAN_API int FORT_CALL nfmpi_def_dim_ ( int *v1, char *v2
>>>>> FORT_MIXED_LEN(d2), MPI_Offset *v3, MPI_Fint *v4 FORT_END_LEN 
>>>>> (d2) )
>>>>>
>>>>> Since MPI_Offset can be 64-bits if compiled with OBJECT_MODE 64 on
>>>>> the IBM,
>>>>> passing NF_UNLIMITED (32-bits) as the third argument is incorrect.
>>>>>
>>>>> John
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: owner-parallel-netcdf at mcs.anl.gov
>>>>>> [mailto:owner-parallel-netcdf at mcs.anl.gov]On Behalf Of John
>>>>>> Michalakes
>>>>>> Sent: Tuesday, October 24, 2006 3:30 PM
>>>>>> To: parallel-netcdf at mcs.anl.gov
>>>>>> Subject: Issue with "integer" arguments in Fortran API for  
>>>>>> PNetCDF
>>>>>>
>>>>>>
>>>>>> I'm having a problem adapting parallel NetCDF as an option in
>>>>>> the WRF
>>>>>> (Weather Research and Forecast) model I/O API. WRF currently
>>>>>> supports
>>>>>> non-parallel NetCDF, and we're now trying to extend the model to
>>>>>> use the new
>>>>>> parallel NetCDF code. Have run into a problem with some of the
>>>>>> arguments in
>>>>>> the API for parallel-NetCDF:
>>>>>>
>>>>>> The original NetCDF Fortran API defines lengths, starts, and
>>>>>> other arguments
>>>>>> as INTEGER. PnetCDF recasts some (but not all) of these
>>>>>> arguments as
>>>>>> MPI_Offset. We compile WRF with OBJECT_MODE 64 on the IBMs where
>>>>>> KIND=MPI_OFFSET_KIND works out to 8 bytes. Thus, the calls in WRF
>>>>>> that pass
>>>>>> these arguments as 32-bit INTEGERs from Fortran are causing
>>>>>> PNetCDF to see
>>>>>> garbage in the high four bytes of the dummy argument. For  
>>>>>> example,
>>>>>> the
>>>>>> length argument to NFMPI_DEF_DIM ends up being 73 + a very-large-
>>>>>> garbage
>>>>>> value instead of 73.
>>>>>>
>>>>>> I was hoping for a relatively quick drop-in of PnetCDF into WRF
>>>>>> I/O API but
>>>>>> this now seems unlikely. There is a large amount of NetCDF
>>>>>> interface code in
>>>>>> WRF that will need to be gone through.  Or I can write a wrapper
>>>>>> lib for all
>>>>>> these routines.
>>>>>>
>>>>>> Has anyone done this already? What's needed is for the wrapper
>>>>>> routine to
>>>>>> accept INTEGER arguments and copy them to INTEGER
>>>>>> (KIND=MPI_OFFSET_KIND) to
>>>>>> be used as arguments to the actual NFMPI_* routines in PNetCDF  
>>>>>> and
>>>>>> (in the
>>>>>> case of return values) copy them back to INTEGER again.
>>>>>>
>>>>>> Not arguing, but curious: since PNetCDF is supposed to be a
>>>>>> parallel
>>>>>> implementation of the NetCDF API, why was the API altered this  
>>>>>> way
>>>>>> to use
>>>>>> arguments of type MPI_Offset instead of INTEGER? At least for  
>>>>>> what
>>>>>> I'm
>>>>>> trying to do, it is a significant impediment.
>>>>>>
>>>>>> I really appreciate that parallel NetCDF is being developed. It
>>>>>> is very much
>>>>>> needed, especially now as we try moving to Petascale. Kudos to  
>>>>>> the
>>>>>> developers.
>>>>>>
>>>>>> John
>>>>>>
>>>>>> -----------------------------------------------------------
>>>>>> John Michalakes, Software Engineer        michalak at ucar.edu
>>>>>> NCAR, MMM Division                   voice: +1 303 497 8199
>>>>>> 3450 Mitchell Lane                     fax: +1 303 497 8181
>>>>>> Boulder, Colorado 80301 U.S.A.        cell: +1 720 209 2320
>>>>>>         http://www.mmm.ucar.edu/individual/michalakes
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>
>>>>
>>>
>>
>