Parallel netcdf & wrf

[John Michalakes]

Hi Rob,

I've isolated one of the problems we're seeing on Blue Gene to a very small test
case. The script is attached to this email. There is a relatively small data
file you can test this with at:

   http://www.mmm.ucar.edu/wrf/WG2/wrfinput_d01

It is a CDF 1 file (about 7MB), but it still shows the problem we've been seeing
with the larger CDF 2 files we've been trying to read. In a nutshell, the call
to set_vara_fileview in mpinetcdf.c around line 2401 is not doing the right
thing. The file view remains at the beginning of the file, even though the
offset to the text field we're trying to read is something like 26872 bytes in.
So when MPI_File_read_all is called in ncmpi_get_vara_all, we get a string with
"CDF" and then garbage in it instead of the first value of the Times variable,
"2000-01-24_12:00:00".

On an IBM Power5 machine (bluevista.ucar.edu) compiled with OBJECT_MODE=64 the
test program works the way it is supposed to:

 p.F 24 0
 p.F 26 0
 p.F 28 0
 p.F 31 0
 p.F 33 0
 p.F 39 0
 stat  0
 Times 2000-01-24_12:00:00  <- this is correct

However, on BG (frost.ucar.edu) it gives:

 p.F 24 0
 p.F 26 0
 p.F 28 0
 p.F 31 0
 p.F 33 0
 p.F 39 0
 stat  0
 Times CDF  <- This is the first 3 bytes from the beginning of the file.

This is with the latest version of pnetcdf, the pre-release issued last week.

Thanks for all your help.

John

PS... also attaching the config.log and config.status files for the Blue Gene
install of parallel-netcdf-1.0.2pre1 . (Jim E: I copied the install over to my
home dir on frost so I could put debugging prints in it).

-----------------------------------------------------------
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
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