filename prefixes
michael
michael.bane at manchester.ac.uk
Wed Aug 11 18:54:02 CDT 2010
Isn't there a WRF configure option to use HDF5 (par) with netcdf4 to
give you much the same thing? In which case there may be something in
the relevant external/ (or externio?) (from mem!) subdir to peek at?
Michael
http://www.twitter.com/mkbane_mcr
On Wed, 2010-08-11 at 18:47 -0500, Gerald Creager wrote:
> On the system I'm working with, I can't use the MPICH envVars such as:
> MPICH_MPIIO_HINTS_DISPLAY 1
> MPICH_MPIIO_HINTS “wrfout*:striping_factor=64”
>
> Therefore, to set striping on the wrfout files, with a Lustre file
> system and SGE for the batch queuing environment, I've gotta find where
> the wrfout file creation instance occurs and add a couple lines of code
> to make it create the wrfouts with stripe-counts appropriately set
> (somewhere between 16-64, I think). What I intend to do eventually, is
> to get that folded back into WRF as a namelist parameter, so that those
> of us using pnetcdf (needed if proc count gets past ~512 or so on this
> system) can have a simplified granular method of using striping on
> parallel file systems (specifically with pnetcdf).
>
> I've looked at Johnsen's work to use Lustre on the Cray XT5. It dowsn't
> apply to my environment, more's the pity.
>
>
> Thanks, Gerry
>
> Don Morton wrote:
> > I've used pnetcdf with WRF, using the nocolons option. I'm not sure
> > specifically what you're asking now, but I can send you my notes if it
> > helps...
> >
> > On Wed, Aug 11, 2010 at 3:13 PM, Gerald Creager <gerry.creager at tamu.edu
> > <mailto:gerry.creager at tamu.edu>> wrote:
> >
> > It's a namelist.input spec: NOCOLONS
> >
> > I'm sorting thru some other issues with pnetcdf and WRF right now...
> > I'm having to change it so it'll create wrfout_dxx files with the
> > striping info correct at file creation. If anyone's had to do this,
> > I'd appreciate a clue...
> >
> > gerry
> >
> > Jim Edwards wrote:
> >
> > Hi Johnny,
> >
> > I think that the real problem may be that WRF uses the colon
> > character in filenames and the filesystem reserves this same
> > character for special use. I think that there is a compile
> > option for wrf not to use colons.
> >
> > Jim
> >
> > On Wed, Aug 11, 2010 at 4:44 PM, Johnny Chang
> > <Johnny.Chang at nasa.gov <mailto:Johnny.Chang at nasa.gov>
> > <mailto:Johnny.Chang at nasa.gov <mailto:Johnny.Chang at nasa.gov>>>
> > wrote:
> >
> > Hello,
> >
> > I am helping a user trouble-shoot a runtime error using
> > parallel-netcdf version 1.1.1 and mvapich2/1.2p1/intel-PIC.
> >
> > The error message is:
> >
> > 0: MPI_File_open : File does not exist, error stack:
> > ADIO_RESOLVEFILETYPE_PREFIX(546): Invalid file name
> > wrfout_d01_2006-07-25_00:00:00
> > open_hist_w : error opening wrfout_d01_2006-07-25_00:00:00 for
> > writing. ***
> >
> > While googling the ADIO_RESOLVEFILETYPE_PREFIX error, we
> > found the
> > ad_fstype.c code containing:
> >
> > 477 /*
> > 478 ADIO_FileSysType_prefix - determines file system
> > type for
> > a file using
> > 479 a prefix on the file name. upper layer should have
> > already determined
> > 480 that a prefix is present.
> > 481 482 Input Parameters:
> > 483 . filename - path to file, including prefix (xxx:)
> > 484 485 Output Parameters:
> > 486 . fstype - pointer to integer in which to store file
> > system
> > type (ADIO_XXX)
> > 487 . error_code - pointer to integer in which to store
> > error code
> > 488 489 Returns MPI_SUCCESS in error_code on
> > success. Filename
> > not having a prefix
> > 490 is considered an error. Except for on Windows systems
> > where the default is NTFS.
> > 491 492 */
> > 493 static void ADIO_FileSysType_prefix(char *filename, int
> > *fstype, int *error_code)
> > 494 {
> > 495 static char myname[] = "ADIO_RESOLVEFILETYPE_PREFIX";
> > 496 *error_code = MPI_SUCCESS;
> > 497 498 if (!strncmp(filename, "pfs:", 4) ||
> > !strncmp(filename,
> > "PFS:", 4)) {
> > 499 *fstype = ADIO_PFS;
> > 500 }
> >
> > ...
> >
> >
> > 557 #else
> > 558 *fstype = 0;
> > 559 /* --BEGIN ERROR HANDLING-- */
> > 560 *error_code = MPIO_Err_create_code(MPI_SUCCESS,
> > MPIR_ERR_RECOVERABLE,
> > 561 myname,
> > __LINE__,
> > MPI_ERR_NO_SUCH_FILE,
> > 562 "**filename",
> > "**filename %s", filename);
> > 563 /* --END ERROR HANDLING-- */
> > 564 #endif
> > 565 }
> > 566 }
> >
> > which seems to indicate that the MVAPICH2 library is expecting
> > parallel-netcdf
> > to pre-pend a prefix on the filename passed to the MVAPICH2
> > library.
> >
> > We are running on a Lustre filesystem. So, we think that the
> > parallel-netcdf
> > library should have passed the "lustre:" or "LUSTRE:" prefix
> > along
> > with the
> > actual filename. Are we right in this interpretation of the
> > error?
> >
> > If so, then perhaps the parallel-netcdf library was not built
> > correctly?
> >
> > Here is the beginning part of config.log:
> >
> >
> > ------------------------------------------------------------------------
> >
> > This file contains any messages produced by compilers while
> > running configure, to aid debugging if configure makes a mistake.
> >
> > It was created by configure, which was
> > generated by GNU Autoconf 2.61. Invocation command line was
> >
> > $ ./configure --prefix=/nasa/parallel-netcdf/1.1.1/mvapich2
> > --with-mpi=/nasa/mvapich2/1.2p1/intel-PIC
> >
> > ## --------- ##
> > ## Platform. ##
> > ## --------- ##
> >
> > hostname = pbspl1
> > uname -m = x86_64
> > uname -r = 2.6.16.60-0.42.5.03schamp-nasa
> > uname -s = Linux
> > uname -v = #1 SMP Tue Nov 10 20:46:20 UTC 2009
> >
> > /usr/bin/uname -p = unknown
> > /bin/uname -X = unknown
> >
> > /bin/arch = x86_64
> > /usr/bin/arch -k = unknown
> > /usr/convex/getsysinfo = unknown
> > /usr/bin/hostinfo = unknown
> > /bin/machine = unknown
> > /usr/bin/oslevel = unknown
> > /bin/universe = unknown
> >
> > PATH: /nasa/intel/Compiler/11.1/046/bin/intel64
> > PATH: /nasa/intel/Compiler/11.1/046/mkl/tools/environment
> > PATH: /nasa/mvapich2/1.2p1/intel-PIC/bin
> > PATH: /u/jrappley/bin
> >
> > If the problem is in the parallel-netcdf build, let us know
> > what is the fix.
> >
> > Thanks in advance!
> >
> > Johnny
> > -- Johnny Chang
> > 650-604-4356
> >
> >
> >
> > --
> > Gerry Creager -- gerry.creager at tamu.edu <mailto:gerry.creager at tamu.edu>
> > Texas Mesonet -- AATLT, Texas A&M University
> > Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
> > Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX 77843
> >
> >
> >
> >
> > --
> > Arctic Region Supercomputing Center
> > http://weather.arsc.edu/
>
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