[Wrf-users] Wrf-users Digest, Vol 92, Issue 5

Tue Apr 17 05:17:48 MDT 2012

Hi Dr. Andrew,
Thanks for the web link. The documentation on wrf performance optimization
provided on this link has been quite useful. I tried to install pnetcdf
(Aragonne Lab) on our Bluegene/P with IBM XLF compilers and it appears to
be built properly however, when I turned on the io_form_hisotry switch for
pnetcdf (option 11), the simulation crashed and I got netcdf related
errors. 

I did the following to compile pnetcdf on our system

./configure --host powerpc-bgp-linux --build powerpc64-suse-linux
--with-mpi=/bgsys/drivers/ppcfloor/comm --prefix=/home/basitali/pnetcdf
CC=mpixlc MPICC=mpixlc FC=mpixlf90 MPIF77=mpixlf90 F77=mpixlf90
F90=mpixlf90

make <enter>
make install <install>

When I run the simulation with io_form_history=11, and debug_level=100, I
got the following error:

0: MPI_File_delete : File does not exist, error stack:
ADIO_RESOLVEFILETYPE_PREFIX(567): Invalid file name
wrfout_d01_2010-06-19_00:00:00
  NetCDF error: Can not open/create file
  NetCDF error in ext_pnc_open_for_write_begin wrf_io.F90, line 1269
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
- - - - -
- - - - -
- - -- - 
- - - - - 
Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
  Warning WRITE READ ONLY FILE in wrf_io.F90, line 2397
Timing for Writing wrfout_d01_2010-06-19_00:00:00 for domain        1:
0.31000 elapsed seconds.

After this last line 'Timing for Writing ŠŠ.." simulation just crashed.
Could you please advise how to fix this.

Secondly the above mentioned documentation suggests to put 11 (parallel
io) for io_form_restart, io_form_input and io_form_boundary options also
whereas the wrf documentation does not provide option 11 for these three
options. So I believe If I would use 11 for these options I may get error.
I will greatly appreciate if you could advise on this also.

Cheers,

----
Basit A. Khan, Ph.D.

Postdoctoral Research Fellow

Division of Physical Sciences & Engineering

Office# 3204, Level 3, Building 1,

King Abdullah University of Science & Technology

4700 King Abdullah Blvd, Box 2753, Thuwal 23955 6900,

Kingdom of Saudi Arabia.

Office: +966(0)2 808 0276,  Mobile: +966(0)5 0860 3617

E-mail: basitali.khan at kaust.edu.sa

Skype name: basit.a.khan

On 4/11/12 9:00 PM, "wrf-users-request at ucar.edu"
<wrf-users-request at ucar.edu> wrote:

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>Today's Topics:
>
>   1. Re: optimizing wrf run (Andy Porter)
>   2. Problem when run wrf_cape_3d.ncl (Nguyen Ngoc Bich Phuong)
>   3. gen_be plots (Sean Crowell)
>   4. WRF WPP Wind u and v components (Rambler)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 10 Apr 2012 10:30:08 +0100
>From: Andy Porter <andrew.porter at stfc.ac.uk>
>Subject: Re: [Wrf-users] optimizing wrf run
>To: <wrf-users at ucar.edu>
>Message-ID: <4F83FDA0.2060209 at stfc.ac.uk>
>Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
>
>> I am using WRFV3.3.1 on our BlueGene/P compiled wit XLF compilers and
>> mpi openmpi implementation. I intend to run a large wrf simulation
>> (1000x1000x41) and trying to optimize(in terms of simulation speed) the
>> wrf run. I know that nproc_x, nproc_y, tile_sz_x and tile_sz_y options
>> can be used for this purpose but do not know how to do this. I also
>> could not find sufficient details on configuring these options in wrf
>> documentation.
>>
>> I would greatly appreciate if somebody could advise me how to configure
>> these options.
>>
>I experimented with the tiling options. More details here:
>
>http://epubs.cclrc.ac.uk/work-details?w=56300
>
>Hope this helps,
>
>Andy.
>
>-- 
>Dr. Andrew Porter
>Computational Scientist
>Advanced Research Computing Group
>Computational Science and Engineering Dept.
>STFC Daresbury Laboratory
>Keckwick Lane
>Daresbury
>WA4 4AD
>Tel. : +44 (0)1925 603607
>email: andrew.porter at stfc.ac.uk
>
>-- 
>Scanned by iCritical.
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 11 Apr 2012 15:53:14 +0700
>From: "Nguyen Ngoc Bich Phuong" <bichphuong at imh.ac.vn>
>Subject: [Wrf-users] Problem when run wrf_cape_3d.ncl
>To: <wrf-users at ucar.edu>
>Message-ID: <000001cd17c0$8a8516b0$9f8f4410$@ac.vn>
>Content-Type: text/plain; charset="us-ascii"
>
>Dear wrf-users, 
>
>I am trying to display cin/cape of  wrfout using wrf_cape_3d.ncl that I
>attached. I use NCL with version 5.1.0 and I get problem.
>
>Please help me to fix this
>
>Thanks in advance
>
> 
>
>Copyright (C) 1995-2009 - All Rights Reserved
>
> University Corporation for Atmospheric Research
>
> NCAR Command Language Version 5.1.0
>
> The use of this software is governed by a License Agreement.
>
> See http://www.ncl.ucar.edu/ for more details.
>
> 
>
> 
>
>Variable: times
>
>Type: string
>
>Total Size: 4 bytes
>
>            1 values
>
>Number of Dimensions: 1
>
>Dimensions and sizes:   [1]
>
>Coordinates: 
>
>Number Of Attributes: 2
>
>  description :   times in file
>
>  _FillValue :    missing
>
>(0)   2008-04-16_00:00:00
>
>At line 492 of file rip_cape.f
>
>Fortran runtime error: No such file or directory
>
> 
>
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>------------------------------
>
>Message: 3
>Date: Wed, 11 Apr 2012 09:12:04 -0500
>From: Sean Crowell <sean.crowell at noaa.gov>
>Subject: [Wrf-users] gen_be plots
>To: WRF Help <wrfhelp at ucar.edu>
>Cc: wrf-users at ucar.edu
>Message-ID: <03C15B4D-374B-4CD0-BD8D-DCF350328262 at noaa.gov>
>Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>Hi,
>
>I'd really like to understand what the be.dat file says about the
>correlations between the model variables, but I don't know what the
>format of the file is.  Also, the supplied plotting scripts don't
>really have any explanation of what's being plotted.  Is there a way
>that someone could either (1) tell me how to read in the be.dat binary
>file to make my own plots, or (2) point me to some documentation of
>the plots that are being generated by the gen_be_plot_wrapper.ksh
>script?  Thanks!
>
>Sean Crowell
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 11 Apr 2012 11:03:17 +0400
>From: Rambler <soleiman at rambler.ru>
>Subject: [Wrf-users] WRF WPP Wind u and v components
>To: "wrf-users at ucar.edu" <wrf-users at ucar.edu>
>Message-ID: <219EB03C-D84B-41B2-AC46-93EB6C28B383 at rambler.ru>
>Content-Type: text/plain;	charset=us-ascii
>
>Hello to all
>Could some one explain me the wind u and v components  in grib files
>which made by WRF WPP is rotated to the earth coordinate ( north, east)
>or in grid direction (x, y) ? Also they are in mass point or not?
>Thanks. 
>
>Best regards, 
>Suleiman Mostamandy
>
>
>
>
>------------------------------
>
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>
>End of Wrf-users Digest, Vol 92, Issue 5
>****************************************

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