pnetcdf test/DRY RUN Error in wrf simulation

Wed Jun 4 10:54:30 CDT 2014

Hi, Basit

The file wrf_io.F90 should be the one in external/io_pnetcdf.
So the code fragment is like

2399   elseif(DH%FileStatus == WRF_FILE_OPENED_NOT_COMMITTED) then
2400     do NVar=1,MaxVars
2401       if(DH%VarNames(NVar) == VarName ) then
2402         Status = WRF_WARN_2DRYRUNS_1VARIABLE
2403         write(msg,*) 'Warning 2 DRYRUNS 1 VARIABLE (',TRIM(VarName),') in ',__FILE__,', line', __LINE__
2404         call wrf_debug ( WARN , TRIM(msg))
2405         return
2406       elseif(DH%VarNames(NVar) == NO_NAME) then

It looks to me is the file is yet to be closed.

Could you let us know how you build WRF (commands) and the test case (and parameters)
that you run? I may give it a try to see if I can repeat your experiment and observe the same errors.

Wei-keng

On Jun 4, 2014, at 10:09 AM, BasitAli Khan wrote:

> Hi Rob,
> 
> Following is the snippet of the subroutine in wrf_io.F90. Actually line
> 2403 is just a variable declaration.
> 
> 
> 2380 subroutine
> ext_ncd_write_field(DataHandle,DateStr,Var,Field,FieldTypeIn,  &
> 2381   Comm, IOComm, DomainDesc, MemoryOrdIn, Stagger,  DimNames,
>    &
> 2382
> DomainStart,DomainEnd,MemoryStart,MemoryEnd,PatchStart,PatchEnd,Status)
> 2383   use wrf_data
> 2384   use ext_ncd_support_routines
> 2385   implicit none
> 2386   include 'wrf_status_codes.h'
> 2387   include 'netcdf.inc'
> 2388   integer                       ,intent(in)    :: DataHandle
> 2389   character*(*)                 ,intent(in)    :: DateStr
> 2390   character*(*)                 ,intent(in)    :: Var
> 2391   integer                       ,intent(inout) :: Field(*)
> 2392   integer                       ,intent(in)    :: FieldTypeIn
> 2393   integer                       ,intent(inout) :: Comm
> 2394   integer                       ,intent(inout) :: IOComm
> 2395   integer                       ,intent(in)    :: DomainDesc
> 2396   character*(*)                 ,intent(in)    :: MemoryOrdIn
> 2397   character*(*)                 ,intent(in)    :: Stagger ! Dummy for
> now
> 2398   character*(*) ,dimension(*)   ,intent(in)    :: DimNames
> 2399   integer       ,dimension(*)   ,intent(in)    :: DomainStart,
> DomainEnd
> 2400   integer       ,dimension(*)   ,intent(in)    :: MemoryStart,
> MemoryEnd
> 2401   integer       ,dimension(*)   ,intent(in)    :: PatchStart,
> PatchEnd
> 2402   integer                       ,intent(out)   :: Status
> 2403   integer                                      :: FieldType
> 2404   character (3)                                :: MemoryOrder
> 2405   type(wrf_data_handle)         ,pointer       :: DH
> 2406   integer                                      :: NCID
> 2407   integer                                      :: NDim
> 2408   character (VarNameLen)                       :: VarName
> 2409   character (3)                                :: MemO
> 2410   character (3)                                :: UCMemO
> 2411   integer                                      :: VarID
> 2412   integer      ,dimension(NVarDims)            :: Length
> 2413   integer      ,dimension(NVarDims)            :: VDimIDs
> 2414   character(80),dimension(NVarDims)            :: RODimNames
> 2415   integer      ,dimension(NVarDims)            :: StoredStart
> 2416   integer      ,dimension(:,:,:,:),allocatable :: XField
> 2417   integer                                      :: stat
> 2418   integer                                      :: NVar
> 2419   integer                                      :: i,j
> 2420   integer                                      :: i1,i2,j1,j2,k1,k2
> 2421   integer                                      :: x1,x2,y1,y2,z1,z2
> 2422   integer                                      :: l1,l2,m1,m2,n1,n2
> 2423   integer                                      :: XType
> 2424   integer                                      :: di
> 2425   character (80)                               :: NullName
> 2426   logical                                      :: NotFound
> 2427
> 
> 
> 
> 
> 
> 
> 
> Cheers,
> b:)
> ----
> 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)12 808 0276,  Mobile: +966(0)5 0860 3617
> 
> E-mail: basitali.khan at kaust.edu.sa
> 
> 
> 
> 
> Skype name: basit.a.khan
> 
> 
> 
> 
> On 6/4/14 4:58 PM, "Rob Latham" <robl at mcs.anl.gov> wrote:
> 
>> 
>> 
>> On 06/04/2014 01:55 AM, BasitAli Khan wrote:
>>> Hi there,
>>> I sent you the following email a a weak ago regarding pnetcdf  make
>>> check  errors, but did not get response. I used this pnetcdf to compile
>>> netCDF library 4.1.2. The pnetcdf was successfully linked and netCDF was
>>> successfully compiled. I ran a WRF simulation which also was completed
>>> successfully, however, the log file rsl.out.0000 (attached ) has several
>>> (DRY RUN) errors that are originating from pnetCDF. I am wondering what
>>> these errors are and would they be affecting my simulation in anyway?
>>> 
>>> Thanks in advance and please do REPLY this email.
>> 
>> Hello! sorry for the oversight.  Here is my (list-only) reply from last
>> week:
>> 
>> http://lists.mcs.anl.gov/pipermail/parallel-netcdf/2014-May/001574.html
>> 
>> Thanks for subscribing to the mailing list.
>> 
>> There are folks using pnetcdf and WRF on Blue Gene.  I don't know the
>> details, but it apparently is possible.  I think we can get you
>> straightened out.
>> 
>> When you see errors like this:
>> 
>> /bin/sh: line 1:  6418 Illegal instruction     ./nc_test -c -d .
>> 
>> it means you are running back-end code on the login nodes.  Blue Gene is
>> a cross-compile environment: compute node codes cannot run on the login
>> nodes.  (well, technically they can... until they make a system call)
>> 
>> what does line 2403 of wrf_io.f90 look like?
>> 
>> ==rob
>> 
>> 
>> Hi Rob,
> 
> 
>>> 
>>> Best regards,
>>> b:)
>>> ----
>>> 
>>> 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)12 808 0276,  Mobile: +966(0)5 0860 3617
>>> 
>>> E-mail: basitali.khan at kaust.edu.sa <mailto:basitali.khan at kaust.edu.sa>
>>> 
>>> Skype name: basit.a.khan
>>> 
>>> From: KAUST <basitali.khan at kaust.edu.sa
>>> <mailto:basitali.khan at kaust.edu.sa>>
>>> Date: Wednesday, May 28, 2014 3:05 PM
>>> To: "parallel-netcdf at mcs.anl.gov <mailto:parallel-netcdf at mcs.anl.gov>"
>>> <parallel-netcdf at mcs.anl.gov <mailto:parallel-netcdf at mcs.anl.gov>>
>>> Subject: pnetcdf test
>>> 
>>> Hi there,
>>> I am new to pnetcdf. I want to compile it for faster IO  of WRF model on
>>> our bluegeneP with Linux RedHat 10 on it. I apparently successfully
>>> installed the latest version of pnetcdf 1.4.1, however when i run  'make
>>> testing', i got few errors (log file attached).  I would greatly
>>> appreciate if you could have a look and advise where i am going wrong.
>>> 
>>> The compilation of parallel netcdf created 4 directories. The contents
>>> of these dir are as follows:
>>> 
>>> /lib/libpnetcdf.a
>>> /include/pnetcdf.h  pnetcdf.inc  pnetcdf.mod
>>> /bin/ncmpidiff  ncmpidump  ncmpigen  ncmpivalid
>>> /man/man1/ncmpidiff.1  ncmpidump.1  ncmpigen.1  ncmpivalid.1
>>> /man/man3/pnetcdf.3  pnetcdf_f77.3  pnetcdf_f90.3
>>> 
>>> 
>>> Another question is that, do i have to do anything special to use it
>>> with WRF?
>>> 
>>> Thanks in advance and best regards,
>>> 
>>> 
>>> b:)
>>> ----
>>> 
>>> 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)12 808 0276,  Mobile: +966(0)5 0860 3617
>>> 
>>> E-mail: basitali.khan at kaust.edu.sa <mailto:basitali.khan at kaust.edu.sa>
>>> 
>>> Skype name: basit.a.khan
>>> 
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>>> 
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>> 
>> --
>> Rob Latham
>> Mathematics and Computer Science Division
>> Argonne National Lab, IL USA
> 
> 
> ________________________________
> 
> This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.