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[netCDF #GUA-922187]: Problems about using parallel io to manage NF90_UNLIMITED dimensions variables in different groups



Hello,

Which versions of netCDF are you using, specifically what version of 
netCDF-Fortran and the underlying netCDF-C libraries?  We recently had a 
parallel I/O bug fix integrated which may correct the behavior you're seeing; 
the version of netCDF-C with this fix was released yesterday, and is version 
4.4.1, available here:  https://github.com/Unidata/netcdf-c/releases

You might try the latest version of the C and Fortran libraries, and let us 
know if the issue persists.  Thanks!

-Ward

> Hi,
> 
> I'm fresh using parallel IO of netCDF, and I've got a problem that really
> confuse me. I was developing a program to manage a netcdf file in a
> parallel way. The main idea is that the file has some groups named after
> the specific probe, for example x1y1 and x2y2 blablabla. And all the groups
> have the same structure, containing its own recording variables like
> 'Temperature' and 'Velocity(U2)' with UNLIMITED dimension.
> Since not all processors contain probes, so I tried to use some specific
> processors to manage the corresponding probes. For example, Processor 0
> governs the area that contains probe x1y1, then the group 'x1y1' is only
> managed by processor 0. On the other hand, some processors are not
> responsible to write.
> However, when I running the program, it pauses at 'call check(
> nf90_put_var(idgrp(i), idt2(i), tprobe) , "io_probe put:T2")', seems like
> it is waiting for MPI communication.
> 
> So here is my questions:
> 1. Does parallel IO of netCDF support the case that some process inquire
> and overwrite variables in the corresponding groups, and the other
> processors just do nothing?
> 2. Is it matter if I use unlimited dimension? Since I have to set
> nf90_var_par_access(idgrp(i), idt2(i), access = NF90_COLLECTIVE) when using
> unlimited dimension in parallel case I supposed.
> 
> BTW, parallel IO works well when I use all processors writing data to a
> single variable.
> Any help or advice would be greatly appreciated!
> 
> Ding
> 
> example of the file structure:
> ncdump -h PROBE.h5
> 
> netcdf PROBE {
> 
> group: x01y01z01 {
> dimensions:
> NTS = UNLIMITED ; // (0 currently)
> variables:
> double time(NTS) ;
> double X ;
> double Y ;
> double Z ;
> double U2(NTS) ;
> double V2(NTS) ;
> double W2(NTS) ;
> double T2(NTS) ;
> } // group x01y01z01
> 
> group: x01y01z02 {
> dimensions:
> NTS = UNLIMITED ; // (0 currently)
> variables:
> double time(NTS) ;
> double X ;
> double Y ;
> double Z ;
> double U2(NTS) ;
> double V2(NTS) ;
> double W2(NTS) ;
> double T2(NTS) ;
> } // group x01y01z02
> 
> 
> example of the code:
> !########### IO PROBE
> ###########################################################
> !---- NF_OPEN
> !---- open existing netCDF dataset - read-write
> call echo_name('   write: ',fprobe)
> call check( nf90_open(fprobe, ior(nf90_Write,nf90_mpiposix), ncid, &
> comm = mpi_comm_world, info = mpi_info_null) , fprobe )
> !---- WRITE TO FILE
> if (n_probe.ne.0) then !------------- to identify which of the processors
> are responsible to write
> do i=1,n_probe   !------------- loop, if this processor is responsible to
> write, inquiring group and variable ID.
> !------------- NOTICE:
> different processors only manager its own part of the groups, and 'grpname'
> is different for different processors.
> call check( nf90_inq_ncid(ncid, grpname(i), idgrp(i)), "io_probe inq:group")
> call check( nf90_inq_varid(idgrp(i), 'time', idtimep(i)),"io_probe
> inq:time")
> call check( nf90_inq_varid(idgrp(i), 'T2',   idt2(i)), "io_probe inq:u2")
> call check( nf90_var_par_access(idgrp(i), idt2(i), access =
> NF90_COLLECTIVE))
> enddo
> !---------- T probe
> do i = 1,n_probe !------------- loop, writing probe data one by one
> print *, 'ready to write'
> call check( nf90_put_var(idgrp(i), idt2(i), tprobe) , "io_probe put:T2")
> enddo
> endif
> !---- NF_CLOSE
> call check( nf90_close(ncid))
> ---------------------------------------
> Guang-Yu Ding
> Department of Physics
> The Chinese University of Hong Kong
> Tel: (+852) 6380 4211
> 
> 


Ticket Details
===================
Ticket ID: GUA-922187
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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