Re: [petsc-dev] pnetcdf is a big problem

2017-12-20 Thread Blaise A Bourdin 
There are two ways to write parallel netcdf files:

Use netcdf-4 (hdf5 based) files
Use pnetcdf and old-style netcdf files.

Perhaps the best would be to compile netcdf with pnetcdf support only if petsc 
is configured with exodusii? I can send a patch this afternoon.
Greg Sjaardema, the exodus maintainer, has been very responsive, I will try to 
iron out the last exodus / netcdf-4 bugs, but it sure would be noce to be able 
to read / write old style files too…

Blaise



> On Dec 19, 2017, at 5:32 PM, Smith, Barry F.  wrote:
> 
> 
> 
>> On Dec 19, 2017, at 5:30 PM, Jed Brown  wrote:
>> 
>> Does ExodusII write pnetcdf?  It's a different interface from (parallel)
>> NetCDF4.
> 
>   Shudder!
> 
>> 
>> Matthew Knepley  writes:
>> 
>>> Blaise really wants to write in parallel. It would be better to use HDF5,
>>> but evidently
>>> it is broken in ExodusII. Thats what we get for using something from
>>> Sandia. They
>>> finally have their revenge.
>>> 
>>>  Matt
>>> 
>>> On Tue, Dec 19, 2017 at 5:53 PM, Smith, Barry F.  wrote:
>>> 
 
 Do you really need to use pnetcdf? No one uses it and what usefulness
 does it really provide, best to be avoided.
 
  Barry
 
 
> On Dec 19, 2017, at 1:12 PM, Satish Balay  wrote:
> 
> parallel-netcdf-1.9.0.pre1/INSTALL has:
> 
 
> 
> 4. Reporting Installation or Usage Problems
> ===
> 
> Please send an email to parallel-net...@mcs.anl.gov
> 
> <<
> 
> We'll have to send in these bug reports.
> 
> Satish
> 
> 
> On Tue, 19 Dec 2017, Matthew Knepley wrote:
> 
>> The configure is broken, perhaps beyond fixing. I need to give
 --with-mpi
>> to get anything
>> to work because the way it checks for MPI is screwed up. I will see if I
>> can throw away all its idiotic configure stuff in favor of just telling
 it
>> everything, but I am not eager to depend on something so rickety.
>> 
>> Matt
>> 
>> 
> 
 
 
>>> 
>>> 
>>> -- 
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>> 
>>> https://www.cse.buffalo.edu/~knepley/ 
> 

-- 
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin

Re: [petsc-dev] pnetcdf is a big problem

2017-12-20 Thread Satish Balay 
On Wed, 20 Dec 2017, Blaise A Bourdin wrote:

> There are two ways to write parallel netcdf files:
> 
> Use netcdf-4 (hdf5 based) files
> Use pnetcdf and old-style netcdf files.
> 
> Perhaps the best would be to compile netcdf with pnetcdf support only if 
> petsc is configured with exodusii? I can send a patch this afternoon.

Current code already does this. i.e pnetcdf is an optional [i.e not mandatory] 
dependency for netcdf


For now - I'm disabling pnetcdf+exodus from this test case. [until this issue 
gets resolved]

Satish

> Greg Sjaardema, the exodus maintainer, has been very responsive, I will try 
> to iron out the last exodus / netcdf-4 bugs, but it sure would be noce to be 
> able to read / write old style files too…
> 
> Blaise
> 
> 
> 
> > On Dec 19, 2017, at 5:32 PM, Smith, Barry F.  wrote:
> > 
> > 
> > 
> >> On Dec 19, 2017, at 5:30 PM, Jed Brown  wrote:
> >> 
> >> Does ExodusII write pnetcdf?  It's a different interface from (parallel)
> >> NetCDF4.
> > 
> >   Shudder!
> > 
> >> 
> >> Matthew Knepley  writes:
> >> 
> >>> Blaise really wants to write in parallel. It would be better to use HDF5,
> >>> but evidently
> >>> it is broken in ExodusII. Thats what we get for using something from
> >>> Sandia. They
> >>> finally have their revenge.
> >>> 
> >>>  Matt
> >>> 
> >>> On Tue, Dec 19, 2017 at 5:53 PM, Smith, Barry F.  
> >>> wrote:
> >>> 
>  
>  Do you really need to use pnetcdf? No one uses it and what usefulness
>  does it really provide, best to be avoided.
>  
>   Barry
>  
>  
> > On Dec 19, 2017, at 1:12 PM, Satish Balay  wrote:
> > 
> > parallel-netcdf-1.9.0.pre1/INSTALL has:
> > 
>  
> > 
> > 4. Reporting Installation or Usage Problems
> > ===
> > 
> > Please send an email to parallel-net...@mcs.anl.gov
> > 
> > <<
> > 
> > We'll have to send in these bug reports.
> > 
> > Satish
> > 
> > 
> > On Tue, 19 Dec 2017, Matthew Knepley wrote:
> > 
> >> The configure is broken, perhaps beyond fixing. I need to give
>  --with-mpi
> >> to get anything
> >> to work because the way it checks for MPI is screwed up. I will see if 
> >> I
> >> can throw away all its idiotic configure stuff in favor of just telling
>  it
> >> everything, but I am not eager to depend on something so rickety.
> >> 
> >> Matt
> >> 
> >> 
> > 
>  
>  
> >>> 
> >>> 
> >>> -- 
> >>> What most experimenters take for granted before they begin their
> >>> experiments is infinitely more interesting than any results to which their
> >>> experiments lead.
> >>> -- Norbert Wiener
> >>> 
> >>> https://www.cse.buffalo.edu/~knepley/ 
> > 
> 
>