Shared library version of pnetcdf

[Wei-keng Liao]

The error messages you encountered are due to an internal
change of PnetCDF made since 1.7.0.
Please see note and patch from pull request 31.
https://github.com/LLNL/ior/pull/31

Wei-keng

On Sep 25, 2017, at 9:03 AM, Wadud Miah wrote:

> Hi Bruno,
>  
> I am getting the following runtime error message when I run the IOR benchmark when I select the pNetCDF API. Any help will be appreciated.
>  
> [wadudm at nash ~]$ mpirun -n 4 ./IOR -a NCMPI -w -r -o testFile
> IOR-2.10.3: MPI Coordinated Test of Parallel I/O
>  
> Run began: Mon Sep 25 15:01:21 2017
> Command line used: ./IOR -a NCMPI -w -r -o testFile
>  
> Summary:
>                 api                = NCMPI (1.8.1 of 28 Jan 2017)
>                 test filename      = testFile
>                 access             = single-shared-file
>                 ordering in a file = sequential offsets
>                 ordering inter file= no tasks offsets
>                 clients            = 4 (4 per node)
>                 repetitions        = 1
>                 xfersize           = 262144 bytes
>                 blocksize          = 1 MiB
>                 aggregate filesize = 4 MiB
>  
> ** error **
> ERROR in aiori-NCMPI.c (line 282): cannot write to data set.
> ERROR: NetCDF: Not a valid data type or _FillValue type mismatch.
> ** exiting **
> ** error **
> ERROR in aiori-NCMPI.c (line 282): cannot write to data set.
> ERROR: NetCDF: Not a valid data type or _FillValue type mismatch.
> ** exiting **
> ** error **
> ERROR in aiori-NCMPI.c (line 282): cannot write to data set.
> ERROR: NetCDF: Not a valid data type or _FillValue type mismatch.
> ** exiting **
> ** error **
> ERROR in aiori-NCMPI.c (line 282): cannot write to data set.
> ERROR: NetCDF: Not a valid data type or _FillValue type mismatch.
> ** exiting **
> -------------------------------------------------------
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
>  
> Regards,
> Wadud.
>  
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status, thus causing
> the job to be terminated. The first process to do so was:
>  
>   Process name: [[23899,1],2]
>   Exit code:    255
> --------------------------------------------------------------------------
>  
> From: parallel-netcdf [mailto:parallel-netcdf-bounces at lists.mcs.anl.gov] On Behalf Of Wadud Miah
> Sent: 25 September 2017 13:45
> To: Bruno Pagani <bruno.pagani at astrophysics.eu>; Ed Hartnett <edwardjameshartnett at gmail.com>
> Cc: parallel-netcdf at lists.mcs.anl.gov
> Subject: RE: Shared library version of pnetcdf
>  
> Hi Bruno,
> 
> cheers for the info. that seems like it has worked, but I will build and run IOR with the dynamic shard object. 
> 
> Wadud.
> 
> -----Original Message-----
> From: Bruno Pagani [mailto:bruno.pagani at astrophysics.eu] 
> Sent: 25 September 2017 13:30
> To: Ed Hartnett <edwardjameshartnett at gmail.com>; Wadud Miah <wadud.miah at nag.co.uk>
> Cc: parallel-netcdf at lists.mcs.anl.gov
> Subject: Re: Shared library version of pnetcdf
> 
> Le 25/09/2017 à 14:10, Ed Hartnett a écrit :
> > You know, I believe I don't have shared pnetcdf libraries either!
> >
> > So I will echo Wadud's question: how do I build a pnetcdf shared library.
> >
> 
> They apparently build the shared version on Debian, by adding -fPIC to
> {C,CXX,FC,F}FLAGS and then after running make they do the following things:
> 
> cd src/lib && mpicxx -shared -o libpnetcdf.so.0d -Wl,--soname
> -Wl,libpnetcdf.so.0d $(LDFLAGS) -Wl,--whole-archive libpnetcdf.a
> -Wl,--no-whole-archive -lgfortran
> chrpath -d ./src/lib/libpnetcdf.so.0d
> 
> And finally they symlink this lib to libpnetcdf.so
> 
> Hope it helps,
> Bruno
> 
> 
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> 
> Disclaimer
> 
> The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
> 
> This e-mail has been scanned for all viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business.
>