Shared library version of pnetcdf

[Wadud Miah]

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<mailto:edwardjameshartnett at gmail.com>>; Wadud Miah <wadud.miah at nag.co.uk<mailto:wadud.miah at nag.co.uk>>
Cc: parallel-netcdf at lists.mcs.anl.gov<mailto: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. 
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