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[netCDF #LRX-899920]: Netcdf 4.3.3.1 with MPICH compilation error



> Thank you so much for helping! That was the problem.I have one more test that 
> fails, run_par_test.sh.
> Here is the output from nc_test4/test-suite.log.
> http://pastebin.com/F2fned05

That error message indicates a problem with your OpenMPI environment
or configuration. It is not related to netCDF, as no netCDF functions were
called. The error came from early in a simple test of MPI file I/O in running
the program resulting from compiling nc_test4/tst_mpi_parallel.c, using

   mpiexec -n 4 ./tst_mpi_parallel

which is the first test run from the shell script nc_test4/run_par_test.sh.

Make sure the mpiexec used by the run_par_test.sh shell script is the 
one for your version of OpenMPI, as there may be multiple versions of
the mpiexec wrapper installed on your system. You may have to change
your PATH before running that test to avoid using an mpiexec that is
not compatible with your OpenMPI environment. Or maybe your OpenMPI
uses mpirun rather than mpiexec?

I also found these possible solutions via Google:

  http://wp.auburn.edu/morgaia/?p=117
  
http://stackoverflow.com/questions/26901663/error-when-running-openmpi-based-library

It's not a netCDF problem, so I'm not what else to try, other than to
suggest making sure an up-to-date version of OpenMPI is correctly
installed and configured with a parallel file system and mpiexec utility.
The error message seems to indicate an internal problem in the OpenMPI
library during initialization while calling MPI_Init.

--Russ

> On Thursday, May 21, 2015 7:09 PM, Unidata netCDF Support <address@hidden> 
> wrote:
> 
> 
> Evelina,
> 
> Allow me to jump in with a question: were you using "make -j check" to run
> make in parallel, to speed up the testing? If so, that may be the problem, 
> because
> some of the tests depend on previous tests in ways not represented in the make
> rules, which means "make -j check" often fails when "make check" succeeds.
> 
> --Russ
> 
> > Sorry for that. Here is the config.log file:
> > http://pastebin.com/YE21L07h ;
> >
> > Thank you again!
> >
> >
> >
> > On Thursday, May 21, 2015 2:57 AM, Unidata netCDF Support <address@hidden> 
> > wrote:
> >
> >
> > Hello Evelina,
> >
> > Thank you very much for providing the information; I will look it over.
> > When you run 'configure', a file is created, 'config.log', that contains
> > verbose debugging information.  Can you provide this as well? It is
> > different than the output sent to the command line by 'configure'.
> >
> > Thanks!
> >
> > -Ward
> >
> > address@hidden> wrote:
> >
> > > New Client Reply: Netcdf 4.3.3.1 with MPICH compilation error
> > >
> > > hi,
> > > Thank you for the quick response!Here is the configure log:
> > > http://pastebin.com/gRTP1GPD
> > > Tests that fail and pass:http://pastebin.com/BkR7YFea
> > > ncdump/test-suite.loghttp://pastebin.com/z87yeMTy
> > >  ls ./src/netcdf-4.3.3.1/ncgen/c0.nc -la
> > > -rw-r--r-- 1 root root 4828 May 21 02:18 ./src/netcdf-4.3.3.1/ncgen/c0.nc
> > > ls -la ./src/netcdf-4.3.3.1/ncdump/c0.nc
> > > -rw-r--r-- 1 root root 25263946 May 21 02:19 ./src/netcdf-4.3.3.1/ncdump/
> > > c0.nc
> > > ls -la ./src/netcdf-4.3.3.1/ncgen3/c0.nc
> > > -rw-r--r-- 1 root root 4828 May 21 02:18 ./src/netcdf-4.3.3.1/ncgen3/c0.nc
> > >
> > > Best,Evelina
> > >
> > >
> > >
> > >
> > > address@hidden> wrote:
> > >
> > >
> > >  Hello Evelina,
> > >
> > > The thing that leaps out at me from the pastebin link is the following:
> > >
> > >    H5F.c line 604 in H5Fopen(): unable to open file
> > >
> > > This suggests to me that there is an error writing the file, somehow.  Can
> > > you do an 'ls -al c0.nc' so that we can see the permissions and size of
> > > the file?
> > >
> > > You do not need the '--enable-parallel' flag when running configure;
> > > netcdf will query libhdf5, after detecting it, to see if libhdf5 supports
> > > parallel operations.
> > >
> > > Finally, can you provide the 'config.log' file generated when you run
> > > configure for netcdf?  This may provide some additional insight into the
> > > issue.
> > >
> > > Thanks,
> > >
> > > -Ward
> > >
> > > > Hi,
> > > >
> > > > When I try to run the netcdf tests for version 4.3.3.1 I get the
> > > following errors:
> > > > http://pastebin.com/hXaw3hnc
> > > >
> > > > Environment variables for netcdf:  export
> > > CC=/opt/lib/mpi/mpich-3.1.4-gcc/bin/mpicc
> > > >  export CFLAGS="-I/opt/lib/mpi/mpich-3.1.4-gcc/include
> > > -I/opt/lib/hdf5/hdf5-1.8.14-mpich/include"
> > > >  export LDFLAGS="-L/opt/lib/mpi/mpich-3.1.4-gcc/lib
> > > -L/opt/lib/hdf5/hdf5-1.8.14-mpich/lib"
> > > >
> > > > Configure flags:
> > > >  ./configure --prefix=$INSTALL_DIR --disable-shared --enable-parallel
> > > --enable-parallel-tests
> > > >
> > > > Environment variables for hdf5:  export
> > > CC=/opt/lib/mpi/mpich-3.1.4-gcc/bin/mpicc
> > > >  export LDFLAGS=-L/opt/lib/mpi/mpich-3.1.4-gcc/lib
> > > >  export CFLAGS=-I/opt/lib/mpi/mpich-3.1.4-gcc/include
> > > > Configure flags for hdf5
> > > >  ./configure --prefix=$INSTALL_DIR --enable-parallel --disable-shared
> > > >
> > > > What can the problem be?
> > > > Evelina
> > > >
> > > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: LRX-899920
> > > Department: Support netCDF
> > > Priority: Normal
> > > Status: Closed
> > >
> > >
> > >
> > >
> > >
> > >
> > > Ticket Details
> > > ===================
> > > Ticket ID: LRX-899920
> > > Department: Support netCDF
> > > Priority: Normal
> > > Status: Open
> > > Link:
> > > https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=viewticket&ticketid=25658
> > >
> > >
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: LRX-899920
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
> >
> >
> >
> 
> Russ Rew                                        UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> 
> 
> 
> Ticket Details
> ===================
> Ticket ID: LRX-899920
> Department: Support netCDF
> Priority: Normal
> Status: Closed
> 
> 
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: LRX-899920
Department: Support netCDF
Priority: Normal
Status: Closed