MPI_Type_create_hindexed errors from PNetCDF 1.7.0

[Wei-keng Liao]

Hi, Carl

I reported this issue to OpenMPI and they have fixed the bug.
FYI, the links to this issue at OpenMPI:

https://github.com/open-mpi/ompi/issues/1611
https://github.com/open-mpi/ompi-release/pull/1122

Wei-keng

On Apr 24, 2016, at 12:55 AM, Wei-keng Liao wrote:

> Hi, Carl
> 
> I can reproduce the error message you are seeing.
> After some digging, I found the cause comes from OpenMPI.
> 
> That PnetCDF test program will internally make a call to
> MPI_Type_create_hindexed to create a filetype of zero length and
> pass it to MPI_File_set_view which flattens the filetype without
> checking whether the length is zero and hence generates the error message.
> 
> FYI. MPICH handles this case just fine.
> 
> I have added a check in PnetCDF to skip that calling MPI_Type_create_hindexed
> to avoid this problem. See the SVN revision 2406.
> http://trac.mcs.anl.gov/projects/parallel-netcdf/changeset/2406
> 
> Thanks for reporting the error.
> 
> Wei-keng
> 
> On Apr 23, 2016, at 6:25 PM, Carl Ponder wrote:
> 
>> On 05/27/2015 05:41 PM, Carl Ponder wrote:
>>> Here are some oddities from the "make check" that I ran:
>>> ./nf_test       -d .
>>> rank 0: MPI error (MPI_File_delete) : MPI_ERR_IO: input/output error
>>> rank 0: MPI error (MPI_File_delete) : MPI_ERR_IO: input/output error
>>> *** TESTING F77 ./nf_test for CDF-1                                ------ pass
>> On 05/27/2015 06:41 PM, Wei-keng Liao wrote
>>> Those MPI error messages are expected if you are using OpenMPI or older versions of MPICH.
>>> This error happens when trying to delete a non-existing file.
>>> A correct MPI implementation should return MPI_ERR_NO_SUCH_FILE, instead of MPI_ERR_IO.
>>> This has been fixed in the MPI-IO part of the latest MPICH release.
>>> OpenMPI is copying the MPI-IO part of MPICH and has not updated to the latest yet.
>>> You can safely ignore those error messages.
>>> 
>> With the 1.7.0 release of PNetCDF, I've started getting there errors from the "make check":
>> ./nctst        ./testfile.nc
>> [ivb106:6511] *** An error occurred in MPI_Type_create_hindexed
>> [ivb106:6511] *** reported by process [46912098861057,46909632806912]
>> [ivb106:6511] *** on communicator MPI_COMM_WORLD
>> [ivb106:6511] *** MPI_ERR_ARG: invalid argument of some other kind
>> [ivb106:6511] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> [ivb106:6511] ***    and potentially your MPI job)
>> *** TESTING C++ ./nctst for APIs with different netCDF formats     ------ make[2]: [testing] Error 13 (ignored)
>> 
>> ./tst_f90      ./testfile.nc
>> [ivb106:7079] *** An error occurred in MPI_Type_create_hindexed
>> [ivb106:7079] *** reported by process [46912052199425,46909632806912]
>> [ivb106:7079] *** on communicator MPI_COMM_WORLD
>> [ivb106:7079] *** MPI_ERR_ARG: invalid argument of some other kind
>> [ivb106:7079] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
>> [ivb106:7079] ***    and potentially your MPI job)
>> make[2]: [testing] Error 13 (ignored)
>> It looks like the 1.6.1 release passed the same:
>> ./nctst        ./testfile.nc
>> *** TESTING C++ ./nctst for APIs with different netCDF formats     ------ pass
>> 
>> ./tst_f90      ./testfile.nc
>> *** TESTING F90 ./tst_f90                                          ------ pass
>> Can you tell me what the issue is here? I'm using OpenMPI 1.10.2 in both cases.
>> The error happens when I use the Intel 15.0, GCC 4.8.5 and PGI 16.4 compilers, so I don't believe the compiler is the problem.
>> Thanks,
>> 
>>                    Carl Ponder
>> 
>> 
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