Problems with testing PNETCDF 1.6.1

Tue Feb 2 08:27:57 CST 2016

Hi Wei-keng:

I think you sent me the wrong copy of that file — it was identical to what is in 1.7.0.pre1.  But I went ahead and added "cmd" as an argument to subroutine check_err, and that test code compiles and runs.

The large file tests pass in 1.7.0.pre1 as you indicated. However, FLASH-IO still hangs with SGI MPT.  I took your suggestion and tried running this test separately (cd benchmarks/FLASH-IO ; make ptest) but the code still hangs.

I've attached the (gzipped) config.log file from the 1.7.0pre1 installations.

Thanks,

-Eric

Eric M. Kemp (SSAI)
NASA/GSFC
Mail Code: 606
Greenbelt, MD 20771
301.286.9768
eric.kemp at nasa.gov
eric.kemp at ssaihq.com

From: Wei-keng Liao <wkliao at eecs.northwestern.edu<mailto:wkliao at eecs.northwestern.edu>>
Date: Monday, February 1, 2016 5:12 PM
To: Eric Kemp <eric.kemp at nasa.gov<mailto:eric.kemp at nasa.gov>>
Cc: "parallel-netcdf at mcs.anl.gov<mailto:parallel-netcdf at mcs.anl.gov>" <parallel-netcdf at mcs.anl.gov<mailto:parallel-netcdf at mcs.anl.gov>>
Subject: Re: Problems with testing PNETCDF 1.6.1

Hi, Eric,

Thanks for reporting the error. This is another oversight, Sorry.
The fixed file, bigrecords.f, is attached.

Wei-keng

On Feb 1, 2016, at 2:41 PM, Kemp, Eric M. (GSFC-606.0)[SCIENCE SYSTEMS AND APPLICATIONS INC] wrote:

>
> Hi Wei-keng:
>
> Thanks for your quick response. I tried installing 1.7.0.pre1 but I get a
> different error when compiling the tests:
>
> /usr/local/intel/2016/impi/5.1.2.150/bin64/mpif90    -I../../src/lib
> -I./../common   -I../../src/libf -I../../src/libf90 -fpic -O2 -fp-model
> strict  -c bigrecords.f
> bigrecords.f(333): error #6514: A substring must be of type CHARACTER.
> [CMD]
>          msg = '*** TESTING F77 '//cmd(1:XTRIM(cmd))//
> ------------------------------------^
> bigrecords.f(333): error #6054: A CHARACTER data type is required in this
> context.   [CMD]
>          msg = '*** TESTING F77 '//cmd(1:XTRIM(cmd))//
> ------------------------------------^
> compilation aborted for bigrecords.f (code 1)
>
>
>
> This appears to be a legitimate syntax error in the test program, in
> subroutine check_err.  "cmd" is not defined in that subroutine, nor is it
> a global variable.
>
> I will try patching 1.6.1 with the NC_64BIT_DATA constant instead.
>
> -Eric
>
>
>
>
> On 2/1/16 12:02 PM, "Wei-keng Liao" <wkliao at eecs.northwestern.edu<mailto:wkliao at eecs.northwestern.edu>> wrote:
>
>> Hi, Eric
>>
>> For the large file tests, the error is caused by a oversight of using a
>> wrong flag.
>> Line 81 of file large_files.c should have used NC_64BIT_DATA, instead of
>> NC_64BIT_OFFSET.
>> This error has been fixed in the pre-release of 1.7.0.pre1. Could you
>> give it a try?
>> http://cucis.ece.northwestern.edu/projects/PnetCDF/download.html
>>
>> As for the FLASH-IO test, could you try running it alone? I.e. cd to the
>> folder
>> benchmarks/FLASH-IO and run "make ptest" there. In the meantime, please
>> send me
>> the file config.log.
>>
>>
>> Wei-keng
>>
>> On Feb 1, 2016, at 7:32 AM, Kemp, Eric M. (GSFC-606.0)[SCIENCE SYSTEMS
>> AND APPLICATIONS INC] wrote:
>>
>>>
>>> Dear PNETCDF developers:
>>>
>>> I'm attempting to install PNETCDF1.6.1 on a Linux cluster running SLES
>>> 11.3.  I'm using Intel 15 Fortran and C compilers (no C++), and I'm
>>> trying to install for two separate MPI implementations (SGI MPT 2.12 and
>>> Intel MPI 5.1.2).
>>>
>>> I'm encountering two problems when I run 'make ptest'.
>>>
>>> 1)  For both MPI implementations, the large file tests fail with an
>>> integer overflow.  The error message is:
>>>
>>> *** Testing large files, slowly.
>>> line 116 of large_files.c: Overflow when type cast to 4-byte integer.
>>> *** Creating large file ./testfile.nc...srun.slurm: error: borgo018:
>>> task 0: Exited with exit code 1
>>>
>>> I reviewed the README.large_files for guidance, and I can confirm that
>>> both 'MPI_Offset' and 'off_t' are 8 bytes.
>>>
>>> 2) For SGI MPT only, if I disable support for large file tests, 'make
>>> ptest' hangs when testing FLASH-IO:
>>>
>>> make -w -C FLASH-IO ptest
>>> make[2]: Entering directory
>>> `/gpfsm/dnb32/emkemp/NUWRFLIB/svn/trunk/builds/parallel-netcdf-1.6.1/benc
>>> hmarks/FLASH-IO'
>>> mpiexec_mpt -n 4 ./flash_benchmark_io ./flash_io_test_
>>> srun.slurm: cluster configuration lacks support for cpu binding
>>>
>>> The earlier tests with both single and multiple processes work for SGI
>>> MPT. And all tests (again, excluding large file tests) work for Intel
>>> MPI.
>>>
>>> I can provide more information (e.g., output from the configure script)
>>> upon request.
>>>
>>> Thanks,
>>>
>>> -Eric
>>>
>>> Eric M. Kemp (SSAI)
>>> NASA/GSFC
>>> Mail Code: 606
>>> Greenbelt, MD 20771
>>> 301.286.9768
>>> eric.kemp at nasa.gov<mailto:eric.kemp at nasa.gov>
>>> eric.kemp at ssaihq.com<mailto:eric.kemp at ssaihq.com>
>>>
>>
>

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