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<div>Hi Wei-keng:</div>
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<div>I tried rerunning the entire installation with PNETCDF_SAFE_MODE=1. FLASH-IO still hangs with SGI MPT (with no error message), but it works fine with Intel MPI.</div>
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<div>-Eric</div>
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<span style="font-weight:bold">From: </span>Wei-keng Liao <<a href="mailto:wkliao@eecs.northwestern.edu">wkliao@eecs.northwestern.edu</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, February 2, 2016 12:39 PM<br>
<span style="font-weight:bold">To: </span>Eric Kemp <<a href="mailto:eric.kemp@nasa.gov">eric.kemp@nasa.gov</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a>" <<a href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a>><br>
<span style="font-weight:bold">Subject: </span>Re: Problems with testing PNETCDF 1.6.1<br>
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<div class="PlainText">Hi, Eric<br>
<br>
Sorry for sending the wrong file. The correct one is attached, in case you would like<br>
to use it.<br>
<br>
I check your config.log file but could not find any thing fishy.<br>
I just now tested it with Intel compiler 16.0.0.109 without a problem.<br>
Could you try running FLASH-IO under the safe mode? i.e. set the environment<br>
variable PNETCDF_SAFE_MODE to 1. It will enable internal checking for<br>
data inconsistency.<br>
<br>
Just want to make sure for 1.7.0.pre1 that your "make ptest" failed only on FLASH-IO.<br>
Because FLAH-IO is the last test program, this means all other tests have passed.<br>
Let me know. Thanks.<br>
<br>
Wei-keng<br>
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On Feb 2, 2016, at 8:27 AM, Kemp, Eric M. (GSFC-606.0)[SCIENCE SYSTEMS AND APPLICATIONS INC] wrote:<br>
<br>
> <br>
> Hi Wei-keng:<br>
> <br>
> 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.<br>
> <br>
> 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.<br>
> <br>
> I've attached the (gzipped) config.log file from the 1.7.0pre1 installations.<br>
> <br>
> Thanks,<br>
> <br>
> -Eric<br>
> <br>
> Eric M. Kemp (SSAI) <br>
> NASA/GSFC <br>
> Mail Code: 606 <br>
> Greenbelt, MD 20771 <br>
> 301.286.9768 <br>
> <a href="mailto:eric.kemp@nasa.gov">eric.kemp@nasa.gov</a><br>
> <a href="mailto:eric.kemp@ssaihq.com">eric.kemp@ssaihq.com</a><br>
> <br>
> <br>
> From: Wei-keng Liao <<a href="mailto:wkliao@eecs.northwestern.edu">wkliao@eecs.northwestern.edu</a>><br>
> Date: Monday, February 1, 2016 5:12 PM<br>
> To: Eric Kemp <<a href="mailto:eric.kemp@nasa.gov">eric.kemp@nasa.gov</a>><br>
> Cc: "<a href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a>" <<a href="mailto:parallel-netcdf@mcs.anl.gov">parallel-netcdf@mcs.anl.gov</a>><br>
> Subject: Re: Problems with testing PNETCDF 1.6.1<br>
> <br>
> Hi, Eric,<br>
> <br>
> Thanks for reporting the error. This is another oversight, Sorry.<br>
> The fixed file, bigrecords.f, is attached.<br>
> <br>
> <br>
> Wei-keng<br>
> <br>
> <br>
> <br>
> On Feb 1, 2016, at 2:41 PM, Kemp, Eric M. (GSFC-606.0)[SCIENCE SYSTEMS AND APPLICATIONS INC] wrote:<br>
> <br>
> > <br>
> > Hi Wei-keng:<br>
> > <br>
> > Thanks for your quick response. I tried installing 1.7.0.pre1 but I get a<br>
> > different error when compiling the tests:<br>
> > <br>
> > /usr/local/intel/2016/impi/5.1.2.150/bin64/mpif90 -I../../src/lib<br>
> > -I./../common -I../../src/libf -I../../src/libf90 -fpic -O2 -fp-model<br>
> > strict -c bigrecords.f<br>
> > bigrecords.f(333): error #6514: A substring must be of type CHARACTER.<br>
> > [CMD]<br>
> > msg = '*** TESTING F77 '//cmd(1:XTRIM(cmd))//<br>
> > ------------------------------------^<br>
> > bigrecords.f(333): error #6054: A CHARACTER data type is required in this<br>
> > context. [CMD]<br>
> > msg = '*** TESTING F77 '//cmd(1:XTRIM(cmd))//<br>
> > ------------------------------------^<br>
> > compilation aborted for bigrecords.f (code 1)<br>
> > <br>
> > <br>
> > <br>
> > This appears to be a legitimate syntax error in the test program, in<br>
> > subroutine check_err. "cmd" is not defined in that subroutine, nor is it<br>
> > a global variable.<br>
> > <br>
> > I will try patching 1.6.1 with the NC_64BIT_DATA constant instead.<br>
> > <br>
> > -Eric<br>
> > <br>
> > <br>
> > <br>
> > <br>
> > On 2/1/16 12:02 PM, "Wei-keng Liao" <<a href="mailto:wkliao@eecs.northwestern.edu">wkliao@eecs.northwestern.edu</a>> wrote:<br>
> > <br>
> >> Hi, Eric<br>
> >> <br>
> >> For the large file tests, the error is caused by a oversight of using a<br>
> >> wrong flag.<br>
> >> Line 81 of file large_files.c should have used NC_64BIT_DATA, instead of<br>
> >> NC_64BIT_OFFSET.<br>
> >> This error has been fixed in the pre-release of 1.7.0.pre1. Could you<br>
> >> give it a try?<br>
> >> <a href="http://cucis.ece.northwestern.edu/projects/PnetCDF/download.html">http://cucis.ece.northwestern.edu/projects/PnetCDF/download.html</a><br>
> >> <br>
> >> As for the FLASH-IO test, could you try running it alone? I.e. cd to the<br>
> >> folder<br>
> >> benchmarks/FLASH-IO and run "make ptest" there. In the meantime, please<br>
> >> send me<br>
> >> the file config.log.<br>
> >> <br>
> >> <br>
> >> Wei-keng<br>
> >> <br>
> >> On Feb 1, 2016, at 7:32 AM, Kemp, Eric M. (GSFC-606.0)[SCIENCE SYSTEMS<br>
> >> AND APPLICATIONS INC] wrote:<br>
> >> <br>
> >>> <br>
> >>> Dear PNETCDF developers:<br>
> >>> <br>
> >>> I'm attempting to install PNETCDF1.6.1 on a Linux cluster running SLES<br>
> >>> 11.3. I'm using Intel 15 Fortran and C compilers (no C++), and I'm<br>
> >>> trying to install for two separate MPI implementations (SGI MPT 2.12 and<br>
> >>> Intel MPI 5.1.2).<br>
> >>> <br>
> >>> I'm encountering two problems when I run 'make ptest'.<br>
> >>> <br>
> >>> 1) For both MPI implementations, the large file tests fail with an<br>
> >>> integer overflow. The error message is:<br>
> >>> <br>
> >>> *** Testing large files, slowly.<br>
> >>> line 116 of large_files.c: Overflow when type cast to 4-byte integer.<br>
> >>> *** Creating large file ./testfile.nc...srun.slurm: error: borgo018:<br>
> >>> task 0: Exited with exit code 1<br>
> >>> <br>
> >>> I reviewed the README.large_files for guidance, and I can confirm that<br>
> >>> both 'MPI_Offset' and 'off_t' are 8 bytes.<br>
> >>> <br>
> >>> 2) For SGI MPT only, if I disable support for large file tests, 'make<br>
> >>> ptest' hangs when testing FLASH-IO:<br>
> >>> <br>
> >>> make -w -C FLASH-IO ptest<br>
> >>> make[2]: Entering directory<br>
> >>> `/gpfsm/dnb32/emkemp/NUWRFLIB/svn/trunk/builds/parallel-netcdf-1.6.1/benc<br>
> >>> hmarks/FLASH-IO'<br>
> >>> mpiexec_mpt -n 4 ./flash_benchmark_io ./flash_io_test_<br>
> >>> srun.slurm: cluster configuration lacks support for cpu binding<br>
> >>> <br>
> >>> The earlier tests with both single and multiple processes work for SGI<br>
> >>> MPT. And all tests (again, excluding large file tests) work for Intel<br>
> >>> MPI.<br>
> >>> <br>
> >>> I can provide more information (e.g., output from the configure script)<br>
> >>> upon request.<br>
> >>> <br>
> >>> Thanks,<br>
> >>> <br>
> >>> -Eric<br>
> >>> <br>
> >>> Eric M. Kemp (SSAI)<br>
> >>> NASA/GSFC <br>
> >>> Mail Code: 606 <br>
> >>> Greenbelt, MD 20771<br>
> >>> 301.286.9768 <br>
> >>> <a href="mailto:eric.kemp@nasa.gov">eric.kemp@nasa.gov</a><br>
> >>> <a href="mailto:eric.kemp@ssaihq.com">eric.kemp@ssaihq.com</a><br>
> >>> <br>
> >> <br>
> > <br>
> <br>
> <config.log.gz><br>
<br>
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