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[netCDF #GNF-884914]: Error: netcdf-4.2-snapshot2012021222

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  • Subject: [netCDF #GNF-884914]: Error: netcdf-4.2-snapshot2012021222
  • Date: Tue, 28 Feb 2012 13:05:11 -0700
> Yep. What are these raw-data tests of the MPI driver all about?

Sorry, I'm afraid I don't know.  We've lost some of our parallel I/O expertise 
lately, so
all I can suggest is that you try building a later version of mpich2, if 
available.  You
could at least run "make check" with that, to see if it also fails.

--Russ

> Craig
> 
> *** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)...
> =====================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   EXIT CODE: 11
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> =====================================================================================
> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault: 11 (signal 
> 11)
> FAIL: run_par_test.sh
> ================================================
> 1 of 51 tests failed
> Please report to address@hidden
> ================================================
> gnumake[2]: *** [check-TESTS] Error 1
> gnumake[1]: *** [check-am] Error 2
> make: *** [check-recursive] Error 1
> address@hidden:/netcdf-4.2-snapshot2012022722/{122}>
> 
> 
> 
> On Feb 28, 2012, at 2:47 PM, Unidata netCDF Support wrote:
> 
> > Hi Craig,
> >
> > Does "make check" still fail reliably with a sementation fault?
> >
> > --Russ
> >
> >> Update:
> >>
> >> I ignored the errors and installed the build, then built the C++ and 
> >> Fortran interfaces without a hitch.
> >>
> >> The parallel test program builds and runs correctly (below). Guess 
> >> everything is okay?
> >>
> >> Craig
> >>
> >>> set NETCDF_INC = "-I${NETCDF}/include"
> >>> set NETCDF_LIB = "-L${NETCDF}/lib -lnetcdf -lnetcdff"
> >>> ${FC} ${FFLAGS} ${NETCDF_INC} ${NETCDF_LIB} -o simple_xy_par_wr 
> >>> simple_xy_par_wr.f90
> >>
> >>> mpirun -np 16 ./simple_xy_par_wr
> >> *** SUCCESS writing example file simple_xy_par.nc!
> >>
> >>> ncdump simple_xy_par.nc
> >> netcdf simple_xy_par {
> >> dimensions:
> >> x = 16 ;
> >> y = 16 ;
> >> variables:
> >> int data(x, y) ;
> >> data:
> >>
> >> data =
> >> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> >> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> >> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
> >> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
> >> 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
> >> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
> >> 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
> >> 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
> >> 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
> >> 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
> >> 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
> >> 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
> >> 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
> >> 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
> >> 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
> >> 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15 ;
> >> }
> >>
> >> On Feb 28, 2012, at 1:28 PM, Dr. Craig A. Mattocks wrote:
> >>
> >>> Hi again, Russ,
> >>>
> >>> Back to 64-bit mode on Mac OS X 10.7.3, trying to build the NetCDF C 
> >>> interface (netcdf-4.2-snapshot2012022722) with the latest Intel compilers 
> >>> (Version 12.1.3.289 Build 20120130). Any idea what the error below, 
> >>> regarding the MPI-IO driver, means? Do I need to re-build mpich2?
> >>>
> >>> Thank you!
> >>> Craig
> >>>
> >>> Testing simple parallel I/O with 16 processors...
> >>>
> >>> *** Testing more advanced parallel access.
> >>> *** Testing parallel IO for raw-data with MPI-IO (driver)...ok.
> >>> *** Testing parallel IO for meta-data with MPI-IO (driver)...ok.
> >>> *** Testing parallel IO for different hyperslab selections with MPI-IO 
> >>> (driver)...ok.
> >>> *** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)...
> >>> =====================================================================================
> >>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> >>> =   EXIT CODE: 11
> >>> =   CLEANING UP REMAINING PROCESSES
> >>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >>> =====================================================================================
> >>> APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault: 11 
> >>> (signal 11)
> >>> FAIL: run_par_test.sh
> >>> ================================================
> >>> 1 of 51 tests failed
> >>> Please report to address@hidden
> >>> ================================================
> >>> gnumake[2]: *** [check-TESTS] Error 1
> >>> gnumake[1]: *** [check-am] Error 2
> >>> make: *** [check-recursive] Error 1
> >>>
> >>> On Feb 13, 2012, at 1:19 PM, Unidata netCDF Support wrote:
> >>>
> >>>> Hi Craig,
> >>>>
> >>>>> I am trying to build a 32-bit version of NetCDF-4 with the Intel 
> >>>>> compilers on Mac OS X Lion (10.7.3) for a numerical model that does not 
> >>>>> run on 64-bit platforms yet.
> >>>>>
> >>>>> I have successfully built 32-bit versions of szip and hdf5.
> >>>>
> >>>> Did you run "make check" on HDF5, and was it version 1.8.8?
> >>>> I've found that "make check" fails using the llvm-based C compiler that
> >>>> comes with the Xcode-4.2.1 developer tools, but that if you build with
> >>>> the gcc-4.6 that is available from Macports, the HDF5 library passes all
> >>>> the tests from "make check".  I haven't had a chance to check if the
> >>>> resulting library works with the latest netCDF-4.2.snapshot yet.
> >>>>
> >>>>> When I run 'make check | & tee check.log' after building the C version 
> >>>>> of NetCDF-4.2, I get the following error:
> >>>>>
> >>>>> *** Testing NetCDF-4 with user-supplied sample file.
> >>>>> *** testing creation of sample file...ok.
> >>>>> *** Tests successful!
> >>>>> PASS: tst_files4
> >>>>> /bin/sh: line 1: 76866 Segmentation fault: 11  ${dir}$tst
> >>>>> FAIL: tst_vars
> >>>>>
> >>>>> . . .
> >>>>>
> >>>>> ================================================
> >>>>> 1 of 50 tests failed
> >>>>> Please report to address@hidden
> >>>>> ================================================
> >>>>> gnumake[2]: *** [check-TESTS] Error 1
> >>>>> gnumake[1]: *** [check-am] Error 2
> >>>>> make: *** [check-recursive] Error 1
> >>>>>
> >>>>> How can I track down this error? Is it catastrophic or can I plow ahead?
> >>>>
> >>>> I wouldn't advise proceeding without knowing which test in tst_files4 
> >>>> failed,
> >>>> and that would require duplicating the problem and doing some debugging.
> >>>> Sometimes the problems are in the tests, but more often they indicate a 
> >>>> real
> >>>> bug.  Which exact version of netCDF are you using, netCDF-4.2-rc1 or the
> >>>> daily snapshot?
> >>>>
> >>>>> Fortran build fails too.
> >>>>>
> >>>>> What is missing in the link process?
> >>>>
> >>>> It looks like you're using ifort, and the error is
> >>>>
> >>>>> Undefined symbols for architecture i386:
> >>>>> "_netcdf_mp_nf90_create_", referenced from:
> >>>>>   _MAIN__ in f90tst_vars.o
> >>>>
> >>>> Can you see what architecture f90tst_vars.o is compiled for, using
> >>>>
> >>>> otool -L f90tst_vars.o
> >>>>
> >>>> Are you using the procedure described here for building the separate
> >>>> Fortran library:
> >>>>
> >>>> http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2012/msg00019.html
> >>>>
> >>>> --Russ
> >>>>
> >>>>
> >>>>
> >>>> Russ Rew                                         UCAR Unidata Program
> >>>> address@hidden                      http://www.unidata.ucar.edu
> >>>>
> >>>>
> >>>>
> >>>> Ticket Details
> >>>> ===================
> >>>> Ticket ID: GNF-884914
> >>>> Department: Support netCDF
> >>>> Priority: Normal
> >>>> Status: Closed
> >>>>
> >>>
> >>
> >>
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: GNF-884914
> > Department: Support netCDF
> > Priority: Urgent
> > Status: Closed
> >
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: GNF-884914
Department: Support netCDF
Priority: Urgent
Status: Closed