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[netCDF #BOZ-873400]: parallel netcdf make check fails

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  • Subject: [netCDF #BOZ-873400]: parallel netcdf make check fails
  • Date: Tue, 14 Jul 2015 14:06:18 -0600
Hello Julio,

Thanks for providing the test-suite.log file; it provides helpful information.  
It looks like the problem is the missing file, as you point out.  While this is 
a problem on our end, in the short term you can avoid this by dropping the 
'--enable-benchmarks' option when you configure netcdf.   Give this a try and 
let me know if it resolves the issue.

Thanks, have a great day,

-Ward

> Dear Support,
> 
> I am installing NetCDF with parallel HDF5 however I got the error while
> doing make check:
> 
> 
> 
> *FAIL: run_bm_ar4.shFAIL: run_par_bm_test.sh*PASS: run_par_test.sh
> ...
> ============================================================================
> Testsuite summary for netCDF 4.3.3.1
> ============================================================================
> # TOTAL: 72
> # PASS:  70
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  2
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See nc_test4/test-suite.log.
> Please report to address@hidden
> 
> Attached you will find the test-suite.log and config.log
> 
> 
> 
> Looking at the scripts, the next link is empty:
> ftp://ftp.unidata.ucar.edu/pub/netcdf/sample_data/ar4/
> 
> Do you have the sample files in another directory?.
> 
> 
> I am building in a Supermicro 2 socket Workstation with Xeon E5-2690 v3,
> intel compilers. My goal is to get the parallel version of the POM ocean
> model running. My building arguments are:
> 
> export CC=mpiicc
> export CXX=mpiicpc
> export F77=mpiifort
> export F90=mpiifort
> export FC=mpiifort
> 
> RUNPARALLEL='mpiexec.hydra -n $${NPROCS:=8}' I_MPI_C=ifort I_MPI_F90=ifort
> I_MPI_DEBUG=5 HDF5_PARAPREFIX=/apps/Parallel_test FC=mpif90 CXX=mpicxx
> CC=mpiicc CXXFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include" CFLAGS="-fPIC -O2"
> FCFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include" FFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include"
> CPPFLAGS="-I/usr/local/Librerias/zlib-1.2.8/include
> -I/usr/local/Librerias/szip-2.1/include
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include"
> LDFLAGS="-L/usr/local/Librerias/zlib-1.2.8/lib
> -L/usr/local/Librerias/szip-2.1/lib
> -L/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/lib
> -L/usr/local/Librerias/parallel-netcdf/lib" ./configure
> --prefix=/usr/local/Librerias/netcdf-4.3.3.1 --enable-parallel-tests
> --enable-pnetcdf --enable-large-file-tests --enable-benchmarks
> 
> # NetCDF C Configuration Summary
> ==============================
> 
> # General
> -------
> NetCDF Version:         4.3.3.1
> Configured On:          Tue Jul 14 11:49:15 CDT 2015
> Host System:            x86_64-unknown-linux-gnu
> Build Directory:        /home/wrf/Pruebas/Source/netcdf-4.3.3.1
> Install Prefix:         /usr/local/Librerias/netcdf-4.3.3.1
> 
> # Compiling Options
> -----------------
> C Compiler:             /opt/intel/impi/5.0.2.044/intel64/bin/mpiicc
> CFLAGS:                 -fPIC -O2
> CPPFLAGS:               -I/usr/local/Librerias/zlib-1.2.8/include
> -I/usr/local/Librerias/szip-2.1/include
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include
> LDFLAGS:                -L/usr/local/Librerias/zlib-1.2.8/lib
> -L/usr/local/Librerias/szip-2.1/lib
> -L/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/lib
> -L/usr/local/Librerias/parallel-netcdf/lib
> AM_CFLAGS:
> AM_CPPFLAGS:
> AM_LDFLAGS:
> Shared Library:         yes
> Static Library:         yes
> Extra libraries:        -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lm -lcurl
> 
> # Features
> --------
> NetCDF-2 API:           yes
> NetCDF-4 API:           yes
> HDF4 Support:           no
> HDF5 Support:           yes
> PNetCDF Support:        yes
> Parallel Support:       yes
> DAP Support:            yes
> Diskless Support:       yes
> MMap Support:           no
> JNA Support:            no
> 
> 
> Regards.
> 
> Julio Figueroa
> -------------------------------------------------
> Julio Figueroa
> Oceanólogo / Oceanographer
> address@hidden
> 
> 
> Dear Support,
> 
> I am installing NetCDF with parallel HDF5 however I got the error while
> doing make check:
> 
> 
> 
> *FAIL: run_bm_ar4.shFAIL: run_par_bm_test.sh*PASS: run_par_test.sh
> ...
> ============================================================================
> Testsuite summary for netCDF 4.3.3.1
> ============================================================================
> # TOTAL: 72
> # PASS:  70
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  2
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See nc_test4/test-suite.log.
> Please report to address@hidden
> 
> Attached you will find the test-suite.log and config.log
> 
> 
> 
> Looking at the scripts, the next link is empty:
> ftp://ftp.unidata.ucar.edu/pub/netcdf/sample_data/ar4/
> 
> Do you have the sample files in another directory?.
> 
> 
> I am building in a Supermicro 2 socket Workstation with Xeon E5-2690 v3,
> intel compilers. My goal is to get the parallel version of the POM ocean
> model running. My building arguments are:
> 
> export CC=mpiicc
> export CXX=mpiicpc
> export F77=mpiifort
> export F90=mpiifort
> export FC=mpiifort
> 
> RUNPARALLEL='mpiexec.hydra -n $${NPROCS:=8}' I_MPI_C=ifort I_MPI_F90=ifort
> I_MPI_DEBUG=5 HDF5_PARAPREFIX=/apps/Parallel_test FC=mpif90 CXX=mpicxx
> CC=mpiicc CXXFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include" CFLAGS="-fPIC -O2"
> FCFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include" FFLAGS="-fPIC -O2
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include"
> CPPFLAGS="-I/usr/local/Librerias/zlib-1.2.8/include
> -I/usr/local/Librerias/szip-2.1/include
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include"
> LDFLAGS="-L/usr/local/Librerias/zlib-1.2.8/lib
> -L/usr/local/Librerias/szip-2.1/lib
> -L/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/lib
> -L/usr/local/Librerias/parallel-netcdf/lib" ./configure
> --prefix=/usr/local/Librerias/netcdf-4.3.3.1 --enable-parallel-tests
> --enable-pnetcdf --enable-large-file-tests --enable-benchmarks
> 
> # NetCDF C Configuration Summary
> ==============================
> 
> # General
> -------
> NetCDF Version:         4.3.3.1
> Configured On:          Tue Jul 14 11:49:15 CDT 2015
> Host System:            x86_64-unknown-linux-gnu
> Build Directory:        /home/wrf/Pruebas/Source/netcdf-4.3.3.1
> Install Prefix:         /usr/local/Librerias/netcdf-4.3.3.1
> 
> # Compiling Options
> -----------------
> C Compiler:             /opt/intel/impi/5.0.2.044/intel64/bin/mpiicc
> CFLAGS:                 -fPIC -O2
> CPPFLAGS:               -I/usr/local/Librerias/zlib-1.2.8/include
> -I/usr/local/Librerias/szip-2.1/include
> -I/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/include
> -I/usr/local/Librerias/parallel-netcdf/include
> LDFLAGS:                -L/usr/local/Librerias/zlib-1.2.8/lib
> -L/usr/local/Librerias/szip-2.1/lib
> -L/usr/local/Librerias/hdf5-1.8.15-patch1_paralelo/lib
> -L/usr/local/Librerias/parallel-netcdf/lib
> AM_CFLAGS:
> AM_CPPFLAGS:
> AM_LDFLAGS:
> Shared Library:         yes
> Static Library:         yes
> Extra libraries:        -lpnetcdf -lhdf5_hl -lhdf5 -ldl -lm -lcurl
> 
> # Features
> --------
> NetCDF-2 API:           yes
> NetCDF-4 API:           yes
> HDF4 Support:           no
> HDF5 Support:           yes
> PNetCDF Support:        yes
> Parallel Support:       yes
> DAP Support:            yes
> Diskless Support:       yes
> MMap Support:           no
> JNA Support:            no
> 
> 
> Regards.
> 
> Julio Figueroa
> -------------------------------------------------
> Julio Figueroa
> Oceanólogo / Oceanographer
> address@hidden
> 
> 


Ticket Details
===================
Ticket ID: BOZ-873400
Department: Support netCDF
Priority: Normal
Status: Closed