Tests fail after building parallel netcdf with gcc and openmpi

[Wei-keng Liao]

Hi, Greg,

The error message indicates the file access permission.
Could you please check if you have the right permission (file creation especially)?

Another possible cause is the OpenMPI. Have you run an MPI program that
successfully creates/opens a file? Below is a simple MPI program. Please
give it a try and let us know.

#include <stdio.h>
#include <mpi.h>
int main(int argc, char **argv) {
    MPI_File fh;
    MPI_Init(&argc, &argv);
    MPI_File_open(MPI_COMM_WORLD, "testfile", MPI_MODE_CREATE | MPI_MODE_RDWR,
                  MPI_INFO_NULL, &fh);
    MPI_File_close(&fh);
    MPI_Finalize();
    return 0;
}


Wei-keng


On Jan 4, 2012, at 7:13 PM, Greg Schussman wrote:

> Hi.
> 
> I'm having trouble getting a working version of parallel netcdf using gcc and openmpi.   I've tried various combinations of:
> 
>   parallel-netcdf-1.1.1
>   parallel-netcdf-1.2.0
>   gcc 4.5.1
>   gcc 4.6.1
>   openmpi-1.4.3
>   openmpi-1.5
> 
> I'm building using this bash script:
> 
>     MPICC=mpicc MPICXX=mpicxx ./configure \
>     --prefix=$HOME/$NERSC_HOST/Software/parallel-netcdf --disable-fortran
> 
>     make clean
>     make
>     make install
> 
> All that completes with no complaints.  Then to test, I run:
> 
>     ../parallel-netcdf/bin/ncmpidump test/data/test_double.nc 
> 
> Which gives:
> 
>      0: MPI_File_open : MPI_ERR_OTHER: known error not in list
>     ../parallel-netcdf/bin/ncmpidump: test/data/test_double.nc: Can not open/create file
> 
> I have checked that that ncmpidump really is the one created by my build.  I have copied that test_double.nc file to another machine with a working ncmpidump, and the file is not corrupt.
> 
> I've tried running the tests that come with the sources via:
> 
>     cd test/nc_test/
>     make testing
> 
> Which starts this way:
> 
>     ./nc_test -c
>      0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 661 of util.c: ncmpi_create: Can not open/create file
>         FAILURE at line 547 of util.c: ncmpi_def_dim: Not a netCDF id
>         FAILURE at line 547 of util.c: ncmpi_def_dim: Not a netCDF id
>         FAILURE at line 547 of util.c: ncmpi_def_dim: Not a netCDF id
>         FAILURE at line 547 of util.c: ncmpi_def_dim: Not a netCDF id
>         FAILURE at line 547 of util.c: ncmpi_def_dim: Not a netCDF id
>         FAILURE at line 563 of util.c: ncmpi_def_var: Not a netCDF id
>         FAILURE at line 563 of util.c: ncmpi_def_var: Not a netCDF idrm -f scratch.nc
> ./nc_test && ./nc_test -c -2 && ./nc_test
>     *** Testing ncmpi_strerror         ... ok
>     *** Testing ncmpi_open             ...  0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 97 of test_read.c: ncmpi_open of nonexistent file should have returned system error 0: MPI_File_open : MPI_ERR_OTHER: known error not in list
>      0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 107 of test_read.c: ncmpi_open: Can not open/create file
>         FAILURE at line 110 of test_read.c: ncmpi_redef of read-only file should fail 0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 114 of test_read.c: ncmpi_open: Can not open/create file 0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 124 of test_read.c: ncmpi_create: Can not open/create file 0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
> 
> and ends this way:
> 
>         FAILURE at line 5995 of test_iput.c: ncmpi_create: Can not open/create file
>         ### 1 FAILURES TESTING ncmpi_iput_varm_int! ###
>     *** Testing ncmpi_iput_varm_long   ...  0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 6163 of test_iput.c: ncmpi_create: Can not open/create file
>         ### 1 FAILURES TESTING ncmpi_iput_varm_long! ###
>     *** Testing ncmpi_iput_varm_float  ...  0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 6331 of test_iput.c: ncmpi_create: Can not open/create file
>         ### 1 FAILURES TESTING ncmpi_iput_varm_float! ###
>     *** Testing ncmpi_iput_varm_double ...  0: MPI_File_open : MPI_ERR_OTHER: known error not in list
> 
>         FAILURE at line 6499 of test_iput.c: ncmpi_create: Can not open/create file
>         ### 1 FAILURES TESTING ncmpi_iput_varm_double! ###
> 
>     NOTE: parallel-netcdf expects to see 2 failures
>     Total number of failures: 167738
> 
> Thanks in advance for any help.
> 
> Greg
> 
>