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[netCDF #UQN-594171]: error : FAIL: run_par_test.sh
- Subject: [netCDF #UQN-594171]: error : FAIL: run_par_test.sh
- Date: Wed, 22 Jul 2015 12:06:21 -0600
Dhirendra,
There seem to be two problems:
1. Something is wrong with the MPI configuration or installation
2. You need to set LD_LIBRARY_PATH to specify where the HDF5 library is
installed.
More specifically, the test_suite.log you provided showing the "make check"
error
in nc_test4/test-suite.log indicated an error with parallel I/O that's
independent of
netCDF-4 or HDF5, because it gets a failure running a very simple test of MPI
that
doesn't use either of those libraries:
FAIL: run_par_test.sh
=====================
Testing MPI parallel I/O without netCDF...
[weather.jnu.ac.in:25805] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in
file ess_env_module.c at line 367
I'm not sure how to fix that problem, but you have to get that simple MPI
test working before the more complex netCDF parallel tests will work.
The error in finding the installed HDF5 library may be fixed by setting the
LD_LIBRARY_PATH environment variable to the lib/ directory where hdf5
was installed.
I hope this helps.
--Russ
> Dear Support,
>
> I have checked my libhdf5.settings and I found the following option for
> parallel-
> Parallel HDF5: mpicc
>
> as previously my hdf5-1.8.12 was configured using-
> CC=mpicc ./configure --prefix=/export/home/pmaharana/RLIB
> --with-zlib=/export/home/pmaharana/RLIB
> --with-szlib=/export/home/pmaharana/RLIB
>
> when compiled hdf5-1.8.12 with-
>
> CC=mpicc ./configure --prefix=/export/home/pmaharana/RLIB --enable-parallel
> --with-zlib=/export/home/pmaharana/RLIB
> --with-szlib=/export/home/pmaharana/RLIB
>
> which enabled
> Parallel HDF5=yes (in libhdf5.settings)
>
> and then tried to configure netcdf with-
>
> CPPFLAGS=-I/export/home/pmaharana/RLIB/include CC=mpicc
> LDFLAGS=-L/export/home/pmaharana/RLIB/lib LIBS= -ldl ./configure
> --enable-parallel-tests --disable-shared --prefix=/export/home/
> pmaharana/RLIB
>
> configure: error: Can't find or link to the hdf5 library. Use
> --disable-netcdf-4, or see config.log for errors.
>
> anyway for your reference I am attaching the test-suite.log file from the
> previous installation. Please have a look.
>
> Thanking you.
>
> Dhirendra
>
>
> address@hidden> wrote:
>
> > Hi Dhirendra,
> >
> > Could you please send us the file
> >
> > /home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4/test-suite.log
> >
> > from where you built netCDF, in case it contains additional information
> > about the error?
> >
> > Could you also check the file
> >
> > /export/home/pmaharana/RLIB/lib/libhdf5.settings
> >
> > to see whether, under "Features", it has the following line:
> >
> > Parallel HDF5: yes
> >
> > If not, then you will have to rebuild the HDF5 library with the
> > "--enable-parallel"
> > configure option, then re-install it, then rebuild netCDF-4.3.3.1 using
> > the new
> > installed library.
> >
> > --Russ
> >
> > > Dear Folks,
> > >
> > > I am trying to install netcdf-4.3.3.1 on a linux cluster with following
> > > options:
> > >
> > > ./configure CC=mpicc --enable-parallel-tests
> > > --prefix=/export/home/pmaharana/RLIB
> > > CPPFLAGS=-I/export/home/pmaharana/RLIB/include
> > > LDFLAGS=-L/export/home/pmaharana/RLIB/lib --enable-parallel
> > > --disable-shared LIBS=-ldl --with-szlib=/export/home/pmaharana/RLIB
> > >
> > > when I am running make and make check command I am getting the following
> > > error , however make install still works....I am not able to understand
> > > what is it about...please have a look and help me out. I am also
> > attaching
> > > the config.log file for the reference.
> > >
> > > FAIL: run_par_test.sh
> > > make[4]: Entering directory
> > `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[4]: Nothing to be done for `all'.
> > > make[4]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > >
> > ============================================================================
> > > Testsuite summary for netCDF 4.3.3.1
> > >
> > ============================================================================
> > > # TOTAL: 56
> > > # PASS: 55
> > > # SKIP: 0
> > > # XFAIL: 0
> > > # FAIL: 1
> > > # XPASS: 0
> > > # ERROR: 0
> > >
> > ============================================================================
> > > See nc_test4/test-suite.log
> > > Please report to address@hidden
> > >
> > ============================================================================
> > > make[3]: *** [test-suite.log] Error 1
> > > make[3]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[2]: *** [check-TESTS] Error 2
> > > make[2]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[1]: *** [check-am] Error 2
> > > make[1]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make: *** [check-recursive] Error 1FAIL: run_par_test.sh
> > > make[4]: Entering directory
> > `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[4]: Nothing to be done for `all'.
> > > make[4]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > >
> > ============================================================================
> > > Testsuite summary for netCDF 4.3.3.1
> > >
> > ============================================================================
> > > # TOTAL: 56
> > > # PASS: 55
> > > # SKIP: 0
> > > # XFAIL: 0
> > > # FAIL: 1
> > > # XPASS: 0
> > > # ERROR: 0
> > >
> > ============================================================================
> > > See nc_test4/test-suite.log
> > > Please report to address@hidden
> > >
> > ============================================================================
> > > make[3]: *** [test-suite.log] Error 1
> > > make[3]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[2]: *** [check-TESTS] Error 2
> > > make[2]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make[1]: *** [check-am] Error 2
> > > make[1]: Leaving directory `/home/pmaharana/RLIB/netcdf-4.3.3.1/nc_test4'
> > > make: *** [check-recursive] Error
> > >
> > > Thanks in anticipation.
> > >
> > > --
> > > ========================================
> > > Dhirendra Kumar
> > > School of Environmental Sciences, JNU
> > > New Delhi (India)
> > > Contact: +91 9910778043
> > > Alternate email: address@hidden
> > > =========================================
> > >
> > >
> > Russ Rew UCAR Unidata Program
> > address@hidden http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: UQN-594171
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
>
>
> --
> ========================================
> Dhirendra Kumar
> UGC-JRF
> School of Environmental Sciences, JNU
> New Delhi (India)
> Contact: +91 9910778043
> Alternate email: address@hidden
> =========================================
>
>
Russ Rew UCAR Unidata Program
address@hidden http://www.unidata.ucar.edu
Ticket Details
===================
Ticket ID: UQN-594171
Department: Support netCDF
Priority: Normal
Status: Closed