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[netCDF #SEL-204074]: NetCDF-4

Subject: [netCDF #SEL-204074]: NetCDF-4
Date: Mon, 22 Sep 2014 20:43:04 -0600
Hi Carlos,

The problems you are seeing may be caused by having your computer's clock
set wrong.  

> make[2]: warning: Clock skew detected. Your build may be incomplete.
> make[2]: Leaving directory 
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make check-TESTS
> make[2]: Entering directory 
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[2]: Warning: File `.deps/fortlib.Po' has modification time 6.5e+02s in 
> the future

Since "make" uses file modification times to determine what commands to run, it
gets confused if some files appear to have modification dates in the future.  
Apparently
some of you files appeared to have last been modified 650 seconds in the future 
when
you ran "make check".  This can happen if the time wasn't set correctly when 
you last
restarted your computer, or if the clock on your computer and the file server 
from which 
you transfer files are not close.  This can lead to files not getting compiled 
that should
have been.

You can solve the problem temporarily by getting rid of all the compiled files 
from the
future using "make clean" in the top-level directory before running configure, 
make all,
make test, and make install again.  To solve the problem permanently, make sure 
your
computer and the file servers you use have synchronized clocks, by having NTP 
installed
and run on each computer, or find some other way to synchronize the clocks.

> Hello Russ,
> thank you for your answer,
> I did the corrections you suggested,
> but unfortuntally I still don't get a proper compilation...
> I first install hdf5-1.8.13, then, netcdf-c-4.3.3-rc1, then,
> netcdf-cxx4-4.2 and then when trying netcdf-fortran-4.4.1 I get errors.
> 
> $
> CPPFLAGS='-I/data/users/carlos/shares/apps/netcdf-C-libraries/4.3.3/gfortran/include'
> LDFLAGS='-L/data/users/carlos/shares/apps/netcdf-C-libraries/4.3.3/gfortran/lib
> -L/data/users/carlos/shares/apps/netcdf-cxx4/4.4.2/gfortran/lib
> -L/data/users/carlos/shares/apps/hdf5/1.8.13/gfortran/lib' ./configure
> --prefix=/data/users/carlos/shares/apps/netcdf-fortran/4.4.1/gfortran/
> $ make check
> $ make install
> 
> In the latest command, I did implemented the suggestions made and I also
> even tried add the line " LIBS='-lnetcdf -lhdf5_hl -lhdf5 '"
> However, I get this result and I don't know how to solve it.
> I am compiling with gfortran 4.7.2
> 
> $ gfortran --version
> GNU Fortran (GCC) 4.7.2
> Copyright (C) 2012 Free Software Foundation, Inc.
> 
> and I have noticed that in your blogs there was a person with a similar
> problem but still I couldn't get my problem solved.
> Could you please give me some suggestions?
> With kindest regards,
> Carlos
> 
> make[2]: warning:  Clock skew detected.  Your build may be incomplete.
> make[2]: Leaving directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make  check-TESTS
> make[2]: Entering directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[2]: Warning: File `.deps/fortlib.Po' has modification time 6.5e+02
> s in the future
> make[3]: Entering directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[3]: Warning: File `.deps/fortlib.Po' has modification time 6.5e+02
> s in the future
> FAIL: nf_test
> PASS: create_fills.sh
> FAIL: tst_f77_v2
> FAIL: ftst_vars
> FAIL: ftst_vars2
> FAIL: ftst_vars3
> FAIL: ftst_vars4
> FAIL: ftst_vars5
> FAIL: ftst_vars6
> FAIL: ftst_types
> FAIL: ftst_types2
> FAIL: ftst_types3
> FAIL: ftst_groups
> FAIL: ftst_path
> FAIL: ftst_rengrps
> FAIL: f90tst_vars
> FAIL: tst_types
> FAIL: tst_types2
> FAIL: f90tst_vars_vlen
> FAIL: tst_f90_nc4
> FAIL: f90tst_grps
> FAIL: f90tst_fill
> FAIL: f90tst_fill2
> FAIL: f90tst_vars3
> FAIL: f90tst_vars4
> FAIL: f90tst_vars2
> FAIL: f90tst_path
> FAIL: f90tst_rengrps
> FAIL: ftst_v2
> FAIL: ftest
> FAIL: tst_f90
> make[4]: Entering directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[4]: Warning: File `.deps/fortlib.Po' has modification time 6.4e+02
> s in the future
> make[4]: Nothing to be done for `all'.
> make[4]: warning:  Clock skew detected.  Your build may be incomplete.
> make[4]: Leaving directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> ============================================================================
> Testsuite summary for netCDF-Fortran 4.4.1
> ============================================================================
> # TOTAL: 31
> # PASS:  1
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  30
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See nf_test/test-suite.log
> Please report to address@hidden
> ============================================================================
> make[3]: *** [test-suite.log] Error 1
> make[3]: Leaving directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[2]: *** [check-TESTS] Error 2
> make[2]: Leaving directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory
> `/data/users/carlos/paraborrar/netcdf-fortran-4.4.1/nf_test'
> make: *** [check-recursive] Error 1
> 
> 
> 
> On 20/09/2014 12:59, Unidata netCDF Support wrote:
> > Hi Carlos,
> >
> > The first problem is the way you have specified the LDFLAGS environment 
> > variable:
> >
> >    
> > LDFLAGS='-L/data/users/carlos/software/netCDF/installation/lib/lib/:/data/users/carlos/software/netCDF/installation/src/netcdf-cxx/lib/:/data/users/carlos/software/hdf5-1.8.13/installation/src/lib/'
> >
> > Instead of specifying all your library directories as one string with ":" 
> > separators,
> > compilers require that each library directory must be specified separately, 
> > as in
> >
> >    LDFLAGS='-L/data/users/carlos/software/netCDF/installation/lib/lib 
> > -L/data/users/carlos/software/netCDF/installation/src/netcdf-cxx/lib 
> > -L/data/users/carlos/software/hdf5-1.8.13/installation/src/lib'
> >
> > Also, if that doesn't fix the problem and you still need to define a LIBS 
> > envoronment
> > variable, the order must be changed to correspond to which libraries depend 
> > on other
> > libraries.  So instead of
> >
> >    LIBS='-lhdf5 -lhdf5_hl -lnetcdf'
> >
> > you would need to use
> >
> >    LIBS='-lnetcdf -lhdf5_hl -lhdf5 '
> >
> > but you may not even need to specify LIBS if getting the right syntax for
> > LDFLAGS is the real problem.
> >
> > --Russ
> >
> >> It does not work (you will see below these lines all the inputs and
> >> output from the terminal and the config.log file). I have exported the
> >> library (netcdf-c-4.3.3-rc1) and still I can't compile.
> >>
> >> Thank you for your support,
> >> Carlos
> >>
> >> $ export
> >> LD_LIBRARY_PATH=$/data/users/carlos/software/netCDF/installation/lib/lib:${LD_LIBRARY_PAT}
> >>
> >> $
> >> CPPFLAGS="-I/data/users/carlos/software/netCDF/installation/lib/include/" 
> >> LDFLAGS="-L/data/users/carlos/software/netCDF/installation/lib/lib/:/data/users/carlos/software/netCDF/installation/src/netcdf-cxx/lib/:/data/users/carlos/software/hdf5-1.8.13/installation/src/lib/"
> >> LIBS="-lhdf5 -lhdf5_hl -lnetcdf" ./configure
> >> --prefix=/data/users/carlos/software/netCDF/installation/src/netcdf-fortran/
> >> configure: netCDF-Fortran 4.4.1
> >> checking build system type... x86_64-unknown-linux-gnu
> >> checking host system type... x86_64-unknown-linux-gnu
> >> checking target system type... x86_64-unknown-linux-gnu
> >> checking for a BSD-compatible install... /usr/bin/install -c
> >> checking whether build environment is sane... yes
> >> checking for a thread-safe mkdir -p... /bin/mkdir -p
> >> checking for gawk... gawk
> >> checking whether make sets $(MAKE)... yes
> >> checking whether make supports nested variables... yes
> >> checking whether to enable maintainer-specific portions of Makefiles... no
> >> configure: checking user options
> >> checking whether extra valgrind tests should be run... no
> >> checking whether parallel IO tests should be run... no
> >> checking whether netCDF extra tests should be run (developers only)... no
> >> checking for doxygen... no
> >> configure: WARNING: Doxygen not found - documentation will not be built
> >> checking for dot... dot
> >> configure: finding C compiler
> >> checking for gcc... gcc
> >> checking whether the C compiler works... no
> >> configure: error: in
> >> `/data/users/carlos/software/netCDF/netcdf-fortran-4.4.1':
> >> configure: error: C compiler cannot create executables
> >> See `config.log' for more details
> >>
> >>
> >>
> >>
> >>
> >>
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                       http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: SEL-204074
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> 
> 
> 
> 
> 
> 
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: SEL-204074
Department: Support netCDF
Priority: Normal
Status: Closed
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