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[netCDF #XIS-909415]: Problem Installing netcdf-4.3.1

Vic,

OK, this was a different problem, but it's still on the server side,
and we can reproduce it.  It's our problem, so your build may be 
perfectly OK.  Until we get the server-side issue resolved (which 
may be a side effect of fixes to a break-in last Thursday night that
required password changes for all registered Unidata users), your
"make check" will only finish successfully if you configure with 

  --disable-dap-remote-tests

I suspect your installation is fine and would work OK with other
OPeNDAP or TDS servers.

--Russ

> I tied a "make check install" again and got the following results.
> below .Just with one error instead of two like before. I have alos
> attached the ncdap_test-suite.log error file.
> 
> 
> Unidata netCDF Support wrote:
> > Vic,
> > Testsuite summary for netCDF 4.3.1.1
> ============================================================================
> # TOTAL: 12
> # PASS:  11
> # SKIP:  0
> # XFAIL: 0
> # FAIL:  1
> # XPASS: 0
> # ERROR: 0
> ============================================================================
> See ncdap_test/test-suite.log
> Please report to address@hidden
> ============================================================================
> make[5]: *** [test-suite.log] Error 1
> make[5]: Leaving directory
> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> make[4]: *** [check-TESTS] Error 2
> make[4]: Leaving directory
> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> make[3]: *** [check-am] Error 2
> make[3]: Leaving directory
> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> make[2]: *** [check-recursive] Error 1
> make[2]: Leaving directory
> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> make[1]: *** [check] Error 2
> make[1]: Leaving directory
> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> make: *** [check-recursive] Error 1
> 
> > This looks like it might be a symptom of a problem with our test
> > server yesterday, which may have caused time outs on remote access
> > tests.  Could you just try "make check" again, now that our server
> > problems are fixed?
> >
> > --Russ
> >
> >> I removed the hdf5.x86_64 1.8.7-1.el5.rf off of my Centoos 5 system
> >> and installed the 1.8.12-1.with.szip.encoder.el5 version. I did a fresh
> >> ./configure in my netcdf-4.3.1.1 directory which I guess looked to work
> >> with no obvious complaints . Then did the "make check install". looked
> >> like it was going to work but came up short with following message
> >> below. I have attached the ncdap_test/test-suite.log file to this email.
> >> Rats--Thought it was going to work--Took quite awhile for it to get to
> >> this point so I thought it was going to work
> >>
> >> ============================================================================
> >> Testsuite summary for netCDF 4.3.1.1
> >> ============================================================================
> >> # TOTAL: 12
> >> # PASS:  11
> >> # SKIP:  0
> >> # XFAIL: 0
> >> # FAIL:  1
> >> # XPASS: 0
> >> # ERROR: 0
> >> ============================================================================
> >> See ncdap_test/test-suite.log
> >> Please report to address@hidden
> >> ============================================================================
> >> make[5]: *** [test-suite.log] Error 1
> >> make[5]: Leaving directory
> >> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> >> make[4]: *** [check-TESTS] Error 2
> >> make[4]: Leaving directory
> >> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> >> make[3]: *** [check-am] Error 2
> >> make[3]: Leaving directory
> >> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> >> make[2]: *** [check-recursive] Error 1
> >> make[2]: Leaving directory
> >> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> >> make[1]: *** [check] Error 2
> >> make[1]: Leaving directory
> >> `/home/tisone/HELP/NETCDF/netcdf-4.3.1.1/ncdap_test'
> >> make: *** [check-recursive] Error 1
> >>
> >>
> >> Unidata netCDF Support wrote:
> >>> Vic,
> >>>
> >>> My first diagnosis was correct, the old version of HDF5 is the problem.
> >>>
> >>> There was a bug in HDF5-1.8.7 that we didn't test for in the corresponding
> >>> netCDF version 4.1.3 released a month later, so that version could be
> >>> built with HDF5-1.8.7.  The current netCDF version 4.3.1.1 detects the
> >>> HDF5 bug when built with HDF5-1.8.7, but builds fine with HDF5 versions
> >>> 1.8.8 and later.  If you have to rebuild HDF5 from source anyway, I
> >>> would recommend just using the latest version 1.8.12, as that's what
> >>> we've done the most testing with.
> >>>
> >>> --Russ
> >>>
> >>>> Oops, sorry, I can now duplicate the problem you are seeing, so
> >>>> will follow up with a diagnosis and solution.  It has nothing to
> >>>> do with the compiler version!
> >>>>
> >>>> I had been  inadvertantly running in an environment in which the
> >>>> LD_LIBRARY_PATH variable was set to a directory that caused me to
> >>>> be testing a current version of HDF5 rather than HDF5-1.8.7.
> >>>>
> >>>> Sorry about the red herrings :-) ...
> >>>>
> >>>> --Russ
> >>>>
> >>>>>> I have included the config.log file for trying to install netcdf-4.3.1.
> >>>>>> I am trying to install on a CENTOS 5 LINUX system. I checked what I
> >>>>>> installed on the system that I am trying to do the install using yum.
> >>>>>> Below is what I have installed currently for the hdf5,curl and zlib 
> >>>>>> via yum.
> >>>>>>
> >>>>>> hdf5.x86_64           1.8.7-1.el5.rf        installed
> >>>>>> hdf5-devel            1.8.7-1.el5.rf        installed
> >>>>>> curl.x86_64           7.15.5-9.el5_6.2      installed
> >>>>>> curl-devel.x86_64     7.15.5-9.el5_6.2      installed
> >>>>>> zlib.x86_64           1.2.3-3               installed
> >>>>>> zlib-devel.x86_64     1.2.3-3               installed
> >>>>>>
> >>>>>> Did not know if I should have used the ones you have in your download
> >>>>>> site instead of installing them using yum via the Centos 5 system
> >>>>> Installing via yum should be fine, if the problem isn't related
> >>>>> to the older versions of HDF5, libcurl, and zlib that you're
> >>>>> building with.  I tried to duplicate the bug with the same version
> >>>>> of HDF5 you are using, but it worked fine for me, and curl and zlib
> >>>>> don't appear to be involved.
> >>>>>
> >>>>>> After downloading the netcdf-4.3.1 tar file and untarring it, I did
> >>>>>> the simple ./connfigure prefix=/home/tisone/HELP/NETCDF/local
> >>>>>> and then did the make check install that generated the error I sent
> >>>>>> Will have the the netcdf command set that it generates when it works be
> >>>>>> placed on our main fileserver in a common directory that is mounted on
> >>>>>> all of LINUX systems running CENTOS 5 and CENTOS 6 . ...
> >>>>> This is puzzling.  I don't have access to a CENTOS 5 platform, but my 
> >>>>> old
> >>>>> Fedora 14 x86_64 should be pretty close, and your config.log shows only 
> >>>>> a
> >>>>> few differences, but you get the "make check" failure that I don't see.
> >>>>>
> >>>>> The differences are
> >>>>>
> >>>>> - You're using an older curl library without CURLOPT_KEYPASSWD defined
> >>>>> in curl/curl.h, but the ncdump test that's failing has nothing to do
> >>>>> with libcurl or DAP.
> >>>>> - In your older math.h, there are no definitions for the macros isfinite
> >>>>> or signbit, but that shouldn't matter, as configure flags make sure
> >>>>> substitutes are defined when not provided.
> >>>>> - Your compiler version, gcc-4.1.2, is older than the gcc-4.5.1 I'm 
> >>>>> using.
> >>>>>
> >>>>> It's grasping at straws, but there might have been a bug in gcc-4.1.2
> >>>>> that was later fixed and gets past the test failure you're seeing in the
> >>>>> call to an HDF5 function in creating a test file, in
> >>>>> ncdump/tst_h_scalar.c:
> >>>>>
> >>>>> /* Create variable-length string datatype */
> >>>>> if ((vlstr_typeid = H5Tcreate(H5T_STRING, (size_t)H5T_VARIABLE)) < 0) 
> >>>>> ERR;
> >>>>>
> >>>>> that resulted in
> >>>>>
> >>>>> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> >>>>> #000: H5T.c line 1597 in H5Tcreate(): unable to create type
> >>>>> major: Datatype
> >>>>> minor: Unable to initialize object
> >>>>> #001: H5T.c line 2990 in H5T_create(): type class is not appropriate - 
> >>>>> use H5Tcopy()
> >>>>> major: Datatype
> >>>>> minor: Feature is unsupported
> >>>>>
> >>>>> If you have access to gcc-4.5.1 or later on your CENTOS platform, could 
> >>>>> you
> >>>>> try building and testing with that instead?
> >>>>>
> >>>>> If that doesn't work, all I can suggest is using a more current 
> >>>>> HDF5-1.8.12
> >>>>> release ...
> >>>>>
> >>>>> --Russ
> >>>>>
> >>>>>> Unidata netCDF Support wrote:
> >>>>>>> Hi Vic,
> >>>>>>>
> >>>>>>>> I have been trying to install netcdf-4.3.1 on one of our Centos 5
> >>>>>>>> Linux systems --I get the errors that are contained in the atached
> >>>>>>>> test-suite.log file--Not sure what I need to do about it.
> >>>>>>> I thought the problem might be using a pretty old version of HDF5 from
> >>>>>>> 2011 with the latest version of netCDF. but I can't duplicate the 
> >>>>>>> problem
> >>>>>>> here.  NetCDF-4.3.1.1 built with HDF5-1.8.7 seems to work fine and 
> >>>>>>> passes
> >>>>>>> all tests on my RHEL 14 Linux system,
> >>>>>>>
> >>>>>>> Can you send the config.log file generated when you ran configure?
> >>>>>>>
> >>>>>>> Thanks!
> >>>>>>>
> >>>>>>> --Russ
> >>>>>>>
> >>>>>>> Russ Rew                                         UCAR Unidata Program
> >>>>>>> address@hidden                      http://www.unidata.ucar.edu
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Ticket Details
> >>>>>>> ===================
> >>>>>>> Ticket ID: XIS-909415
> >>>>>>> Department: Support netCDF
> >>>>>>> Priority: Normal
> >>>>>>> Status: Closed
> >>>>>> --
> >>>>>> Vic
> >>>>>>
> >>>>>> Victor P. Tisone           Computer System Management Team (CSMT)
> >>>>>> address@hidden            voice: (303)497-1519  fax: (303)497-1589
> >>>>>> High Altitude Observatory  P.O. Box 3000 Boulder CO 80307  USA
> >>>>>>
> >>>>>>
> >>>>> Russ Rew                                         UCAR Unidata Program
> >>>>> address@hidden                      http://www.unidata.ucar.edu
> >>>>>
> >>>>>
> >>>> Russ Rew                                         UCAR Unidata Program
> >>>> address@hidden                      http://www.unidata.ucar.edu
> >>>>
> >>>>
> >>> Russ Rew                                         UCAR Unidata Program
> >>> address@hidden                      http://www.unidata.ucar.edu
> >>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: XIS-909415
> >>> Department: Support netCDF
> >>> Priority: Normal
> >>> Status: Closed
> >> --
> >> Vic
> >>
> >> Victor P. Tisone           Computer System Management Team (CSMT)
> >> address@hidden            voice: (303)497-1519  fax: (303)497-1589
> >> High Altitude Observatory  P.O. Box 3000 Boulder CO 80307  USA
> >>
> >>
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: XIS-909415
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> 
> --
> Vic
> 
> Victor P. Tisone           Computer System Management Team (CSMT)
> address@hidden            voice: (303)497-1519  fax: (303)497-1589
> High Altitude Observatory  P.O. Box 3000 Boulder CO 80307  USA
> 
> 

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



Ticket Details
===================
Ticket ID: XIS-909415
Department: Support netCDF
Priority: Normal
Status: Closed