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[netCDF #XIS-909415]: Problem Installing netcdf-4.3.1
- Subject: [netCDF #XIS-909415]: Problem Installing netcdf-4.3.1
- Date: Sat, 22 Feb 2014 08:54:29 -0700
Vic,
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