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[netCDF #LIC-415919]: netCDF 4.1.1 build problems

Hi Neil.

> I am trying to build netCDF 4.1.1 (without the netCDF 4 extension (HDF5
> etc.)) on a Pentium 4 machine running i686 CentOS release 5.4 (Final).
> 
> I'm using the compiler flags "-march=pentium4 -mfpmath=sse
> -malign-double -O3" for gcc, g++, and gfortran. (Changing O3 to O2
> didn't change the problem.)
> 
> I am failing 1 (or 2) of 11 tests. The tests failed are tst_lengths.sh
> and tst_nccopy3.sh. (However, tst_nccopy3.sh seems to fail only because
> it is expecting files that would be created by tst_lengths.sh, and the
> files don't exist because tst_lengths.sh didn't run to completion. If I
> modify tst_lengths.sh so that it doesn't exit on each failure but echos
> a diagnostic message, I get the following output (and tst_nccopy3.sh no
> longer subsequently fails).

We haven't seen the tst_lengths.sh test fail on any Unix platforms, only
occasionally on Windows running cygwin, and it succeeds on our cygwin
platform, so we've been unable to reproduce the problem here.  I tried 
building with the "-mfpmath=sse -malign-double -O3" flags on our x86_64
Linux platform, but couldn't reproduce any of the errors you saw.

The small.nc and small2.nc files you supplied are readable netCDF files.  The
small2.nc is what's expected, since it's the result of the last test run by
tst_lengths.sh, which succeeded.  The small.nc file has extra padding added
to the end of what's expected in the file to make it 4096 bytes instead of
the expected 68 bytes, but the netCDF library doesn't see those extra bytes
when reading the file.  So your library should work fine and you can install
it, but it creates either larger files than expected with extra 0-byte 
padding for small netCDF files, or files slightly smaller than what are
expected by truncating up to 3 bytes of expected padding when NOFILL is
specified.

Are you by any chance using an experimental file system or a file system
configured in an unusual way?

--Russ

> Output from modified tst_lengths.sh:
> *** testing length of classic file
> *** testing length of classic file written with NOFILL
> Expecting=>68, Measured=>65
> *** testing length of rewritten classic file
> Expecting=>68, Measured=>4096
> *** testing length of rewritten classic file written with NOFILL
> Expecting=>68, Measured=>4096
> *** testing length of 64-bit offset file
> *** testing length of 64-bit offset file written with NOFILL
> Expecting=>72, Measured=>69
> *** testing length of rewritten 64-bit offset file
> Expecting=>72, Measured=>4096
> *** testing length of rewritten 64-bit offset file written with NOFILL
> Expecting=>72, Measured=>4096
> *** testing length of one-record-variable classic file
> *** testing length of one-record-variable classic file written with
> NOFILL
> *** testing length of one-record-variable 64-bit offset file
> *** testing length of one-record-variable 64-bit offset file written
> with NOFILL
> FAIL: tst_lengths.sh
> 
> 1. I am installing from netcdf-4.1.1.tar.gz downloaded from
> http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_1/index.jsp. I
> cannot find a VERSION file, but the date of the archive seems to be
> 2010-04-12.1249.
> 
> 2. The output from "./configure", "make", and "make check" are attached
> as setup.log, make.log, and check.log respectively.
> 
> <<make.log>>  <<check.log>>  <<setup.log>>
> 3. The configure did not fail so I have not included config.log.
> 
> 4. I get the same errors whether I enable or disable large file tests.
> 
> ===
> 
> So I have two questions. 1) Does this file size discrepancy indicate a
> major problem with my build? 2) If it is a problem, how best can I go
> about resolving it?
> 
> I am attaching for reference the small and small2 files that were
> upsetting tst_lengths.sh in case they should be of interest.
> 
> <<small.cdl>>  <<small.nc>>  <<small2.cdl>>  <<small2.nc>>
> Please let me know if any further information is required to
> diagnose/resolve this issue.


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



Ticket Details
===================
Ticket ID: LIC-415919
Department: Support netCDF
Priority: Normal
Status: Closed