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[netCDF #TFK-571541]: Problems when installing NetCDF-4.1.1 for parallel I/O

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  • Subject: [netCDF #TFK-571541]: Problems when installing NetCDF-4.1.1 for parallel I/O
  • Date: Thu, 14 Jun 2012 10:27:32 -0600
Hi Albert,

> I'm a college student in NTHU, Taiwan. I'm
> going to attend the SC12 competition this November. (Student Cluster
> 2012 Competition) I have to install the atmosphere model CAM. And I need
> to install NetCDF first. But now I have difficulties in installing the
> required library NetCDF-1.4.1 for parallel I/O.
> 
> I'm writing to enquire about some help because I really have no idea
> what I should do now. I can use make to build NetCDF-4.1.1 for parallel,
> but it will fail 1 of 59 tests when I use the command "make check."
> 
> 
> Besides, I install ZLIB-1.2.5 &
> MVAPICH2-1.8 & HDF5-1.8.6 in advance and use CentOS
> 6.0 for the operating system.

We haven't tested the combination of netCDF-4.1.1 with HDF5-1.8.6, so I'm
not sure what caused the error you are seeing in testing HDF5 for netCDF,
but it may be an incompatibility from the HDF5-1.8.4-patch1 release that
we originally recommended and tested with for netCDF 4.1.1.

However, I think you should instead use netCDF-4.2 with HDF5 1.8.8 or 1.8.9,
because there have been many improvements since the netCDF-4.1.1 release.

> ./configure --with-hdf5=$HOME/HDF5-1.8.6-intel
> --prefix=$HOME/NetCDF-4.1.1-intel make check install
> 
> Another question is when  I want to use other version newer than
> NetCDF-4.1.1, for example, NetCDF-4.1.2 or NetCDF-4.1.3, it always cannot
> find the HDF5 libraries.  I use the same configure flags as above. I
> would be grateful if you could give me some advice relating to this
> problem. ...

The problem is using the "--with-hdf5=" option for netCDF-4.2.  That worked
OK with 4.1.1, but for 4.2 you have to specify the location of the HDF5
library in a different way, using environment variables, for example:

  CPPFLAGS=-I${HOME}/HDF5-1.8.8-intel/include 
LDFLAGS="-L${HOME}/HDF5-1.8.8-intel/lib" ./configure ...

More on this change is here:

  http://www.unidata.ucar.edu/software/netcdf/docs/build_default.html

and the reason the change from "--with-hdf5=..." is here:

  https://www.unidata.ucar.edu/jira/browse/NCF-20

I hope this works for you.  Let us know if you encounter other problems.

--Russ

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



Ticket Details
===================
Ticket ID: TFK-571541
Department: Support netCDF
Priority: Normal
Status: Closed