[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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

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:

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

More on this change is here:


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


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


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

NOTE: All email exchanges with Unidata User Support are recorded in the Unidata inquiry tracking system and then made publicly available through the web. If you do not want to have your interactions made available in this way, you must let us know in each email you send to us.