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

Albert,

> After seeing your suggestion, I tried to use HDF5-1.8.4-patch1 with 
> NetCDF-4.1.1 & MVAPICH2-1.8 for MPI compiler.But it still have some errors 
> when I run the "make check" command and when I tried to use NetCDF to build 
> the atmosphere model CAM5.0, it seems to have some errors relating to NetCDF.
> But I not really understand what meaning the message is. Could please take a 
> look and give me some advice for what should I do now?I attach the error 
> message for NetCDF using the command make check and partial message relating 
> to NetCDF when I tried to build the application.I really appreciate all the 
> help you gave to me. Thank you very much.

Sorry, but I don't have any software that knows how to read the ".rar" file you 
attached, which is apparently
a compressed Windows archive.  Please either attach the logfile in uncompressed 
form or use something that
can be read on a Linux system, such as tar.gz or .zip.

For CentOS 6, the easiest way to install netCDF is by using the prebuilt 
package for netCDF and a package 
manager, such as "yum". For example, you should be able to use a command such as

  yum install netcdf-4.1.1

or a more specific version such as netcdf-4.1.1-3.el6.2.x86_64

I don't know if any of the prebuilt packages for your system are built for 
parallel I/O.  If not,
you will have to build from source using the --enable-parallel option to 
configure, as described
here:

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

under the "Building with Parallel I/O" link.

--Russ

> > To: address@hidden
> > Subject: [netCDF #TFK-571541]: Problems when installing NetCDF-4.1.1 for 
> > parallel I/O
> > Date: Thu, 14 Jun 2012 10:27:32 -0600
> > CC: address@hidden
> > From: address@hidden
> >
> > 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
> >
> 
> 
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