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[netCDF #YWP-403246]: compiling netCDF



Chad,

> Sean,
> 
> I am using the atest ubuntu 11.0.4, just downloaded and installed las
> week.  Here is the ouput you requested:
> 
> address@hidden:~$ echo $SHELL
> /bin/bash
> address@hidden:~$ ls -la /bin/sh
> lrwxrwxrwx 1 root root 4 May 25 21:07 /bin/sh -> dash*
> address@hidden:~$

The failures you get for `make check` show up when using ifort during the 
tests, and once again ifort is having issues finding the Intel shared objects. 
Just out of curiosity, is /bin/bash also a symlink to /bin/dash? If so, then 
that is the problem - dash is not 100% compatible with bash, and thus the Intel 
scripts may not be fully functional. If it is a link to dash, use apt-get to 
install bash and then try to rebuild.

> 
> I am not sure if I should open a separate support issue for this, but
> I am running into a data incompatibility problem.  I want to use
> Tecplot 360 (tecplot.com) for visualzing and making movies of output
> from WRF.  Tecplot 360 support HDF5 data, but WRF only suports netCDF
> without HDF5, from what I have read and been told by wrfhelp.  How can
> I get my data into Tecplot 360 from a netCDF file that has no HDF5?
> Do you know if WRF planps to upgrade to HDF5 support soon?

I am not sure what the plans are with WRF,as it is not developed at Unidata. 
The folks at NCAR who are involved in the administration of the codebase should 
be able to answer that question (I'd check with WRFhelp). The questions to ask 
would be if/when WRF plans to use netCDF4.

> 
> I suppose we would need to get this netCDF 4 with HDF5 support to
> compile, then I could write a program that read the netCDF without
> HDF5 data, then wrote it back with netCDF with HDF5.  Is netCDF 4 with
> HDF5 backwards compatible with output from say netCDF 363?  So, if I
> write a code using netCDF4 with HDF5, can I read netCDF 363 data and
> then write it back in HDF5 format?  

netCDF4 will read data written with netCDF3 - no problems :-) That said...

> Do you guys have any utiities that
> already do this?  A simple utility that reads in a netCDF 363 data
> file and upgrades it to netCDF4 with HDF5 support?  If you do not, you
> should write one.  It would be simple for you guys that know netCDF so
> well.   If I have to do it, its going to take me a while to figure out
> how.... time I really do not have right now.  

If you check out the netCDF FAQ 
(http://www.unidata.ucar.edu/software/netcdf/docs/faq.html), there is an entry 
about how to do this 
(http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#fv13).

> I can write code in
> Fortran and C, but would prefer to use Python.  Python can usually
> call C libraries, so do you know for sure if Python can link to
> netCDF4 with HDF5 support?   

Since nccopy can do what you need it to do (once we get it to compile, that 
is), it may be of general interest to know that there is a netCDF4 python 
wrapper that is functional, although a few features are missing (see 
http://code.google.com/p/netcdf4-python/). I've compiled and used this on 
MacOSX and it works great so far.

Sean

> If you can think of any other solution to
> this problem, please let me know.
> 
> 
> Many Thanks,
> 
> Chad
> 
> On Wed, Jun 1, 2011 at 3:03 PM, Unidata netCDF Support
> <address@hidden> wrote:
> > Hi Chad,
> 
> 
> 
> Iatest ubuntu 11.0.4, just downloaded and installed las week.  Here is
> the ouput you requested:
> 
> address@hidden:~$ echo $SHELL
> /bin/bash
> address@hidden:~$ ls -la /bin/sh
> lrwxrwxrwx 1 root root 4 May 25 21:07 /bin/sh -> dash*
> address@hidden:~$
> 
> I am not sure if I should
> 
> 
> On Wed, Jun 1, 2011 at 3:03 PM, Unidata netCDF Support
> <address@hidden> wrote:
> > Hi Chad,
> >
> > It seems as though netCDF is still having issues finding the Intel libs. 
> > First, which version of Ubuntu are you running? Second, could you send me 
> > the output from the following two commands:
> >
> > 1) echo $SHELL
> >
> > 2) ls -la /bin/sh
> >
> > Thanks!
> >
> > Sean
> >
> >> Hi Sean,
> >>
> >> I did as you suggested. ÂI cleared all the shell environmental
> >> variables and used
> >> source /opt/intel/bin/iccvars.sh intel64
> >> source /opt/intel/bin/ifortvars.sh intel64
> >>
> >> The configure and make seemed to go ok, but when I ran "make check" it
> >> failed 4 out of 5 of the tests.
> >>
> >> I made log files of each stage and attached them to this email for you
> >> to examine. ÂDo you think gc/gortran would work better or stay with
> >> intel on ubuntu? ÂOthers here at ASU reported better success with
> >> intel compilers, which is why I am using them.
> >>
> >>
> >> Thanks,
> >>
> >> Chad
> >>
> >>
> >> On Tue, May 31, 2011 at 1:00 PM, Unidata netCDF Support
> >> <address@hidden> wrote:
> >> > Greetings Dr. Coulliette!
> >> >
> >> >> Hello,
> >> >>
> >> >> My name is Dr. Chad Coulliette. ÂI am working with Professor Alex
> >> >> Mahalov at Arizona State University. ÂI have been trying to compile
> >> >> netCDF on Ubuntu Linux 64-bit. ÂThe hardware is a MacBook Pro with a
> >> >> Intel Duo Core 64-bit processor. ÂI want to compile and use WRF, but
> >> >> need netCDF first. ÂI have netCDF installed as a package using
> >> >> synaptic, but I suspect there is something deficient about it, so we
> >> >> have been trying to compile and install netCDF from source code. ÂI
> >> >> have netCDF-4.1.2 and have tried with both GNU compilers and Intel
> >> >> compilers. ÂThe GNU compilers seem to compile ok....no errors during
> >> >> make, but when I run "make check" it finds problems, and the message
> >> >> actually says to contact this email address.
> >> >
> >> > From looking through the make-gcc.log, you seem to be using the Intel 
> >> > fortran compiler `ifort` along side the gcc `cc` compiler - this is 
> >> > because .configure could not find any other fortran compiler (i.e. 
> >> > gfortran) in your $PATH. The error you are getting, as indicated in the 
> >> > make-test-gcc.log file, is due to problems finding the Intel shared 
> >> > objects. This is probably because when you building with a GNU 
> >> > environment in mind and so you didn't source ifortvars.sh. If you want 
> >> > to go the GNU route, try installing gfortran .
> >> >
> >> >> With the Intel
> >> >> compilers, it crashes during the make. ÂI included log files of the
> >> >> configure, make and make check for the GNU compilers, and included log
> >> >> files for the configure and make for the Intel compilers.
> >> >>
> >> >> For the Intel compiler, I have been following the instructions at
> >> >>
> >> >> http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers/
> >> >>
> >> >> Are these the best compile instructions? ÂThey might be too old,
> >> >> because I noticed a complaint about the compiler flag -xT being
> >> >> depreciated. ÂI tried to take it out and run everything over, but the
> >> >> results were the same.
> >> >>
> >> >
> >> > The instructions above are for an older version of netCDF. I would check 
> >> > out the Unidata netCDF docs, which can be found here:
> >> >
> >> > http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/Building-on-Unix.html#Building-on-Unix
> >> >
> >> > These docs do not specifically look at using the Intel compiler, but it 
> >> > should give you some general reference.
> >> >
> >> > What happens if you do not set any flags by hand, but only source 
> >> > iccvars.sh and ifortvars.sh before building?
> >> >
> >> > Cheers!
> >> >
> >> > Sean Arms
> >> >
> >> >> Could you examine the log files and let me know what to do?
> >> >>
> >> >>
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Chad
> >> >>
> >> >>
> >> >
> >> >
> >> > Ticket Details
> >> > ===================
> >> > Ticket ID: YWP-403246
> >> > Department: Support netCDF
> >> > Priority: Normal
> >> > Status: Open
> >> >
> >> >
> >>
> >>
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: YWP-403246
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
> 
> 


Ticket Details
===================
Ticket ID: YWP-403246
Department: Support netCDF
Priority: Normal
Status: Open


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