Frequently Asked Questions

How to solve problems with a short variable?

I have problems with a felt-file with a variable of type 'short'. fimex abborts with

change in scaling-factor for parameter: 31,2,1000 consider using float or double datatpye

What should I do?

While the netcdf-format allows for only 1 scaling-factor per variable, the felt-format can have a scaling-factor per 2d-slice per variable (that are level*time scaling-factors). You should change the type of the variable and its _FillValue attribute from short to float in the file felt2nc_variables.xml.

If you want to save disk-space, and you know that all data of the variable can be subscribed sufficiently with a packed short data-array, use the ncml-configuration as follows:

<?xml version="1.0" encoding="UTF-8"?>
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2 ncml-2.2.xsd ">
<!-- change the type of a variable, repack -->
<variable name="precipitation_amount" type="short">
<attribute name="_FillValue" value="-32767" type="short" />
<attribute name="scale_factor" value="0.1" type="float" />
<attribute name="add_offset" value="0" type="double" />
</variable>
</netcdf>

In this example, the precipitation will be described with an accuracy of 0.1mm and up to 3276.7mm. The ncml-configfile will be applied right before writing with the --ncml.config=....ncml fimex-option.

What does this error-message mean?

CDMException: Felt_File_Error: FeltError: cannot read gridParameters: no Felt_Array2 available

The config-file for felt-files must at least define 1 existing parameter in the corresponding felt-file. Update your config-file (e.g. felt2nc_variables.xml) with the output from the felt-index, which can be read by felt-tools like rfinh.

CDMException: Can't open HDF5 attribute

This error-message is unfortuneatly very misleading. In many cases, the _FillValue type does not correspond to the variables type. Please check your config-file. Unless really required, it's recommended to remove the _FillValue.

How can I read grib-message which are split over several files?

since fimex 0.40.1, it is possible to give multiple optional file-sources:

fimex --input.file=/opdata/lameps/mle/eceps_201211260000_ens00.mars \
--input.type=grb --input.config=/home/heikok/Programme/MetSis/Fimex/share/etc/cdmGribReaderConfig.xml \
--input.optional=/opdata/lameps/mle/eceps_201211260000_ens01.mars \
--input.optional=/opdata/lameps/mle/eceps_201211260000_ens02.mars \
--output.file=eceps.nc4

How to use fimex as opendap-client?

Install netcdf with integrated dap-support

Prerequisites

netcdf4 (4.1.1) from unidata

curl library: sudo apt-get install libcurl4-gnutls-dev (on ubuntu hardy)

make sure to remove the libnetcdf4-dev package (on ubuntu hardy): apt-get remove libnetcdf4-dev

Build

Configuring, without HDF-file support (can be added if desired). Important: include dap-support via curl; build shared libraries (libtool autodetect dependencies)

./configure --prefix=/usr/local/netcdf4.1.1 --enable-dap --with-curl-config=/usr/bin/curl-config --enable-shared --disable-static
make -k # there might be errors building the man-pages depending on tex-installation
make check
make -k install

Fimex and OpENDAP

Build

./configure --with-netcdf=/usr/local/netcdf4.1.1

Running an extraction from opendap

fimex --input.file=http://thredds.met.no/thredds/dodsC/topaz/dataset-topaz3-arc-myocean-be \
--input.type=netcdf \
--output.type=netcdf \
--output.file=test.nc \
\
--extract.selectVariables=time \
--extract.selectVariables=x \
--extract.selectVariables=y \
--extract.selectVariables=depth \
--extract.selectVariables=longitude \
--extract.selectVariables=latitude \
--extract.selectVariables=temperature \
\
--extract.reduceTime.start=2010-10-05 \
--extract.reduceTime.end=2010-10-07 \
\
--extract.reduceToBoundingBox.south 55.0 \
--extract.reduceToBoundingBox.north 80.0 \
--extract.reduceToBoundingBox.east 20.0 \
--extract.reduceToBoundingBox.west -5.0

Why takes linking with ''g++ -g'' ages?

This happens with older versions of gcc, seen with 3.3 on debian sarge.

Use -gstabs or -ggdb instead of -g. For debugging, this is better suited to c++ code and works with the GNU utils and most other debugger, too. (But unfortunately not with /valgrind/.