What are namespaces?
A namespace in ecCodes is just a fancy word for a grouping of related keys. The following are available:
ls:This is the namespace used by the grib_ls and bufr_ls tools and has the most-commonly used keys e.g. centre, shortName, level etc
parameter:Contains keys like paramId, shortName, units which relate to the meteorological parameter
statistics: Contains keys that relate to the statistics of the data values e.g. maximum, minimum, average, standard deviation etc
time: Contains keys that describe the forecast runs e.g. forecast date, validity date, steps etc
geography: Contains keys that describe the grid geometry e.g. bounding box of the grid, number of points along a parallel etc
vertical: Contains keys that describe the levels and layers e.g. type of the level, list of coefficients of the vertical coordinate etc
mars: Contains the list of MARS (ECMWF's Meteorological Archive and Retrieval System) keywords like class, stream, type etc
Why am I not able to set the missing value in the GRIB message?
Missing values cannot be encoded in a GRIB message. The GRIB format does keep track of missing values but through the use of a bitmap It does not allow the specification of a missing value. Setting the missing value is a feature that can be used only when encoding the data values stored in a GRIB message. This of course means that is the responsibility of the user to know what missing value is meaningful to the data. A default value of 9999 is set for the missing value in the library (not the GRIB message!). That means that when retrieving the values from a message without having set the missing value key, all missing values in the data will be replaced with the default value of 9999.
A small example on the use of the missing value during encoding can be found here: grib_set_bitmap.
During decoding it is advisable to query the bitmap directly to discover missing data values. See example here: grib_iterator_bitmap
How do I detect keys whose values are missing in a BUFR message?
Each element in the data section of a BUFR can be missing. ecCodes provides a simple way for the user to check if the value of an element is missing by comparing with two constants:
These constants are available in Python, Fortran 90 and C and the user needs to compare with the appropriate constant depending on the type of the variable used. This is an example of Fortran 90 code:
How do I append messages to an existing GRIB file?
Try using grib_open_file (Fortran interface) with mode "a" instead of "w". The "a" mode means: Append to a file. Writing operations append data at the end of the file. The file is created if it does not exist.
How do I delete a message from a file?
The tools never change the input file(s). You have to create a new one without the offending message and then do a rename. E.g.
This can also be done using the grib_filter (or bufr_filter) where a more complex condition can be entered.
How do I copy a selected number of messages from a GRIB file?
Say you want to copy the first 3 messages. This can be done with:
% grib_copy -w count=1/2/3 in.grib out.grib
But it is better to write a rules file and use grib_filter:
Then run this as follows:
% grib_filter -o out.grib my.filter in.grib
Of course you can make the IF condition more complicated e.g. select a range of messages to be copied:
How can I change from second_order to simple packing?
You may be tempted to try it like this:
% grib_set -s packingType=grid_simple second_order.grib simple.grib
But this will not work and issue errors re codedValues and bitsPerValue! You need to use the repacking option as shown:
% grib_set -r -s packingType=grid_simple second_order.grib simple.grib
Also see the code example: grib_precision
Issues converting from grid_complex_spatial_differencing to simple packing?
There are GRIB messages whose packingType is "grid_complex_spatial_differencing" where the missing values are not in a bitmap but stored in the Data Section (as coded values).
In these cases conversion to simple packing can fail.
A workaround is to set the key "bitmapPresent" to 1 before the conversion. This ensures a bitmap is created for the output GRIB and the missing values correctly stored:
After the conversion, check the statistics of the input and output files to ensure correctness:
This will still work even if the input did not have any missing values.
How do I set the product definition template in a GRIB2 message?
Let's say you want your message to use the product definition template 40 (The full list is defined in Code table 4.0):
Now you can do a "grib_dump -O" to inspect the section 4 (Product definition section) of the output.grib2 file to see the new keys.
What happens when I set the packingType to "grid_jpeg" on a GRIB1 message?
Actually nothing! The JPEG packing is not supported for GRIB edition 1 but rather than fail, the library leaves the message as is. This was designed for cases where a file (or set of files) containing a mix of grib1 and grib2 messages is being processed to use JPEG encoding. We convert grib2 messages and leave the grib1 messages alone.
How do I know what the native type of a key value is?
For the moment there is no simple way of knowing what the type of a key value is. However, the library provides a function that can be used to find out what the native type of a key value is. The function, available only in the C API, is called 'grib_get_native_type'. Possible key value types are the following: undefined, long, double, string, bytes, section, label or missing. It is not possible at the moment to know if the value of a key is of type scalar or vector.
How do I use an OR condition (logical disjunction) in a "where" clause?
For example in grib_get you may want to show all messages which have level of 100, 150 or 200. The way to do this is to use the "/" (forward slash) character in the "where" clause (for the -w switch)
% grib_get -w level=100/150/200 ...
This can be combined with an "AND" condition (logical conjunction). So if I want to show all messages whose level is either 0 or 1 and whose type is "an":
% grib_ls -w level=0/1,dataType=an ...
This would be equivalent to the pseudo-code:
grib_filter/bufr_filter: How can I check if a key exists (is defined) in a message?
Easy peasy. Use the "defined" function which takes a single key name as argument. e.g.
grib_filter/bufr_filter: How do I control the format of array printing?
One can add several 'modifiers' to a key in square brackets to control number of columns, separator string and format:
c -> number of columns
F -> C-style formatting
S -> separator string
How do I know if I am dealing with a multi-field grib file?
At the moment, the only possible way of detecting if a grib file is multi-field is by using the grib tools or the API to turn the support for multiple fields in a single grib message on or off and observe the results. For example you can do a "grib_count" and compare the result with "grib_ls", in a multi-field grib file the latter will report more messages than the former.
The use of the multi-field feature is not recommended.
Why can I read certain parameters using the grib tools, but not from my program?
Your file may be encoded as a multi-field grib file. By default, grib tools have multi-field support enabled and the API disabled. Check the examples to know how to enable this feature on your program:
Confused about stepUnits?
The key stepUnits is a transient key and it is not written in the grib message. So, you cannot expect to get the same stepUnits as when you have encoded the data. By convention, when encoding, ecCodes will choose the best unit to encode the step in so that it fits the space available in the grib message. When decoding, ecCodes will return the step in hours by default.
Note: The "step" key (as well as startStep, endStep and stepRange) were added purely for the MARS system here at ECMWF and MARS only deals with steps in units of hours.
The stepUnits can only be set in the following situations:
- before encoding, in order to tell ecCodes what units are we dealing with
- when decoding, in order to tell ecCodes what units to get the step in
One can also set values in a grib message before printing its contents with tools like grib_ls and grib_get.
Confused about key types?
Some keys like shortName are strings (native type string) and it doesn't make any sense to set them as an integer or float as they are not possible values for the key.
Some keys are native type integer like perturbationNumber and you can set/get them as integer, float or string as you like.
Some keys are codetables and for them you have a code (integer) and an abbreviation (string) like for example "centre". You can set them as a string or as an integer, not as a float because there is no mapping for those keys into a float. An example is:
Some keys are concepts and they are usually strings like stepType, gridType, packingType. Again setting them as integer doesn't make any sense as they don't have any mapping as integers.
A concept is a key with a special association with other keys. Let's take shortName as an example. Its definition in the .def files is made with a long list of entries like:
this means that if you set shortName="cape" ( as a string ) ecCodes will automatically set the keys listed in curly brackets to the corresponding values.
Conversely when you get shortName, ecCodes looks for the best match of the keys listed in the full definition of shortName (not only cape) and will return "cape" only if the following are true:
in the message and there isn't a better match of keys in the list.
Again saying shortName=123 doesn't make any sense as in the context of shortName we don't need numbers.
The idea is that the user should know what to set before choosing the type to use. In the sense that the user should know the meaning of the key before setting it to a value. For this purpose we have built the documentation and I agree that we need to do a big review (with your help) of it to fix all the wrong things and to add what is missing.
There was a bit of confusion regarding the type of step and paramId for the following reason:
For me step was a string because you can have values like 24-36 which you cannot represent as numbers. In mars the step is only the endStep and therefore I had to modify ecCodes to be mars compliant. Now the step is an integer and is step=endStep. As we need a step indicating a range I have introduced stepRange which is a string and cannot be set as an integer and will never be set as an integer because it allows values like stepRange=24-36. It is true that most of the time you have stepRange=36 or stepRange=24 or another single number, but this is because in those cases you have also stepType=instant and endStep=startStep and we don't want to write stepRange=24-24 which is only redundant. We also use to write stepRange=24 when stepRange=0-24 (mars compatibility which I don't like). If you prefer to set the step as an integer instead of using a string you have starStep, endStep which are integers and they can also be set as string because it is possible to convert for example the number 24 into the string "24". Therefore you can do:
It is a concept like shortName and unfortunately in the previous version the native type for a concept was string even if the meaning of it is number. In the new version paramId is still a concept, but it has native type number. This means that it can be set as a number, but cannot be set as a string because only the numbers are valid values for paramId. You can still get it as a string because it is possible to convert a number into a string. You cannot set it as a string because it isn't always possible to convert a string into a number.
Why I cannot set negative values for the longitude in GRIB 2
GRIB 1 regulates that the longitude can be in either [-180, 180] or [0,360], GRIB 2 regulates that the longitude can only be in the interval [0,360]. ecCodes does comply with these regulations and in the case of GRIB 2, it will scale the longitude to fall in the interval [0,360]. ecCodes does not offer an edition independent view of the longitude because of the uncertainty brought by GRIB 1, where you do not know what interval a longitude is in exactly.
For GRIB edition 1, why does the centre change when I set stepType?
This happens for stepType of "max" and "min". Unfortunately edition 1 does not support maximum and minimum in its "Time Range Indicator" table (Table 5). So we invented our own centre-specific combination to support this. There is no such issue in GRIB edition 2.
Why is the "bottomLevel" of Soil Temperature level 4 reported as MISSING?
The parameter 236 (Soil temperature level 4) specifies that its top level is 100cm and its bottom level is 289cm so to encode this information in GRIB edition 1 we would need to set the value of the key "bottomLevel" to 289 (octet 12 in section 1. See GRIB edition 1 section 1 spec).
However since this key is only one octet it cannot accommodate any value larger than 255! Therefore it is not possible to encode levels larger than that value in GRIB1 so we simply set all the bits to 1 (which means MISSING).
GRIB edition 2 addresses this shortcoming.
Possible GOTCHA with wave spectra fields
In the wave spectra, all frequency/direction components with values less than some (field-dependent) threshold are set to 'missing' when encoded in GRIB; values larger than this threshold are encoded as log10 of the actual value to an accuracy of 9 bits (bitsPerValue=9).
To interpret these values correctly, the user should do:
What environment variables are there?
Here are the environment variables that are used by ecCodes:
ECCODES_DEFINITION_PATH: Set to the list of directories containing the set of definition files you want to use instead of the default one.
ECCODES_SAMPLES_PATH: Set to the list of directories containing the set of sample files you want to use instead of the default one.
ECCODES_DEBUG: If set to -1, will enable brief debug-level logging messages to be displayed by the library. If set to 1, you will get very verbose output.
ECCODES_FAIL_IF_LOG_MESSAGE: If set to 1, will cause the library to exit when an error or warning is encountered.
ECCODES_IO_BUFFER_SIZE: Defines the size in bytes of the buffer used in the IO calls from Fortran and in the tools.
ECCODES_NO_ABORT: When set to 1 it causes ecCodes not to abort execution on failing asserts.
ECCODES_GRIB_WRITE_ON_FAIL: When set to 1 it will write the last processed GRIB message to a file named $PID_$FILEID_error.grib on failure in a fortran function used without the return code argument.
ECCODES_GRIBEX_MODE_ON: When set to 1 it will enable the GRIBEX compatibility mode and ecCodes will produce GRIB messages readable by GRIBEX.
ECCODES_GRIB_IEEE_PACKING: Accepted values 32 or 64 for 32 or 64 bits IEEE floating point respectively. The GRIB message produced will contain data written in IEEE floating point without packing.
ECCODES_LOG_STREAM: This controls the output stream for warning/error messages. Accepted values are "stdout" or "stderr" (default is stderr)
ECCODES_BUFRDC_MODE_ON: This is for BUFR decoding functionality. When set to 1 it will enable the BUFRDC compatibility mode (e.g. we tolerate problems like wrong data section length)
ECCODES_BUFR_SET_TO_MISSING_IF_OUT_OF_RANGE:This is for BUFR encoding functionality. When set to 1 ecCodes will allow out-of-range values (BUFRDC compatibility mode). In this mode encoding does not fail and a missing value is encoded in place of the out-of-range value.
If the library is built with only one of the jpeg libraries (jasper or openjpeg) it will work without any environment variable. If ecCodes is built with both, then you have always to link both and you can switch from one to the other with the variable:
This env. variable was only for debugging/development purposes, but it can be used by users. There is also another variable ECCODES_GRIB_DUMP_JPG_FILE=filename which provides a dump of the JPEG image on a separate file, again for debugging purposes.
How can I remove the PV array (list of vertical coordinates)?
This can be done by setting the key "deletePV" as shown:
% grib_set -s deletePV=1 in.grib out.grib
Which is in fact equivalent to setting the number of coordinate values to 0 and clearing the "pv" array:
% grib_set -s PVPresent=0,NV=0 in.grib out.grib
Failure setting key changeDecimalPrecision
If you issue the command "grib_set -s changeDecimalPrecision=1 spectral.grib output", you can get an error
ECCODES ERROR : COMPLEX_PACKING : Cannot compute binary_scale_factor
This is because that key does not work for spectral_complex! So first check the packingType key.
grib_compare: Is there an alternative to blacklisting keys?
For example if you are interested in comparing the differences between the data values of two GRIB files, you can blacklist (exclude) certain keys which show up in the comparison e.g.
You can also include what you want to compare rather than exclude with a blacklist. E.g.
Now only the values array is compared. Now you can use the -P, -R and -A flags to control the tolerances.
What are the GRIB keys numberOfDataPoints, numberOfValues and numberOfMissing?
numberOfDataPoints: This is the total number of points on the grid and includes missing as well as 'real' values
numberOfValues (=numberOfCodedValues): These two keys are the same (one is an alias for the other). This is the number of 'real' values in the field and excludes the number of missing ones
numberOfMissing: You guessed it. The number of missing values in the field
So you can write the equation:
numberOfDataPoints = numberOfCodedValues + numberOfMissing
BUFR: How can I set keys for a subset?
You have to use the "by rank" syntax i.e. "
#n#key". For example using the bufr_filter rules:
This sets the 4th instance of the key "airTemperature" to 3.14.
Note: Although you can use the "by condition" syntax for getting values of keys, this method cannot be used for setting such keys i.e. The following will not work:
Also see Setting keys by rank.
How can I multiply a GRIB field values by a constant?
One way is to use grib_set with the key "scaleValuesBy". Let's say you have a field in orig.grib whose values you want to multiply by 2.1. First check the original data value statistics:
You could have also checked the statistics by "grib_ls -n statistics orig.grib".
Now let's scale all values up by a factor of 2.1:
And check the new values after the multiplication:
For adding or subtracting a constant, you can use the key "offsetValuesBy".
grib_to_netcdf: Why do I get the error "Wrong number of fields... Try using the -T option"?
You try to retrieve data from the ECMWF data archive in NetCDF format but the retrieval fails with this message:
This can occur if:
- you request forecast data in NetCDF format
- your data request contains overlapping "time"+"step" specifications
For example, for the ERA-Interim dataset there are two daily forecasts (00:00, 12:00), with 3-hourly forecast steps. So one could specify in a data retrieval script:
With the above specification you get data for the following validity times:
- time 00:00 + step 3 → validity time 2016-12-01, 03:00
- time 00:00 + step 6 → validity time 2016-12-01, 06:00
- time 00:00 + step 9 → validity time 2016-12-01, 09:00
- time 00:00 + step 12 → validity time 2016-12-01, 12:00
- time 00:00 + step 15 → validity time 2016-12-01, 15:00
- time 12:00 + step 3 → validity time 2016-12-01, 15:00
- time 12:00 + step 6 → validity time 2016-12-01, 18:00
- time 12:00 + step 9 → validity time 2016-12-01, 21:00
- time 12:00 + step 12 → validity time 2016-12-02, 00:00
- time 12:00 + step 15 → validity time 2016-12-02, 03:00
In this example you get two data values at the same validity time 2016-12-01, 15:00. The NetCDF format does not support multiple data values at a single time, hence the creation of the output NetCDF file fails, triggering the error message.
The solution is:
- Retrieve the data in its native
Then convert the data from GRIB to NetCDF format using the grib_to_netcdf tool with the -T option. format, which supports multiple data values at any one validity time.
- Retrieve data for each forecast "time" separately, for example for ERA-Interim:
- first with time = 00:00 and all required steps
- then with time = 12:00 and all required steps
Is ecCodes thread-safe?
Yes, but the package needs to be built with either Pthreads (POSIX Threads) or OpenMP support. To do so, you need to make sure that one of the following options is present in your cmake configure command.
These options are mutually exclusive.
Note: there are known thread safety issues when GRIB multi-field support is enabled.
Building on High Performance Computer systems
Some HPC batch systems have a different hardware architecture for their login (or frontend node) to the batch node, but the frontend compilation system is targeted at the batch nodes. This is known as cross-compilation. If this is the case you may see failures in the 'make check' stage because the checks, although compiled for the backend batch nodes, are being run on the frontend nodes and therefore may not work correctly. If this is the case on your system, we recommend using a batch job to do the 'cmake; make; make check; make install' steps.
In some cases, the batch system cannot be used for compilation at all. In this case, you have to compile on the frontend but without extra flags 'configure' will assume the build is for the frontend. You can make use of the --host option to ensure the build is correct for the architecture of the batch system. Again though, the tests will fail, a small serial batch job is recommended to make sure ecCodes is installed correctly.
Note if you plan on using ecCodes in your own software that runs on the frontend nodes you will need to install ecCodes twice; one for the batch system and again for the frontend system.
If you have any questions installing ecCodes in this type of environment, please contact: firstname.lastname@example.org for assistance.
How do I create my own local GRIB definitions?
Can I use my own GRIB/BUFR sample files?
Yes. You can add your own samples, either to the installation directory (if you have access) or by defining the environment variable
ECCODES_SAMPLES_PATH. The latter works like a normal Unix PATH where you have a colon separated list of directories for ecCodes to search when a sample is required.
One important requirement is that the sample file must have the extension "
To set this environment variable properly we have first to find the samples directory used by ecCodes. For this we can use the tool
codes_info which provides some configuration information about the library:
Let's say you place your own sample files in
/home/eccodes/samples. We have to set the environment variable ECCODES_SAMPLES_PATH as follows:
Another cool trick is to use the codes_info tool itself for this purpose, rather than hard-coding the installation path with a specific version:
Refer to the codes_info help page for its options.
Now when you refer to a sample file (e.g. the C function
codes_bufr_handle_new_from_samples), at run-time ecCodes will search for it in the first directory and if it is not there, it will search in the second directory (and so on)
How can I get verbose output when running tests?
When you run the tests via CMake (which actually runs ctest), you are only told if it passed or failed. After a failure you want to re-run the test and see all of what the test was doing.
In order to do this just set the environment variable ECCODES_TEST_VERBOSE_OUTPUT to 1.
So for example you run the tests first:
Now let's assume you see the test "t_bufr_ls" has failed. Now set the environment variable and re-run just that test (not everything)
ctest -VV -R t_bufr_ls
You need the -VV switch as well to tell ctest not to suppress its output. The presence of the environment variable will do a "set -x" inside the running shell script so you get to see everything it did.
How can I set the verbosity level to see debug output?
There is an environment variable called ECCODES_DEBUG: If set to -1, it will enable brief debug-level logging messages to be displayed by the library. If set to 1, you will get very verbose output.
For example let's say we want to change the grid type of a GRIB message to be "Lambert Conformal":
Here the debugging output tells us setting the key "gridType" (whose type is "string") causes a low-level key "gridDefinitionTemplateNumber" (whose type is "long" i.e. integer) to be 30 (Also see http://apps.ecmwf.int/codes/grib/format/grib2/templates/3/30).
Another example showing what happens when you set the "shortName":
Now you can see the cascading effect of setting a key which causes others to be set. Try it when you convert from GRIB1 to GRIB2 to see how much happens behind the scenes!
Where can I find ecCode's version history?
The ecCodes version history is here.
Note: ecCodes is an evolution of GRIB-API. For the version history of GRIB-API please see here