Changeset 5b0708b in flex_extract.git
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- Aug 20, 2019, 2:52:30 PM (5 years ago)
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README.md
r3fc6232 r5b0708b 1 # flex_extract 1 # flex_extract 2 2 3 `flex_extract` is a software package to support retrieving meteorological fields from the E CMWF MARS archiveas input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system.3 `flex_extract` is a software package to support retrieving meteorological fields from the European Centre for Medium-Range Weather Forecasts' (ECMWF) Meteorological Archival and Retrieval System (MARS) as input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system. 4 4 5 `FLEXPART` (“FLEXible PARTicle dispersion model”) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes. 6 7 `FLEXPART` expects GRIB files containing a set of meteorological fields separated by time. The format of these file names look like: `<prefix>YYMMDDHH`, where `<prefix>` can be defined by the user (usually it should be limited to "2" characters because of further processing reasons). 8 9 The MARS (Meteorological Archival and Retrieval System) archive from ECMWF saves a number of different data sets, such as the ERA-Interim and ERA 5 reanalysis and the daily operational data. More can be found here: <https://confluence.ecmwf.int/display/UDOC/MARS+content> 10 11 To define the data set and its composition of, e.g. time, field types and paramaters, `flex_extract` uses `CONTROL` files to set a number of MARS keywords and `flex_extract` specific control parameters. Detailed description can be found in the documentation and a set of example `CONTROL` files are also distributed with `flex_extract`. 5 `FLEXPART` (“FLEXible PARTicle dispersion model”, http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes. 12 6 13 7 8 ## Installation and Usage 14 9 10 There is a documentation within the flex_extract directory which contain all information necessary. 11 Please open the file Documentation/html/index.html in your prefered browser to learn about installation and usage of flex_extract. 15 12 13 ## Project website 16 14 17 ## ECMWF DATA 15 https://www.flexpart.eu/wiki/FpInputMetEcmwf 18 16 17 ## Authors 19 18 20 There are two modes for accessing ECMWF data sets: the **_full access_** and the **_public access_** mode. 21 A description of these two modes and links to the available data sets is available here: https://www.ecmwf.int/en/forecasts/datasets/archive-datasets 19 Anne Philipp, Leopold Haimberger and Petra Seibert 22 20 23 #### Important note for public users 21 ## License 22 (C) Copyright 2014-2019. 24 23 25 If you want to extract public data sets from the ECMWF servers you first have to register at the ECMWF. Do this by following the instructions at: https://software.ecmwf.int/wiki/display/WEBAPI/Access+MARS 24 SPDX-License-Identifier: CC-BY-4.0 26 25 27 Afterwards you **_need to accept the licenses_** of the data sets you want to extract: 28 29 https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets 30 31 Now your able to use `flex_extract` in public mode (command line parameter "*--public=1*"). 32 33 34 35 36 37 38 ## Application modes 39 40 There are 4 different modes of running `flex_extract` : 41 1. Remote (*): ***flex_extract*** is installed and executed directly on the ECMWF Linux member state server ecgate. Users have to be a registered member-state user. 42 2. Gateway (*): ***flex_extract*** is installed on a local machine and the scripts are submitted to ECMWF 43 computer facilities via a member-state gateway server. Users have to be a registered member-state user. 44 3. Local member state (*): ***flex_extract*** is installed and executed on a local machine. Users have to be a registered member-state user. 45 4. Local public (**): ***flex_extract*** is installed and executed on a local machine. Users do not have to be a member-state user. A normal registration at the ECMWF website is enough. 46 47 *(\*) To get a ms (member-state) user access, users have to be a resident of a [member state](https://www.ecmwf.int/en/about/who-we-are/member-states) and have to contact their national meteorological center for granting access.* 48 49 *(\*\*) To get a public user account, the user can just register at the ECMWF website following the instructions [here](https://apps.ecmwf.int/registration/)!* 50 51 52 53 54 <!-- 55 [![NPM Version][npm-image]][npm-url] 56 [![Build Status][travis-image]][travis-url] 57 [![Downloads Stats][npm-downloads]][npm-url] 58 59 60 ![](header.png) 61 --> 62 63 64 65 66 67 68 69 70 ## Installation 71 72 73 74 ### Requirements 75 76 77 To run the python part of flex_extract a [Python 3](https://docs.python.org/3/) environment is needed.<br> 78 We tested `flex_extract` with a normal Linux Python package distribution and Anaconda Python. 79 * [Python3](https://www.python.org/downloads/) or [Anaconda Python 3](https://www.anaconda.com/distribution/#download-section) 80 * [numpy](http://www.numpy.org/) 81 * [ecmwf-api-client](https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home) 82 * [cdsapi](https://cds.climate.copernicus.eu/api-how-to) 83 * [genshi](https://genshi.edgewall.org/) 84 * [eccodes for python](https://packages.debian.org/sid/python3-eccodes) (e.g. manually from source or from distribution package) or [eccodes for conda](https://anaconda.org/conda-forge/eccodes) 85 86 For the Fortran part of flex_extract we need: 87 88 * [gfortran](https://gcc.gnu.org/wiki/GFortran) 89 * [fftw3](http://www.fftw.org) 90 * [eccodes](https://software.ecmwf.int/wiki/display/ECC) 91 * [emoslib](https://software.ecmwf.int/wiki/display/EMOS/Emoslib) 92 93 94 95 ### Prepare the environment 96 97 98 ##### On ecgate 99 100 All libraries and software packages needed by flex_extract are already installed on the ECMWF servers. They can be loaded by a module management system. In general, `flex_extract` is managing the correct settings of modules if you submit to the `ecgate` or `cca` queue. If the user works directly on ecgate, he has to assure that a Python3 environment is loaded before starting `flex_extract`. 101 102 ```bash 103 # on ecgate 104 module unload python 105 module load python3 106 ``` 107 108 ##### On a local and a gateway machine 109 110 The easiest way to install all required packages is to use the package management system of the Linux distribution. If you have any problems with this method, you can ask for support or just try to install specific packages from source. 111 112 _We are not describing the installation of a gateway server since this is out of scope. Please see [here](https://confluence.ecmwf.int/display/ECAC/ECaccess+Home)!_ 113 114 On a Linux Debian or Ubuntu system: 115 116 ```sh 117 # on your local system, do: 118 sudo apt -PV install python3 119 sudo apt -PV install pip3 120 sudo apt -PV install gfortran 121 sudo apt -PV install fftw3-dev 122 sudo apt -PV install libeccodes-dev 123 sudo apt -PV install libemos-dev 124 sudo apt -PV install python3-eccodes 125 pip3 install cdsapi 126 pip3 install ecmwf-api-client 127 pip3 install genshi 128 pip3 install numpy 129 ``` 130 131 Afterwards, check the availability of the python packages: 132 ```python 133 # check in python3 console 134 import eccodes 135 import cdsapi 136 import ecmwfapi 137 import genshi 138 ``` 139 Additionally, start simple test retrievals for both API's: 140 ```python 141 #!/usr/bin/env python3 142 from ecmwfapi import ECMWFDataServer 143 144 server = ECMWFDataServer() 145 146 server.retrieve({ 147 'stream' : "oper", 148 'levtype' : "sfc", 149 'param' : "165.128/166.128/167.128", 150 'dataset' : "interim", 151 'step' : "0", 152 'grid' : "0.75/0.75", 153 'time' : "00/06/12/18", 154 'date' : "2014-07-01/to/2014-07-31", 155 'type' : "an", 156 'class' : "ei", 157 'target' : "download_ecmwfapi.grib" 158 }) 159 ``` 160 ```python 161 #!/usr/bin/env python 162 import cdsapi 163 c = cdsapi.Client() 164 c.retrieve("reanalysis-era5-pressure-levels", 165 { 166 "variable": "temperature", 167 "pressure_level": "1000", 168 "product_type": "reanalysis", 169 "year": "2008", 170 "month": "01", 171 "day": "01", 172 "time": "12:00", 173 "format": "grib" 174 }, 175 "download_cdsapi.grib") 176 ``` 177 178 179 180 ### Some important notes for a manual installation process: 181 - Use the same compiler and compiler version for all libraries and the Fortran program of `flex_extract`. 182 - Don't forget to set all library paths to the `LD_LIBRARY_PATH` variable. 183 - Don't forget to adapt the makefile for the Fortran program. 184 - Please follow the instructions on the websites of the libraries. 185 186 For the manual installation of these libraries it is useful to consider the official documentation (and also the hints from the ECMWF) rather than trying to explain every detail in here. Nevertheless, if you have to do the manual installation, we recommend doing the installation in the following order (see links to the libraries in the table above): 187 188 189 1. Read `Emoslib` [installation instructions](https://confluence.ecmwf.int/display/EMOS/Installation+Guide). 190 2. Read [ECMWF blog about gfortran](https://software.ecmwf.int/wiki/display/SUP/2015/05/11/Building+ECMWF+software+with+gfortran). 191 3. [Install `FFTW`](http://www.fftw.org/). 192 4. [Install `EMOSLIB`](https://confluence.ecmwf.int/display/EMOS/Emoslib) (Hint: Apply make 2 times! One time without any options and one time with single precision option). 193 5. [Install `ECCODES` from source](https://confluence.ecmwf.int/display/ECC/ecCodes+installation) from source (for python and fortran). `ECCODES` is downward compatible with `GRIB_API`. `GRIB_API` support was expire at the end of 2018. 194 6. For local usage and as public user, install the ECMWF key by following step 1 [here](https://confluence.ecmwf.int/display/WEBAPI/Access+ECMWF+Public+Datasets). 195 7. [Install `ECMWF_Web API.`](https://confluence.ecmwf.int/display/WEBAPI/Access+ECMWF+Public+Datasets#AccessECMWFPublicDatasets-python) 196 8. [Install `CDS API.`](https://cds.climate.copernicus.eu/api-how-to) 197 9. Check `LD_LIBRARY_PATH `environment variable if it contains all paths to the libs. 198 10. Do some tests as listed above. 199 200 201 202 203 204 205 ### Installation of `flex_extract` 206 207 208 To install `flex_extract` you have to first decide which application mode you want to use and then, if you choosed one of the local version, edit the corresponding Makefile for the Fortran programm. Makefiles for ECMWF server are already fixed. 209 For example: 210 ```bash 211 cd flex_extract_v7.1/source/fortran 212 nedit Makefile.local.gfortran 213 ``` 214 Edit the pathes to the ECCODES library on your local machine in this file: 215 ```sh 216 ECCODES_INCLUDE_DIR=/usr/lib/ 217 ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm 218 ``` 219 Now go to the root directory and open the setup.sh file: 220 ```bash 221 cd ../../ 222 nedit setup.sh 223 ``` 224 In this file edit the labelled block for "AVAILABLE COMMANDLINE ARGUMENTS TO SET" 225 ```bash 226 # ----------------------------------------------------------------- 227 # AVAILABLE COMMANDLINE ARGUMENTS TO SET 228 # 229 # THE USER HAS TO SPECIFY THESE PARAMETER 230 # 231 TARGET='ecgate' 232 MAKEFILE='Makefile.gfortran' 233 ECUID='uid' 234 ECGID='gid' 235 GATEWAY='server.example.edu' 236 DESTINATION='example@genericSftp' 237 FLEXPARTDIR="" 238 JOB_TEMPLATE="job.template" 239 CONTROLFILE="CONTROL_EA5.testgrid" 240 ``` 241 242 243 244 245 246 247 248 249 250 ``` 251 ./setup.sh 252 ``` 253 254 255 On ECMWF servers a makefile named "Makefile.gfortran" is already provided in the "source/fortran"-directory. It is also the default makefile, so that the parameter does not have to be set when calling "install.py". 256 257 If the ***flex_extract*** is to be installed within a ***FLEXPART*** environment it should be called with the parameter `flexpart_root_scripts` to let ***flex_extract*** know about the path to ***FLEXPART***. 258 259 The installation was successful if the compilation of the Fortran program ``CONVERT2`` didn't fail and is displayed in the terminal. 260 261 #### Installation using a gateway server (***flex_extract*** mode 2 only) 262 263 --- 264 265 If the user has a gateway server and the Ecaccess toolkit available, ***flex_extract*** can be installed such that it is executed on the local machine and a job script is submitted to the ECMWF server. The final ***FLEXPART*** input files are then send back via the Ecaccess command line tool "ectrans". To use this tool, the user has to create an association directly on the local gateway server via the localhost ecaccess.ecmwf.int and provide the association name as the "destination"-parameter when calling "install.py". 266 267 The gateway server has to be registered at ECMWF. For information about a gateway server see: 268 - https://software.ecmwf.int/wiki/display/ECAC/Releases+-+Gateway+package 269 - and the Software Installation Plan (SIP.pdf) in the docs/ directory. 270 271 Afterwards ***flex_extract*** can be installed with the following command: 272 ``` 273 ./install.py --target=local --makefile=Makefile.gfortan --ecuid=<id> --ecgid=<gid> --gateway=<servername> --destination=<destinationname> 274 ``` 275 276 If the installation was successful the user gets an email with a success note! 277 278 279 280 281 ## How to use flex_extract 282 283 A few motivating and useful examples of how your product can be used. Spice this up with code blocks and potentially more screenshots. 284 285 _For more examples and usage, please refer to the [Wiki][wiki]._ 286 287 288 289 290 This section provides the absolut basics on how ***flex_extract*** is to be used. For more information about possible settings, performance, parameter combinations and so one, the user is referred to the SIP.pdf and SUT.pdf documents and the www.flexpart.eu community website. It is also possible to ask for help by writing to the ***FLEXPART*** user email list (registration needed) or by creating a ticket on the community website. 291 292 #### CONTROL file 293 294 ***flex_extract*** is controlled by providing "CONTROL"-files with a list of parameter settings. These parameter are described in detail in the *Software User Tutorial (SUT.pdf)*. 295 The "CONTROL"-files specifies which ECMWF data set is to be retrieved, the time and spatial resolution, the format of the grib file and many more. In the `python` directory are some example `CONTROL` files for the different data sets and access modes which can be retrieved with ***flex_extract***: 296 297 ``` 298 CONTROL_CERA 299 CONTROL_CV 300 CONTROL_EA5.public 301 CONTROL_FC.pure 302 CONTROL_OD.highres.gauss 303 CONTROL_CERA.public 304 CONTROL_EA5 305 CONTROL_EI.global 306 CONTROL_FC.twiceaday 307 CONTROL_OPS.4V 308 CONTROL_CF 309 CONTROL_EA5.highres 310 CONTROL_EI.public 311 CONTROL_OD.highres.eta 312 CONTROL.temp 313 ``` 314 315 For information about all the possible parameter settings and explanation, please see the SUT.pdf document in the `docs/` directory. 316 317 `CONTROL`-files with a `.public` ending is usable for the public access mode. The main difference is the parameter ``dataset`` which explicitly specifies the public data sets. Additionally, not all meteorological fields and times were archived in the public data sets and are considered in the public `CONTROL`-files. 318 319 #### Python scripts 320 321 * `submit.py` 322 323 This is the main program for doing both, retrieving ECMWF data and generating the ***FLEXPART*** input files. It combines the two sub-programs `getMARSdata.py` and `prepareFLEXPART.py` which can also be run by themselves for debugging purposes. 324 Use the `-h` option to get the parameter options: 325 326 ``` 327 usage: submit.py [-h] [--start_date START_DATE] [--end_date END_DATE] 328 [--date_chunk DATE_CHUNK] [--basetime BASETIME] [--step STEP] 329 [--levelist LEVELIST] [--area AREA] [--inputdir INPUTDIR] 330 [--outputdir OUTPUTDIR] 331 [--flexpart_root_scripts FLEXPART_ROOT_SCRIPTS] [--ppid PPID] 332 [--job_template JOB_TEMPLATE] [--queue QUEUE] 333 [--controlfile CONTROLFILE] [--debug DEBUG] [--public PUBLIC] 334 335 Retrieve FLEXPART input from ECMWF MARS archive 336 337 optional arguments: 338 -h, --help show this help message and exit 339 --start_date START_DATE 340 start date YYYYMMDD (default: None) 341 --end_date END_DATE end_date YYYYMMDD (default: None) 342 --date_chunk DATE_CHUNK 343 # of days to be retrieved at once (default: None) 344 --basetime BASETIME base such as 00/12 (for half day retrievals) (default: 345 None) 346 --step STEP steps such as 00/to/48 (default: None) 347 --levelist LEVELIST Vertical levels to be retrieved, e.g. 30/to/60 348 (default: None) 349 --area AREA area defined as north/west/south/east (default: None) 350 --inputdir INPUTDIR root directory for storing intermediate files 351 (default: None) 352 --outputdir OUTPUTDIR 353 root directory for storing output files (default: 354 None) 355 --flexpart_root_scripts FLEXPART_ROOT_SCRIPTS 356 FLEXPART root directory (to find grib2flexpart and 357 COMMAND file) Normally flex_extract resides in the 358 scripts directory of the FLEXPART distribution 359 (default: None) 360 --ppid PPID Specify parent process id for rerun of prepareFLEXPART 361 (default: None) 362 --job_template JOB_TEMPLATE 363 job template file for submission to ECMWF (default: 364 job.temp) 365 --queue QUEUE queue for submission to ECMWF (e.g. ecgate or cca ) 366 (default: None) 367 --controlfile CONTROLFILE 368 file with control parameters (default: CONTROL.temp) 369 --debug DEBUG Debug mode - leave temporary files intact (default: 0) 370 --public PUBLIC Public mode - retrieves the public datasets (default: 371 0) 372 ``` 373 374 *Optional arguments are listed in squared brackets.* 375 376 377 * `getMARSdata.py` 378 379 This program retrieves the ECMWF data from ECMWF servers using [ECMWF WebApi](https://software.ecmwf.int/wiki/display/WEBAPI/ECMWF+Web+API+Home) or [Mars](https://software.ecmwf.int/wiki/display/UDOC/MARS+user+documentation), depending on your user status and your selection of the running mode. It requires the `ECMWF WebApi` python library (see Requirements below). Check with your local IT group as it may be already available. 380 381 382 * `prepareFLEXPART.py` 383 384 This program generates FLEXPART input files from the retrieved meteorological fields. It requires python interface to grib_api or eccodes and the Fortran program `CONVERT2` (located in `src` directory). `CONVERT2` needs a namelist which is generated from the python program. 385 386 387 #### execute flex_extract locally (member-state user) 388 389 Almost every command line parameter for the `submit.py` script call has a default value or is read from the specified `CONTROL` file. 390 Therefore, for a local extraction of ERA-Interim data as a member-state user the script can be called simply by passing a `CONTROL` file and a starting date with the following command: 391 ``` 392 ./submit.py --controlfile=CONTROL_EI.global --start_date=20101201 393 ``` 394 If there was just a starting date without an end date, ***flex_extract*** retrieves just this one day of meteorological data. The `CONTROL_EI.global` file has a set of default values which needs to be adjusted regarding users needs. It is also possible to set the dates within the `CONTROL`-file instead of passing it via command line parameter. 395 396 397 #### execute flex_extract locally (public user) 398 399 As a public user one has to use the `CONTROL` file with the `.public` extension and the parameter `public`: 400 ``` 401 ./submit.py --controlfile=CONTROL_EI.public --start_date=20101201 --public=1 402 ``` 403 Otherwise, except of the different data available, the usage of ***flex_extract*** is the same as for member-state users. 404 405 #### execute flex_extract via gateway server 406 407 If ***flex_extract*** was installed via a gateway server and a file "*ECMWF_ENV*" is available in the ``python``-directory, the ``submit.py`` script can be called with the `--queue` option. A job script is then prepared and submitted to the ECMWF server (in this case, "ecgate") . 408 409 ``` 410 ./submit.py --queue=ecgate --controlfile=CONTROL_EI.global --start_date=20101201 411 ``` 412 413 The job status can then be checked by typing: 414 ```` 415 ecaccess-job-list 416 ```` 417 418 If the parameters *ecuid*, *ecgid*, *gateway* and *destination* were set correctly during installation and the gateway server is running, the resulting ***FLEXPART*** input files can be directly transferred to the local gateway by setting the paramter ``ectrans`` in the ``CONTROL``-file to ``1``. 419 420 Regardless of the job being successful or not, the user will receive an email with the log messages. 421 422 423 424 425 ## Development setup 426 427 install more python modules and run some tests, describe here 428 429 Describe how to install all development dependencies and how to run an automated test-suite of some kind. Potentially do this for multiple platforms. 430 431 ```sh 432 make install 433 npm test 434 ``` 435 436 ## Release History 437 438 * 7.1 439 * Completely revised/refactored python section 440 * restructured program directories 441 * simplified installation process 442 * CHANGE: upgraded to Python3 443 * CHANGE: applied PEP8 style guide 444 * CHANGE: use of genshi templates 445 * CHANGE: modularization of python source code 446 * CAHNGE: upgrade from grib_api to ecCodes 447 * ADD: first UNIT tests 448 * ADD: some regression tests 449 * ADD: more detailed documentation 450 * ADD: local retrieval via CDS API for ERA 5 data 451 * 7.0.4 452 * FIX: ERA 5 retrieval 453 * FIX: CERA-20C retrieval 454 * FIX: in BASETIME retrieval option 455 * FIX: `CONVERT2` FORTRAN program: initialise fields to 0. 456 * ADD: Ensemble retrieval for ENFO and ELDA stream (ZAMG specific with extra ensembles for ELDA stream) 457 * 7.0.3 458 * CHANGE: 459 * ADD: output of mars requests to an extra file 460 * ADD: CERA-20C download 461 * ADD: ERA 5 download 462 * ADD: public user interface with ECMWF Web API 463 * ADD: use of ECMWF Web API for local retrieval version 464 * 7.0.2 465 * Python based version 466 * CHANGE: korn shell scripts were substituted by python scripts 467 * v0.1 - v6.0 468 * old versions which should no longer be used anymore 469 470 # SUPPORT 471 472 ##### FLEXPART's community website: <http://flexpart.eu> 473 474 ##### flex_extract information: [https://www.flexpart.eu/wiki/FpInputMetEcmwf](https://www.flexpart.eu/wiki/FpInputMetEcmwf) 475 476 ##### Git-repository: <https://www.flexpart.eu/browser/flex_extract.git> 477 478 ##### Mailing list: [FP-dev(at)lists.univie.ac.at](mailto:fp-dev@lists.univie.ac.at) 479 480 ##### Ticket system: <https://www.flexpart.eu/report/1> 481 482 483 If you have any problems please open a ticket at <http://flexpart.eu> or send an e-mail to: <br> 484 [FP-dev(at)lists.univie.ac.at](mailto:fp-dev@lists.univie.ac.at) 485 486 487 488 489 # COPYRIGHT AND LICENSE 490 © Copyright 2014-2019. 491 Anne Philipp and Leopold Haimberger 492 493 <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br /> 494 495 This work is licensed under the <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>. <br /> 496 To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. 497 498 499 <!-- 500 [npm-image]: https://img.shields.io/npm/v/datadog-metrics.svg?style=flat-square 501 [npm-url]: https://npmjs.org/package/datadog-metrics 502 [npm-downloads]: https://img.shields.io/npm/dm/datadog-metrics.svg?style=flat-square 503 [travis-image]: https://img.shields.io/travis/dbader/node-datadog-metrics/master.svg?style=flat-square 504 [travis-url]: https://travis-ci.org/dbader/node-datadog-metrics 505 [wiki]: https://github.com/yourname/yourproject/wiki 506 --> 26 This work is licensed under the Creative Commons Attribution 4.0 27 International License. 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