of Earth system modelling
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1. There is evidently little point in repeating the spin up for each and every model experiment that might similar except in a single detail e g testing a variety of different CO emissions scenarios all starting from current year 2009 conditions A facility is thus provided for requesting that a restart is used starting a new experiment from the end of a previous one usually a spin up that has been run explicitly for the purpose of generating a starting point restart for subsequent experiments to continue on from A restart can be requested by setting the 5 optional parameter when entering in the old_rungenie sh command A spin up of the preindustrial Earth system based on an 8 level resolution of the ocean model and near identical to that described in Ridgwell et al 2007a is provided modern_SPINUP which can be found in the genie_output directory The experiment exp3_modern can be told to use a restart state by adding an appropriate 5 parameter at the command line e g ee Run the exp3_modern experiment interactively using the restart The run time output should now look noticeably different There should be no very little drift in any of the various variable values outputted to the screen 5 1 5 3 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Model output The first thing to note about output i e saved results files from GENIE is th2. To get a read only copy of GENIE from your home directory in the SSH Shell Window type svn co http source ggy bris ac uk subversion genie tags rel 2 5 0 username genie user genie NOTE All this must be typed continuously on ONE LINE with aS P A C E before username and before genie You my or may not be asked for a password if so it is g3nle user Don t mix up the ONE 1 with an el T Change directory see Appendix I to genie genie main and type make This compiles the default configuration of GENIE It serves to check that you have the software environment correctly configured If you are unsuccessful here too bad Try editing user mak or user sh which are located in genie genie main and which set the environment Next make assumedgood This creates a gold standard set of experimental results for GENIE 2 GENIE with the dynamical ICGM atmosphere against which your version of GENIE 2 can subsequently be check to ensure that you have not broken it in any way There are a bunch of tests that check the integrity of the code and results but you can assume that the tagged release you have installed has already been extensively checked and is good to go The tests are make test short tests that check against your newly created assumed good experimental results make testebgogs the EMBM based climate model make testbiogem climate model plus ocean bioge
3. SciTE to automatically open the model configuration files in the Secure File Transfer Client go to Edit then Settings and from the SECOND File Transfer section of the list in the left hand panel there are TWO File Transfer section entries and you are after the one near the bottom of the lest click on the button for If a file association is missing use this application to open the file Then from Program Files on the C drive of the Windoz machine find the SciTE editor directory and its program executable inside Click on OK to close the Settings dialogue box Then under File in the main menu Save Settings It should now be possible to double click on a file in the Secure File Transfer Client and it will open like magic almost Try opening old_rungenie sh in your home directory in this way If you edit and save the file you will be asked whether you want to transfer it back to the remote machine and also whether you want to over write the original file Simply click Yes to both If you log out of Windoz then you may have to re do these settings 2 1 2 2 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Running the model interactively in a shell window The strategy for running the model is as follows DON T TYPE ANYTHING YET JUST READ THIS SECTION At the command line in the root home of your account you will be entering in a command old_r
4. e journals or from www seao2 org pubs html or http www genie ac uk publications papers htm Other GENIE resources can be found at http mygenie seao2 org 0 0 0 1 0 2 0 3 0 4 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Before anything else For some of you the mechanics of running the model will be about as much fun as sticking you tongue in an electrical outlet GENIE has traditionally been configured and accessed via the command line of the linux or Mac equivalent operating system The command line is a place where you type text and when you press Return something hopefully good happens Typically the stuff you type started with a Command word and often followed by one or more options and or parameters The Command word and any options parameters MUST be separated by SPACEs The command line will look something like The is call the prompt and is prompting you to type some input Commands swear words etc See the computer is just sat there waiting for you to command it to go do something stupid Often you will also be informed reminded of the username and computer name and current directory at the prompt e g mushroom almond Which is user mushroom on computing cluster almond and the current directory is the home directory Now you can see why pe
5. ocean sea ice cover and thickness biogem_series_ocn_sal res mean ocean surface and whole ocean salinity biogem_series_ocn_temp res mean ocean surface and whole ocean temperature The contents of the files can be viewed by changing directory into the results directory i e cd genie_output expl_modern biogem and opening a file in the vi editor But I promised that we would not do anything quite so unpleasant in this workshop Instead change to the experiment results directory and then to the BIOGEM sub directory in the Secure File Transfer Client and try double clicking on one of the res files listed above For biogem_series_ocn_temp res you should see 3 columns time mean whole ocean temperature C mean sea surface temperature SST C and mean benthic temperature C Other results files may differ in the numbers of columns but all should be identifiable from the header information Excel or MUTLAB if you prefer can be used to graph the time series results Either way you will have to deal with the header line s that are present at the top of the file and preceding the rows of data In Excel Chose File then Open You will want to select Files of Type All Files In the Text Import Wizard window you can request that Excel skips the first few lines to start the import on the 2 or 3 line of the text file Alternatively set appropriate column widths manually in Excel to ensure that the c
6. 1 the 1 time slice often year mid point 0 5 rather than the experiment end 2 auto scaling of the color scale 3 global zonal averaging of lat depth plots Be careful when opening a new plot that you are looking at what you think you are looking at Explore different data fields and play with different ways of displaying them Aim for a set of display properties that show the information you are interested in want to present in the clearest possible manner Try different years time slice number depth level for a lat long plot or longitude for a vertical section Note that gray cells represent dry grid points i e continental or oceanic crust To save plots in Panoply File Save Image As Then select the location filename and graphics format There is also a set of MUTLAB script for plotting the BIOGEM and SEDGEM NetCDF output See http mygenie seao2 org under Miscellaneous Note that you may need to install MUTLAB NetCDF libraries which are invoked by the init_netcdf m which note is configured for a specific location of the library files on a PC and will probably need to be edited appropriately You are pretty much on you own here see the instructions assessable via http www giss nasa gov tools panoply for what library files are required where to get them from and where to install them 11 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth s
7. C concentration umol kg lt ALK gt global mean ocean alkalinity ALK concentration ueq kg The choice of what information to display on screen as the model is running is rather arbitrary but the chosen metrics do tend to summarize some of the main properties of the climate system and carbon cycle for my own personal convenience rather than reflecting any fundamental scientific truth This information is reported at the same intervals as time series data see later amp refer to the User Manual is saved and is indicated by gt gt gt SAVING BIOGEM TIME SERIES year Interleaved with these lines are lines reporting the saving of time slice data the 2 and 3 D model states more of which later and in the User Manual These appear as gt gt gt SAVING BIOGEM TIME SLICE year When the model ends after 11 years as per the value you specified at the command line a bunch more lines of diagnostics things are reported If you scroll up the screen of the terminal window you can get back to where the time dependent information appears while the model was running Alternatively you can run the model again but after a few years hit lt Ctrl C gt CONTROL key C key which will halt the model Try both letting the experiment take its natural course and end after 11 years and terminating it part way through which makes it easier to browse the run time output HINT
8. File Transfer Client display needs to be refreshed DON T FORGET THIS I know you will 1 5 1 6 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics You will see that your account contains the following files and directories the highlighted files and directories are the ones you have just created or downloaded genie a directory containing the model source code and input data directory tree genie_archive a directory containing archived model results genie_output a directory containing a set of subdirectories one for the results of each model experiment genie_forcings a directory containing a series of sub directories for applying geochemical forcings e g prescribing CO emissions genie_log a directory containing redirected run time output and error messages genie_userconfigs a directory containing a series of files configuring specific experiments one for each model experiment to be run old_rungenie sh a run script for the GENIE model Appendix C of the GENIE User Manual http mygenie seao2 org contains a fuller but more tedious explanation of the directory structure and file contents as well as a schematic diagram overview The final setup step specific to this workshop is to instill some files you will be needing for running some pre configured experiments From http mygenie seao2 org and under GENIE resources WORKSHOPS and
9. Make your Secure Shell Client window full screen in order for the run time information to be formatted properly and thus fully legible Now run the same experiment but this time for 101 years substitute 101 for 11 as the 4 parameter in the line where you issue the old_rungenie sh command Just from examining the screen output how close to steady state does the system appear to have come after this time Are all the elements of the Earth system converging at equivalent rates i e SST vs atmospheric CO2 This is something to think about later on has the model reached steady state What are the slowest responding parts of the Earth system 3 0 3 1 3 2 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Submitting experiment jobs to a cluster This bit is no particular fun at all but it is a very handy trick for running the model in the background and maximizes drinking time in the pub vs sat bored watching a computer screen Running jobs interactively is all very well but there are three important limitations 1 The connection between your terminal and the server computer running the model must remain unbroken Anything more than a fleeting loss of internet connectively may result in the experiment terminating 2 You can only run one experiment at a time unless you want to have thousands of separate Secure Shell Client windows open I thou
10. PC username and password which will only get you into the Windoz PC and the username and password for the computer cluster There are TWO sets of passwords and usernames Because there are 2 different computers involved You should now have a dull blank look window with the command prompt see previous page If you have a window that looks something like a file manager directory display you have mixed up steps 1 2 below and 1 1 Does not matter For displaying directory contents and transferring model results files we are going to be using the SSH file transfer program One of the icons towards the middle of the icon bar in the SSH terminal window you have opened is called New File Transfer Window it should be the 2 icon to the right of the search binoculars icon Click on this to open a file transfer window You should now have TWO windows open a shell window lines of text on an otherwise blank screen and a file manager transfer window Ensure that you have both these before moving on The next step is to download and test a copy of the source code for the GENIE model The instructions for downloading installing and testing the model code are summarized in the Super quick start guide at the end of this hand out Follow all the steps 1 7 in the Super quick start guide before continuing on to 1 4 A more generic version can be obtained from the mygenie http mygenie seao2 org w
11. PRACTICAL CLASSES and UoB 26th 27th August 2009 download the rather improbably named file GENIEworkshop UoB 090826 tar gz to your local machine PC and then using the file transfer manager transfer across the home directory of your account on the almond computing cluster Extract the contents of this archive by typing at the command line in the Secure Shell Client tar xfz GENIEworkshop UoB 090826 tar gz If you now view the contents of the genie_userconfigs and genie_forcings directories you will see that they have been populated with a number of files and subdirectories respectively Later on you will be editing some configuration files So now might be a good time to check that you can use the editor You will also be using the same editor to view some of the model output You have two alternative options for editing and viewing text files depending on whether you are a UNIX nerd with no life or prefer anything to do with computers to be wrapped in cotton wool and covered with dollops of treacle EITHER Use the linux vi application if you are familiar with it I think that this pretty much sucks as a text editor and life is far too short and brutal so we will not bother in this workshop OR Use a suitable linux friendly text editor NOT Micro oft Notepad in conjunction with the Secure File Transfer Client Just such an editor SciTE is provided on the desktop machine To set
12. T have executable permissions chmod u x old_rungenie sh Note that you run old_rungenie sh from your home directory NOT genie genie main which confusingly is where the tests are run from Finally for running GENIE 1 using rungenie create see Appendix I the following directories genie_archive genie_forcings genie_log genie_userconfigs
13. UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics A Hitchhikers Guide to the Black Arts of Earth system modelling SESSION 1a GENIE 1 Earth system model basics Stuff to keep in mind e GENIE 1 is a model Models ARE NOT the real World Don t get confused e The very low for a 3 D ocean circulation model resolution of GENIE 1 precludes its explicit applicability to very short time scales and because the simplified atmospheric component cannot calculate winds there is no atmospheric dynamics or inter annual variability e GENIE 1 is best thought of as a discovery and exploring tool for learning how the Earth system works rather than a detailed simulation tool e Have fun or at least try Background reading The following references provide primary model description and critical evaluation discussion Edwards and Marsh 2005 Climate Dynamics 24 415 433 description and calibration of the climate model component of GENIE 1 Hargreaves et al 2004 Climate Dynamics 23 745 760 description of data assimilation methodology and calibrated climatology of the climate model component of GENIE 1 Ridgwell et al 2007a Biogeosciences 4 87 104 description of a basic PO based carbon cycle in the ocean and calibration of the climate model component of GENIE 1 Ridgwell et al 2007b Biogeosciences 4 481 492 description of the calibra
14. ar 5 50 314 638 8 022 8935 6 412 8 578 34 902 2238 528 2363 233 SAVING BIOGEM TIME SLICE year 5 50000000000000 SAVING BIOGEM TIME SERIES year 6 50 317 108 8 085 82133 6 630 9 317 34 902 2238 239 2363 256 SAVING BIOGEM TIME SERIES year 7 50 319 071 8 125 7 910 6 736 9 946 34 903 2238 009 2363 276 SAVING BIOGEM TIME SERIES year 8 50 320 618 8 147 7 936 6 736 10 487 34 903 223 TOS 2363 292 SAVING BIOGEM TIME SERIES year 9 50 321 817 8 155 7 981 6 731 10 963 34 904 2237 695 2363 307 SAVING BIOGEM TIME SERIES year 10 50 322 734 8 152 8 092 6 858 11 406 34 904 2237995 23635319 SAVING BIOGEM TIME SLICE year 10 5000000000000 After do the looping gt the very first line contains header information describing the columns of numbers that follow below Thereafter all the lines contain summary information about the state of the model with the year time at which the values are reported in the first column The remaining columns after model year are as follows pco2 uatm mean atmospheric CO concentration in units of atm d13C02 mean C value of atmospheric CO o NOTE only valid if C is selected AMO Sv Atlantic meridional overturning circulation Sv assuming modern continents ice global sea ice fraction lt SST gt global sea surface temperature SST C lt SSS gt global sea surface salinity SSS o lt DIC gt global mean ocean dissolved inorganic carbon DI
15. at every science module saves its own results in its own sub directory and sometimes in very different and difficult to fathom ways All the sub directories of results plus copies of input parameters and the model executable are gathered together in a directory that is assigned the same name as the experiment and the same as the user config file name The overall experiment result directory is located within genie_output and will be assigned a directory name something like runl_modern Within this are each module s results sub directories We will consider primarily only results saved by the ocean biogeochemical module BIOGEM biogem The results files will thus be found in genie_output runl_modern biogem BIOGEM has a flexible and powerful facility of saving results by means of spatially explicit time slices and as a semi continuous time series of a single global or otherwise representative mean variable In contrast ATCHEM does not save its own results BIOGEM can save information about atmospheric composition and air sea gas exchange while SEDGEM essentially saves results only at the very end of a model experiment BIOGEM can also save the spatial distribution of sediment composition as time slices as well as mean composition as a time series Furthermore in order to attain a common format for both ocean physical properties and biogeochemistry BIOGEM can save a range of ocean results in addition to te
16. b_go_gs_ac_bg genie_userconfigs expl_modern 11 parameter number 1 T 2 T 3 T 4 REMEMBER This must be entered on a single CONTINUOUS LINE The single S P A C E S are vital Take care not to confuse an el 1 with a one 1 when typing this in First you will have to wait a little while as all the components of GENIE are compiled from the raw source code FORTRAN When it has finished doing this the model will initialize and carry out some self checking Only then will it start actually running and doing something and at this point you will see output of the format 2 3 do t UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics he looping model year pCO2 uatm d13c02 AMO Sv ice lt SST gt lt SSS gt lt DIC gt uM lt ALK gt uM SAVING BIOGEM TIME SERIES year 0 50 285 160 6 812 13 816 0 211 1 393 34 901 2242 457 2363 077 SAVING BIOGEM TIME SLICE year 0 500000000000000 SAVING BIOGEM TIME SERIES year 1 50 295 241 be2tt 13 201 2 247 3 545 34 901 2240 918 2363 122 SAVING BIOGEM TIME SERIES year 2 50 302 269 7 580 L231 4 377 5279 34901 2240 016 2363 147 SAVING BIOGEM TIME SLICE year 2 50000000000000 SAVING BIOGEM TIME SERIES year 350 307 521 7 786 11 061 5 509 6 633 34 901 2239 3 76 2363 175 SAVING BIOGEM TIME SERIES year 4 50 311 502 7 926 9 865 6 078 7 703 34 902 2238 900 2363 205 SAVING BIOGEM TIME SERIES ye
17. e queue status information when you issue a qgstat f command You should see your job appear on one of the 8 compute nodes numbered from 0 0 to 0 7 although it might briefly be a PENDING JOB For an 8 level ocean based configuration of GENIE 1 being run for 11 years the job should remain there in the queue for a few good tens of seconds before disappearing your clue that it has finished or died If you periodically re issue a qst at f command you can follow your job s progress 4 0 4 1 4 2 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Restarts Not much fun here either but again an important and time saving increased drinking time modelling technique to learn to use By default model experiments start from cold i e the ocean is at rest and uniform in temperature and salinity while the atmosphere is uniform in temperature and humidity All biogeochemical tracers in the ocean have uniform concentrations and or are zero and there are no biogenic materials in deep sea sediments From this state it will take several thousand years kyr for the climate system to reach steady state closer to 10 kyr for ocean biogeochemical cycles and atmosphere CO to reach steady state and approaching 100 kyr for sediment composition to re balance weathering Reaching this the equilibrium state is called the spin up phase of the model
18. ebpage under GENIE resources DOCUMENTATION Note the username and password for accessing the repository where the code lives are different from the password used to log onto the PC and different from the username and password used to access the computing cluster almond So many different passwords Don t confuse them You will not need the code repository username and password again they are used only once to install the model Note2 Make sure that you have set the correct permissions to the old_rungenie sh script as per the instructions in the Super quick start Guide Note3 To create the required directories step 7 refer to Appendix 1 linux 101 for the required command in linux Or folders can be created using the Secure File Transfer Client under the Operation menu item Take a moment to familiarize yourself with the contents of your home directory as an alternative to the linux command line Command 1s consult the right hand display listing in the Secure File Transfer Client Note that the file listing in the Secure File Transfer Client does not automatically refresh and newly created files directories will not necessarily be displayed click on the Refresh icon or press F5 I repeat the file listing in the Secure File Transfer Client does not automatically refresh Hence if in subsequent experiments you cannot see your results appearing 9 times closer to 10 actually out of 10 it will be because the Secure
19. ght not 3 Any cluster or computer you are likely to be accessing using a shell will not have many computing cores either because it is a single machine with only one or two processors or if a cluster by using a shell you a running on the head node which will have similar computing core limitations to running on a single machine The more experiments you run simultaneously the slower they will all run The alternative is to submit your experiment as a job to a queuing system which then manages what compute resources are used to run the model Once you have submitted the experiment that is it you can go straight to the pub Section 3 4 in the GENIE User Manual explains how to use the queue on the almond cluster you have been provided with an account on But for now just take the suggested options to the qsub command on trust The options following qsub and before 0old_rungenie sh re direct screen output and error messaging to a file and specify which linux shell to assume Run the next experiment exp2_modern for 11 years and submit the experiment as a job to the cluster queue Use a command line like nen ery ees ee ema en Note that you should not include the bit before old_rungenie sh unlike before The status of the cluster queue can be checked by qstat f as detailed in the User Manual After submitting an experiment you receive a job number This number appears in the first column in th
20. he experiment in years this must be entered as an integer even though GENIE will actually be treating it as a real There is also one optional 5 parameter 5 is the full path and name of any model experiment that you wish to continue on from the end of called a restar file If the 5th optional parameter is not passed then GENIE will run from cold If the 5th parameter is present then GENIE will attempt to run from a previously generated restart state Restarts will be discussed later The GENIE User Manual and Tutorial documents contain a fuller and rather more boring description of the above as well as examples of the command line syntax see http mygenie seao2 org As an example of running the GENIE Earth system model you are going to start a modern experiment similar to the preindustrial experiment described in the GENIE Tutorial The relevant configuration files have already been provided for you You will need the following details in order to construct the appropriate run command parameter 1 The base config is genie_eb_go_gs_ac_bg parameter 2 The user config directory is genie_userconfigs parameter 3 The user config file is exp1_modern parameter 4 Run the experiment for eleven years 11 parameter 5 There is no restart file and so no 5 parameter needs to be passed The full command you need to enter from your home directory then looks like old_rungenie sh genie_e
21. mething that is indistinguishable form magic in a sufficiently retarded civilization adapted from A C Clarke When you open the NetCDF file you will be presented with a Datasets and Variables window on the left hand side of the application window This contains a list of all the parameters available that you can display You will find that the Long Name description of the variable will be the most helpful to identify the one you want Simply double click on a variable to display For the 3 D fields you will be asked first whether you want a Lon Lat or Lat Vert plot for the 2 D fields the plot display will immediately open For the Lon Lat plots there are multiple levels depth layers in the ocean of data that can be plotted form the surface to the abyssal ocean For the Lat Vert plots there are multiple possible longitudes to plot slices from The default is the global mean meridional distribution You can interpolate the data or not often you may find that it is clearer not to interpolate the data but to leave it as blocky colors corresponding to the resolution of the model change the scale and colors overlay continental outline change the projection etc etc Gray cells represent dry grid points i e continental or oceanic crust There may be multiple time slices i e you can plot data saved form different years NOTE The default settings in Panoply can mislead
22. mperature and salinity such as velocities sea ice extent mixed layer depth convective frequency etc Time slices One of the most informative data sets that can be saved is that of the spatial distribution of properties such as tracers or physical ocean attributes However saving full spatial distributions a 36x36x8 array for any or all of the tracers each and every time step is clearly not practical not only in terms of data storage but also because of the detrimental effect that repeated file access has on model run time Instead BIOGEM will save the full spatial distribution of tracer properties only at one or more predefined time points years These are called time slices At the specified time points a set of spatially explicit data fields are saved for all the key tracer flux and physical characteristics of the system However rather than taking an instantaneous snapshot the time slice is constructed as an average over a specified integration interval the default is set to 1 0 years Time series The second data format for model output is much more closely spaced in time Model characteristics must then be reducible to a single meaningful variable for this to be practical i e saving the time varying nature of 3 D ocean tracer distributions is not Suitable reduced indicators would be the total inventories in the ocean and or atmosphere of various tracers or equivalently the mean global concentrations partial pressures
23. ochemsitry BIOGEM Because the results of the EMBM based climate model are not chaotic these tests compare the result against a known good set of results files that are held on SVN and installed along with the code in genie genie knowngood Run just a single test for now make testbiogem There may be some Warnings reported sloppy programming but these are not detrimental to the ultimate science results we hope Success of this test is indicated at the end if you get kTEST OK and you can then be certain that the model you have installed is producing identical within tolerance results to everyone else in the World who has ever installed GENIE At this point the science modules are currently compiled in a grid and or number of tracers configuration that is unlikely to be what you want for running experiments Clean up remove all the compiled GENIE modules ready for re compiling afresh from the source code by typing make cleanall That is it as far as basic installation goes Except to read the user manual You will be using a script mini program if you like to think of it in that way that carries out some basic configuration tasks and packages up the results old_rungenie sh which can be downloaded from mygenie seao2 org and under GENIE resources WORKSHOPS and PRACTICAL CLASSES the link to UoB 26th 27th August 2009 This file should be installed in your home directory and MUS
24. olumns of data are correctly imported MUTLAB will ignore lines starting with a which the time series starts with However it may be that the header line wraps around and there is in effect a 2 header line but without a In this case extra care or a quick edit of the header in the ASCH file will be required to load the data into MUTLAB 10 7 1 7 2 7 3 74 7 5 7 6 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Viewing time slice output of 2 D and 3 D environmental property fields For the time slice NetCDF nc files you will be using a program called Panoply If you want your own FREE copy of this utility you can get it here and is available for Windoz Mac and linux operating systems http www qgiss nasa gov tools panoply The first time that you try and view a NetCDF file you will need to associate the file format the nc file format extension with the Panoply program To do this 1 copy across to a local directory either the 2 D or 3 D NetCDF results file from the BIOGEM results sub directory 2 right mouse button click over the file and chose Open With 3 Browse and find the Panoply program file select and tick Always use the selected program to open this kind of file Hopefully all you have to do now is to double click on the nc file icon in the File Transfer window and the time slice will be displayed like so
25. ople so willingly let Billy Gates suck all their blood in return for a copy of Windoz 10 Read quickly through Appendix 1 which is a quick summary of some of the more important useful linux Commands you can use at the command line You may want to refer to this later NOTE In the following workshop instructions example lines to be typed at the command line are or grey when photocopied Be VERY CAREFUL that spaces are not missed out Also be careful not to confuse the number one 1 for the letter el 1 Mis spelling typing will probably be the primary reason for any wailing and gnashing of teeth during the workshop But coming soon is a GUI graphical user interface for GENIE that will relieve you of tedious mucking about at the linux command line However in depth science will always probably be done at the command line as it give the maximum access to the inner workings of the model and offers the greatest flexibility in designing experiments DO NOT RACE AHEAD AND SKIP OVER BITS THAT YOU CAN T BE BOTHERED TO READ OR DO IT WILL ALL GO HORRIBLY PEAR SHAPED BEFORE YOU CAN SAY WHAT MUPPET WROTE THESE STUPID INSTRUCTIONS Some warnings and reminders are repeated over and over and over and over again This is because you will forget immediately each time Additional documentation can be found on http mygenie seao2 org under GENIE resources DOCUMENTATION in particular i The GENIE User Man
26. respectively Like the time slices the data values saved in the time series files represent averages over a specified integration interval the default is set to 1 0 years View the BIOGEM results directory of one of the two experiments that you ran previously You should see the following files i biogem is the re start file created form the run you have just complete and can be ignored li biogem_series_ res these are the time series files in ASCII plain text format iii biogem_year_ _diag_GLOBAL res these contain global diagnostics summary information and are saved at the same frequency as the time slices also as ASCII plain text iv fields_biogem_2d nc 2 D fields of ocean and atmosphere properties as NetCDF v fields_biogem_3d nc 3 D fields of ocean properties as NetCDF 6 1 6 2 6 3 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Viewing time series output A descriptive summary of all the time series biogem_series_ res data files is given in the GENIE User Manual if you are really that bored The files of most immediate use relevance are biogem_series_atm_humidity res mean atmospheric surface humidity biogem_series_atm_temp res mean atmospheric surface air temperature biogem_series_misc_opsi res mean ocean overturning stream function Atlantic and global min max biogem_series_misc_seaice res mean
27. tion and application of the pH responsive pelagic calcification parameterization Ridgwell and Hargreaves 2007 Global Biogeochemical Cycles 21 doi 10 1029 2006GB002764 description and calibration of the sediment model component SEDGEM and response to fossil CO release Lenton et al 2006 Climate Dynamics 26 doi 10 1007 s00382 006 0109 9 description calibration and application of the ENTS land surface vegetation scheme The following provide a taste of mostly paleo applications Chikamoto M O K Matsumoto and A Ridgwell 2008 JGR 113 doi 10 1029 2007JG00066 analysis of the deep sea CaCO sediment and atmospheric CO response to Atlantic meridional overturning circulation shutdown Panchutk K A Ridgwell and L R Kump 2008 Geology 36 315 318 configuration of GENIE 1 for end Paleocene marine carbon cycling interpretation of the CO release associated with the PETM Ridgwell 2007 Paleoceanography 22 doi 10 1029 2006PA001372 description of sediment core modeling in SEDGEM application to the interpretation of CCD changes due to massive CO release e g PETM Singaraye J S D A Richards A Ridgwell P J Valdes W E N Austin and J W Beck 2008 GRL 35 doi 10 1029 2008GL034074 analysis of the role of changing ocean circulation in atmospheric radiocarbon variability during the Younger Dryas Copies of these references can be obtained from the usual places i
28. ual 11 A set of Tutorials iii A HOW TO potted explanations of how to get useful stuff done iv A table of namelist parameters in the model for controlling what GENIE does v A Quick start Guide referred to later OK now log into the PC 1 0 1 1 1 2 1 3 1 4 UoB Earth system modelling workshop 26 27 August 2009 SESSION 1a GENIE 1 Earth system model basics Starting off You are going to be installing the model from scratch why Why not Hell it saves me installing it a dozen times Actually having gone through the install and testing procedure once you should be able to install GENIE for real another time If you dare ever use it again Log in to the account that has been created for you on the almond computing cluster To do this first start the SSH Secure Shell program you can find this via the All Programs menu tree from the Start icon in Windoz Run the Secure Shell Client rather than the Secure File Transfer Client to start off Click on the Quick Connect icon in the main Secure Shell Client window A Connect to Remote Host dialogue box will appear In the first box Host Name enter almond ggy bris ac uk and your computing cluster user name on the line below this User Name When and only when you click on the Connect button will you be asked for your password in a new dialogue window that will appear Don t get confused between the
29. ungenie sh so named because it utilizes the old way of configuring and launching the model together with a list of parameters that will be passed to the model and as if by magic the model will run or sometimes not old_rungenie sh 1 2 3 4 5 Now pay attention there are 4 FOUR parameters separated by S PACE S that MUST follow the old_rungenie sh command on a single continuous line even if it wraps around across 2 lines 1 is the name of the required base configuration base config of the model We will mostly be using the base config genie_eb_go_gs_ac_bg initially which specifies the GENIE 1 climate model components GOLDSTEIN ocean go GOLDSTEIN sea ice gs EMBM atmosphere eb together with ocean bg and atmosphere ac carbon cycle modules The ocean circulation component is configured with 8 vertical levels and is forced with annual average insolation This configuration is basically as described in Ridgwell et al 2007 2 is the full path of the directory containing the user configuration user config file i e the file containing the specification of a particular experiment In the particular file structure adopted here it will be genie_userconfigs 3 is the name of the experiment There must be a file in the directory specified in parameter 2 genie_userconfigs with exactly the same name as you enter here for parameter 3 4 is the run length of t
30. ystem model basics Appendix 1 linux 101 Throughout the GENIE tutorials and documentation your home directory will be represented by Thus for example the output directory path will be written genie_output Viewing directories moving around the file system At the command line prompt in linux you can view the current directory contents ls or for a more complete output ls la To go down a directory genie_output is cd genie_output and to go back up one is cd You can always return to your home directory by typing cd or cd Copying and moving files To copy a file myconfig to myconfig_new cp myconfig myconfig_new To move myconfig to the GENIE user config directory mv myconfig genie_userconfigs myconfig To rename myconfig to useless_config mv myconfig useless_config Creating directories To create a directory mydirectory mkdir mydirectory Repeating command lines You do not have to re enter lines of commands and options in their entirety each time by pressing the UP cursor key you get the last command you issued If you keep pressing the UP cursor key you can recover progressively older commands you have previously entered When you have recovered a helpful line you can simply just edit it navigating along with the LEFT and RIGHT cursor keys press RETURN when you are done 12 GENIE Super quick start Guide Andy Ridgwell August 25 2009
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