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https://source.geography.bristol.ac.uk/mediawiki/api.php?action=feedcontributions&feedformat=atom&user=VickyLee SourceWiki - User contributions [en] 2026-04-06T01:17:03Z User contributions MediaWiki 1.35.8 https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4679 Nemo 2008-02-05T15:53:06Z

<p>VickyLee: /* AGRIF package */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the [[AGRIF package]].<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry '''and''' high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are <br /> * <code>create_coordinates.exe </code> generates the longitude, latitude and metrics for the child grid, <br /> * <code>create_bathy.exe </code> generates the bathymetry, <br /> * <code>create_data.exe </code> generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and <br /> * <code>create_restart.exe </code> interpolates the global restart file to the child grid.<br /> <br /> These executables use one '''namelist'''. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin. To run the example copy coordinates.nc, bathy_level.nc, bathy_meter.nc, taux_1m.nc, tauy_1m.nc, data_1m_potential_temperature_nomask.nc, data_1m_potential_temperature_nomask.nc, flx.nc, runoff_1m_nomask.nc and geothermal_heating.nc from ORCA2_LIM test case to Nesting_tools/bin. You will also need to acquire bathymetry_meter_ORCA_R05.nc, which I found it by typing the filename into google. Alternatively, try setting <code>new_topo = false</code>. Run the executables in Nesting_tools/bin in order using<br /> <br /> <code>./create_*.exe pacifique_topical</code><br /> <br /> where * is coordinates, bathy and then data (you don't need to do restart). Output has the form 1_globalname.nc, where 1_ signifies child grid and globalname is the name of the file copied from the test case, such as bathy_level, tauy_1m etc.<br /> <br /> For a new regional model copy pacifique_tropical and rename it as namelist_Amundsen, say. Set <code>imin, imax, jmin</code> and <code>jmax</code> to the indices on the global grid corresponding to your region, where (imin, jmin) is the south-west corner and (imax, jmax) is the north-east corner of your region. These indices must lie inside the global grid. Set <code>rho</code>, which is the grid refinement ratio to values between 2 and 5 (AGRIF recommendation). I suggest setting <code>type_bathy_interp = 2</code> for bilinear interpolation of the bathymetry as it seems more robust then the other options. Add <code>'runoff_1m_nomask.nc'</code> to the list of forcing files.<br /> <br /> ===High resolution bathymetry===<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4678 Nemo 2008-02-05T15:03:55Z

<p>VickyLee: /* AGRIF package */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the [[AGRIF package]].<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry '''and''' high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are <br /> * <code>create_coordinates.exe </code> generates the longitude, latitude and metrics for the child grid, <br /> * <code>create_bathy.exe </code> generates the bathymetry, <br /> * <code>create_data.exe </code> generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and <br /> * <code>create_restart.exe </code> interpolates the global restart file to the child grid.<br /> <br /> These executables use one '''namelist'''. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin. To run the example copy coordinates.nc, bathy_level.nc, bathy_meter.nc, taux_1m.nc, tauy_1m.nc, data_1m_potential_temperature_nomask.nc, data_1m_potential_temperature_nomask.nc, flx.nc, runoff_1m_nomask.nc and geothermal_heating.nc from ORCA2_LIM test case to Nesting_tools/bin. You will also need to acquire bathymetry_meter_ORCA_R05.nc, which I found it by typing the filename into google. Alternatively, try setting <code>new_topo = false</code>. Run the executables in Nesting_tools/bin in order using<br /> <br /> <code>./create_*.exe < pacifique_topical</code><br /> <br /> where * is coordinates, bathy and then data (you don't need to do restart). Output has the form 1_globalname.nc, where 1_ signifies child grid and globalname is the name of the file copied from the test case, such as bathy_level, tauy_1m.nc etc.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4677 Nemo 2008-02-05T13:19:12Z

<p>VickyLee: /* AGRIF package */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the [[AGRIF package]].<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry '''and''' high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are <br /> * <code>create_coordinates.exe </code> generates the longitude, latitude and metrics for the child grid, <br /> * <code>create_bathy.exe </code> generates the bathymetry, <br /> * <code>create_data.exe </code> generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and <br /> * <code>create_restart.exe </code> interpolates the global restart file to the child grid.<br /> <br /> These executables use one '''namelist'''. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin. To run the example copy coordinates.nc, bathy_level.nc, bathy_meter.nc, taux_1m.nc, tauy_1m.nc, data_1m_potential_temperature_nomask.nc, data_1m_potential_temperature_nomask.nc, flx.nc, runoff_1m_nomask.nc and geothermal_heating.nc from ORCA2_LIM test case to Nesting_tools/bin. You will also need to acquire bathymetry_meter_ORCA_R05.nc, which I found it by typing the filename into google. Alternatively, try setting <code>new_topo = false</code>. Run the executables in Nesting_tools/bin in order using<br /> <br /> <code>./create_*.exe < pacifique_topical</code><br /> <br /> where * is coordinates, bathy and then data (you don't need to do restart).<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4676 Nemo 2008-02-05T12:55:01Z

<p>VickyLee: /* Regional model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the [[AGRIF package]].<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry '''and''' high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are <br /> * <code>create_coordinates.exe </code> generates the longitude, latitude and metrics for the child grid, <br /> * <code>create_bathy.exe </code> generates the bathymetry, <br /> * <code>create_data.exe </code> generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and <br /> * <code>create_restart.exe </code> interpolates the global restart file to the child grid.<br /> <br /> These executables use one namelist. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4675 Nemo 2008-02-05T11:24:42Z

<p>VickyLee: /* AGRIF package */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the AGRIF package.<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. It is possible to genrate the child bathymetry by interpolating from the global bathymetry '''and''' high resolution topography. It blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are <br /> * <code>create_coordinates.exe </code> generates the longitude, latitude and metrics for the child grid, <br /> * <code>create_bathy.exe </code> generates the bathymetry, <br /> * <code>create_data.exe </code> generates the necessary input files (nav_lon and nav_lat in the child files aren't correct but NEMO doesn't use them) and <br /> * <code>create_restart.exe </code> interpolates the global restart file to the child grid.<br /> <br /> These executables use one namelist. AGRIF provides an example namelist, pacifique_tropical, in Nesting_tools/bin.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4674 Nemo 2008-02-05T10:44:02Z

<p>VickyLee: /* AGRIF package */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the AGRIF package.<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine regional grids (child grids) in a form that NEMO can read in from a coarse NEMO global grid. The idea is to run the fine grid '''with''' the global grid to provide local increased resolution where the model needs it. The package blends the coarse and fine resolutions over a few cells at the edges of the child grid. It also creates input files for the child grid from the global input files.<br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interpolation schemes. The executables are create_coordinates.exe, create_bathy.exe, create_data.exe and create_restart.exe.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4652 Nemo 2008-02-04T17:56:16Z

<p>VickyLee: </p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the AGRIF package.<br /> <br /> ==Bathymetry==<br /> <br /> There are some pre-processing packages available on the NEMO website. I don't recommend using the bathymetry package OPABAT. It uses idl and fortran routines contained in IDL_OPABAT3.tar. The instructions are in French and some of the files are missing. Instead, use the AGRIF nesting tools. The instructions are clear and the package also interpolates the input files from the ORCA2_LIM test case.<br /> <br /> ===AGRIF package===<br /> <br /> AGRIF is designed to create fine grids (child grids) from a coarse global grid. <br /> <br /> You can download the source code (Nesting_tools_NEMO.tar) and the user's manual (doc_nesting_tools.pdf) from the NEMO website. The manual tells you how to untar and make the executable files, run the executables and gives some theory about the interploation schemes. The excutables are create_coordinates.exe, create_bathy.exe, create_data.exe and create_restart.exe.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4619 Nemo 2008-02-01T11:50:30Z

<p>VickyLee: /* Regional model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> # Generate input data from the ORCA2_LIM test case files using the AGRIF package.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4618 Nemo 2008-02-01T11:46:48Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ===Model Compilation===<br /> <br /> In the steps below, I'm assuming that you are interested in the ORCA2_LIM version of the model.<br /> <br /> If you follow the steps described on the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage], you will be able to download and compile the model, with one caveat. When using newer versions of the NetCDF libraries--such as v3.6.2 installed on the Quest cluster--you will need to change line 210 of modipsl/util/AA_make.gdef to "NCDF_INC = /usr/local/netcdf/3.6.2/pgi-251/include" and line 211 to "NCDF_LIB = -L/usr/local/netcdf/3.6.2/pgi-251/lib -lnetcdf -lnetcdff".<br /> <br /> ===Running the Model===<br /> <br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. The run simulates one year. The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website or can be copied from ~ggdaqw/NEMO_forcing as detailed below. <br /> <br /> The instructions for running the model are not so clear. You will need two things to run the model; (i) some forcing files; and (ii) a run script. Assuming you are running on the Quest cluster, you can obtain forcing files for an example job by copying the directory ~ggdagw/NEMO_forcing and it's contents to you home directory. If you adopt the same directory name, you will be able to use [[Nemo_example_runscript|this runscript]]. Place the runscript into the directory modipsl/config/ORCA2_LIM/EXP00. I named it Job_EXP.new. You will need to create the directory "$DUMP2HOLD/NEMO" in your home directory to collect the output. You can submit the job by typing "qsub Job_EXP.new", check whether it is running using "showq", and obviously look in the output directory.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> Sediment cores recovered from the Mediterranean Sea reveal distinct layers of organic rich material thought to be associated with deep water anoxia, caused by either a shut down in deep water circulation, an increase in productivity, or both. One of the ways this could have happened is by a large increase in fresh water runoff into the basin. We intend to use a Mediterranean configuration of NEMO to study how point sources of freshwater, represented by low delta-18-O, are circulated around the Mediterranean, and compare the modeled distribution with records of delta-18-O during these "Mediterranean Anoxic Events".<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> <br /> <br /> ==Regional model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4266 Nemo 2007-11-09T20:43:40Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Alter <code>jpjed</code> and/or <code>jpjef</code> if the open boundary covers only part of the eastern face. Similarly for <code>lp_obc_west</code>, <code>jpjwd</code>, <code>jpjwf</code>, <code>lp_obc_north</code>, <code>jpind</code>, <code>jpinf</code> and <code>lp_obc_south</code>, <code>jpisd</code>, <code>jpisf</code>.<br /> # In the input file namelist set <code>n_cla</code> to 0. Assuming you have no closed seas, i.e. Mediterranean and Red Sea in ORCA2.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4265 Nemo 2007-11-09T20:17:29Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Mediterranean or the Red Sea that are grid dependent. <br /> # Set the new domain resolution in '''par_oce.F90''' in modipsl/modeles/NEMO/OPA_SRC/. Parameters for the resolution are <code>jpidta</code> and <code>jpjdta</code>.<br /> # Set parameters in '''obc_oce.F90''' and '''obc_par.F90''' in modipsl/modeles/NEMO/OPA_SRC/OBC/.<br /> #* obc_oce.F90: <code>nbobc</code> is the number of open boundaries, i.e. set to 1, 2, 3 or 4. <br /> #* obc_par.F90: set logical parameter <code>lp_obc_east</code> to <code>.true.</code> if open boundary conditions are to be applied to part or all of the eastern face of the domain. Similarly for <code>lp_obc_west</code>, <code>lp_obc_north</code> and <code>lp_obc_north</code>.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4264 Nemo 2007-11-09T19:38:58Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> # '''TIP''': modify '''tradmp.F90''' in modipsl/modeles/NEMO/OPA_SRC/TRA/. Replace the line <code>if (cp_cfg=="orca" .AND. (ndmp > 0 .OR. ndmp==-1)) then </code> with <code>if (ndmp > 0 .OR. ndmp==-1) then</code>. If you don't make the change you'll get the error message <code>tra_dmp: You should not have seen this print error?</code>. With this change you can apply tracer damping as in the ORCA configurations (i.e. global models for various resolutions) without special treatment for particular areas such as the Meditarrean<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4263 Nemo 2007-11-09T19:07:50Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you're not running a global model and add <code>key_obc</code> to invoke [[open boundary conditions]] instead.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4262 Nemo 2007-11-09T19:02:36Z

<p>VickyLee: /* Region model */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case:<br /> <br /> # Create a new configuration for the regional model.<br /> #* In directory '''modipsl/config/''' create a new directory AMUNDSEN, for example, and copy the contents of the ORCA2_LIM directory into AMUNDSEN.<br /> #* Edit file '''fait_config''' in modipsl/modeles/UTIL/. Add <code>\n AMUNDSEN</code> to <code>LIST =</code> and add the line <code>set -A DIR_AMUNSDEN OPA_SRC C1D_SRC NST_SRC</code>.<br /> # Change CPP keys by editing '''BB_make.ldef''' in modipsl/config/AMUNDSEN/scripts/. Remove <code>key_orca_r2</code> since you aren't run a global model and add <code>key_obc</code> to invoke open boundary conditions instead.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4261 Nemo 2007-11-09T18:14:32Z

<p>VickyLee: /* Projects using Nemo at Bristol */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ==ORCA2_LIM test case==<br /> <br /> Nemo provides a test case, ORCA2_LIM, for a global ocean run coupled with the sea-ice model. <br /> The run simulates one year.<br /> <br /> The configuration for ORCA2_LIM is downloaded through CVS when getting Nemo and the necessary forcing files are provided through a link on the Nemo website. <br /> <br /> ==Region model==<br /> <br /> How to set up a regional model starting from the ORCA2_LIM test case.<br /> <br /> ==Open boundary conditions==<br /> <br /> ==Wiki example==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4260 Nemo 2007-11-09T17:34:49Z

<p>VickyLee: /* Welcome to the Bristol Nemo Page! */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Here are a few tips and comments based on Bristol's experiences compiling and running NEMO. Hopefully, you will find some useful.<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage] before continuing with this page.<br /> <br /> ==Projects using Nemo at Bristol==<br /> <br /> ===Mediterranean Sea===<br /> <br /> ===Amundsen Sea===<br /> <br /> Thinning of the Pine Island Glacier, West Antarctica, has been observed during the 1990s. <br /> It has been suggested that relatively warm water at the base of the ice shelf has triggered the thinning. <br /> The source of and mechanism driving this warm water is unknown.<br /> <br /> We are constructing a regional model of the Amunsden Sea using Nemo to investigate ocean circulation close to <br /> Pine Island Bay. <br /> Input data at the sea surface and at the open boundaries are constructed using output data from the [http://www.soc.soton.ac.uk/JRD/OCCAM/ OCCAM global ocean model].<br /> <br /> ===Wiki example===<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4243 Nemo 2007-11-09T15:49:01Z

<p>VickyLee: /* Welcome to the Bristol Nemo Page! */</p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> Please take a look the [http://www.lodyc.jussieu.fr/NEMO/ official NEMO webpage].<br /> <br /> ===Wiki example===<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4230 Nemo 2007-11-09T14:48:19Z

<p>VickyLee: </p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4229 Nemo 2007-11-09T14:46:55Z

<p>VickyLee: </p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [http://www.google.com|a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4228 Nemo 2007-11-09T14:45:53Z

<p>VickyLee: </p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order<br /> <br /> An external link is [www.google.com|a search engine]<br /> <br /> A link to another wiki page is [[GENIE|the genie project]]</div>

VickyLee https://source.geography.bristol.ac.uk/mediawiki/index.php?title=Nemo&diff=4227 Nemo 2007-11-09T14:44:40Z

<p>VickyLee: </p> <hr /> <div>==Welcome to the Bristol Nemo Page!==<br /> <br /> This text '''is very imprtant'''. This ''is less so''.<br /> <br /> Listen very carefully, I shall say this only once:<br /> <br /> # put kettle on<br /> # find mug<br /> # add water to tea bag--'''in mug!'''<br /> <br /> * slurp<br /> * read<br /> * slurp<br /> <br /> can be done in any order</div>

VickyLee