Changeset 4193 for branches/2013/dev_r3867_MERCATOR1_DYN/DOC
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- 2013-11-14T12:04:31+01:00 (11 years ago)
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branches/2013/dev_r3867_MERCATOR1_DYN/DOC/NEMO_book.tex
r3294 r4193 23 23 \usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions 24 24 \usepackage{enumitem} % allows non-bold description items 25 \usepackage{longtable} % allows multipage tables 25 26 %\usepackage{colortbl} % gives coloured panels behind table columns 26 27 -
branches/2013/dev_r3867_MERCATOR1_DYN/DOC/TexFiles/Chapters/Chap_DIA.tex
r3764 r4193 1 1 % ================================================================ 2 % Chapter ÑI/O & Diagnostics2 % Chapter I/O & Diagnostics 3 3 % ================================================================ 4 4 \chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)} … … 16 16 17 17 The model outputs are of three types: the restart file, the output listing, 18 and the output file(s). The restart file is used internally by the code when18 and the diagnostic output file(s). The restart file is used internally by the code when 19 19 the user wants to start the model with initial conditions defined by a 20 20 previous simulation. It contains all the information that is necessary in … … 25 25 that it is saved in the same binary format as the one used by the computer 26 26 that is to read it (in particular, 32 bits binary IEEE format must not be used for 27 this file). The output listing and file(s) are predefined but should be checked 27 this file). 28 29 The output listing and file(s) are predefined but should be checked 28 30 and eventually adapted to the user's needs. The output listing is stored in 29 31 the $ocean.output$ file. The information is printed from within the code on the … … 31 33 "\textit{grep -i numout}" in the source code directory. 32 34 33 In the standard configuration, the user will find the model results in 34 NetCDF files containing mean values (or instantaneous values if 35 \key{diainstant} is defined) for every time-step where output is demanded. 36 These outputs are defined in the \mdl{diawri} module. 37 When defining \key{dimgout}, the output are written in DIMG format, 38 an IEEE output format. 39 40 Since version 3.2, an I/O server has been added which provides more 41 flexibility in the choice of the fields to be output as well as how the 42 writing work is distributed over the processors in massively parallel 43 computing. It is presented in next section. 44 35 By default, diagnostic output files are written in NetCDF format but an IEEE binary output format, called DIMG, can be choosen by defining \key{dimgout}. 36 37 Since version 3.2, when defining \key{iomput}, an I/O server has been added which provides more flexibility in the choice of the fields to be written as well as how the writing work is distributed over the processors in massively parallel computing. The complete description of the use of this I/O server is presented in the next section. 38 39 By default, if neither \key{iomput} nor \key{dimgout} are defined, NEMO produces NetCDF with the old IOIPSL library which has been kept for compatibility and its easy installation. However, the IOIPSL library is quite inefficient on parallel machines and, since version 3.2, many diagnostic options have been added presuming the use of \key{iomput}. The usefulness of the default IOIPSL-based option is expected to reduce with each new release. If \key{iomput} is not defined, output files and content are defined in the \mdl{diawri} module and contain mean (or instantaneous if \key{diainstant} is defined) values over a regular period of nn\_write time-steps (namelist parameter). 45 40 46 41 %\gmcomment{ % start of gmcomment … … 53 48 54 49 55 Since version 3.2, iom\_put is the NEMO output interface. It was designed to be simple to use, 56 flexible and efficient. Two main functionalities are covered by iom\_put: 57 (1) the control of the output files through an external xml file defined by the user ; 58 (2) the distribution (or not) of all task related to output files on dedicated processors. 59 The first functionality allows the user to specify, without touching anything into the code, 60 the way he want to output data: \\ 61 - choice of output frequencies that can be different for each file (including real months and years) \\ 62 - choice of file contents: decide which data will be written in which file (the same data can be 63 outputted in different files) \\ 64 - possibility to extract a subdomain (for example all TAO-PIRATA-RAMA moorings are already defined) \\ 65 - choice of the temporal operation to perform: mean, instantaneous, min, max \\ 66 - extremely large choice of data available \\ 67 - redefine variables name and long\_name \\ 68 In addition, iom\_put allows the user to output any variable (scalar, 2D or 3D) in the code 69 in a very easy way. All details of iom\_put functionalities are listed in the following subsections. 70 An example of the iodef.xml file that control the outputs can be found here: 71 NEMOGCM/CONFIG/ORCA2\_LIM/EXP00/iodef.xml 72 73 The second functionality targets outputs performances when running on a very large number of processes. 74 The idea is to dedicate N specific processes to write the outputs, where N is defined by the user. 75 In the current version, this functionality is technically working however, its performance are usually poor 76 (for known reasons). Users can therefore test this functionality but they must be aware that expected 77 performance improvement will not be achieved before the release 3.4. 78 An example of xmlio\_server.def NEMOGCM/CONFIG/ORCA2\_LIM/EXP00/xmlio\_server.def 79 80 81 \subsection{Basic knowledge} 82 50 Since version 3.2, iomput is the NEMO output interface of choice. It has been designed to be simple to use, flexible and efficient. The two main purposes of iomput are: 51 \begin{enumerate} 52 \item The complete and flexible control of the output files through external XML files adapted by the user from standard templates. 53 \item To achieve high performance and scalable output through the optional distribution of all diagnostic output related tasks to dedicated processes. 54 \end{enumerate} 55 The first functionality allows the user to specify, without code changes or recompilation, aspects of the diagnostic output stream, such as: 56 \begin{itemize} 57 \item The choice of output frequencies that can be different for each file (including real months and years). 58 \item The choice of file contents; includes complete flexibility over which data are written in which files (the same data can be written in different files). 59 \item The possibility to split output files at a choosen frequency. 60 \item The possibility to extract a vertical or an horizontal subdomain. 61 \item The choice of the temporal operation to perform, e.g.: average, accumulate, instantaneous, min, max and once. 62 \item Control over metadata via a large XML "database" of possible output fields. 63 \end{itemize} 64 In addition, iomput allows the user to add the output of any new variable (scalar, 2D or 3D) in the code in a very easy way. All details of iomput functionalities are listed in the following subsections. Examples of the XML files that control the outputs can be found in: 65 \begin{alltt} 66 \begin{verbatim} 67 NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml 68 NEMOGCM/CONFIG/SHARED/field_def.xml 69 and 70 NEMOGCM/CONFIG/SHARED/domain_def.xml. 71 \end{verbatim} 72 \end{alltt} 73 74 The second functionality targets output performance when running in parallel (\key{mpp\_mpi}). Iomput provides the possibility to specify N dedicated I/O processes (in addition to the NEMO processes) to collect and write the outputs. With an appropriate choice of N by the user, the bottleneck associated with the writing of the output files can be greatly reduced. 75 76 Since version 3.5, the iom\_put interface depends on an external code called \href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}. This new IO server can take advantage of the parallel I/O functionality of NetCDF4 to create a single output file and therefore to bypass the rebuilding phase. Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to an HDF5 library that has been correctly compiled (i.e. with the configure option $--$enable-parallel). Note that the files created by iomput through XIOS are incompatible with NetCDF3. All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3. 77 78 Even if not using the parallel I/O functionality of NetCDF4, using N dedicated I/O servers, where N is typically much less than the number of NEMO processors, will reduce the number of output files created. This can greatly reduce the post-processing burden usually associated with using large numbers of NEMO processors. Note that for smaller configurations, the rebuilding phase can be avoided, even without a parallel-enabled NetCDF4 library, simply by employing only one dedicated I/O server. 79 80 \subsection{XIOS: the IO\_SERVER} 81 82 \subsubsection{Attached or detached mode?} 83 84 Iomput is based on \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS}, the io\_server developed by Yann Meurdesoif from IPSL. The behaviour of the io subsystem is controlled by settings in the external XML files listed above. Key settings in the iodef.xml file are {\tt using\_server} and the {\tt type} tag associated with each defined file. The {\tt using\_server} setting determines whether or not the server will be used in ''attached mode'' (as a library) [{\tt false}] or in ''detached mode'' (as an external executable on N additional, dedicated cpus) [{\tt true}]. The ''attached mode'' is simpler to use but much less efficient for massively parallel applications. The type of each file can be either ''multiple\_file'' or ''one\_file''. 85 86 In attached mode and if the type of file is ''multiple\_file'', then each NEMO process will also act as an IO server and produce its own set of output files. Superficially, this emulates the standard behaviour in previous versions, However, the subdomain written out by each process does not correspond to the {\tt jpi x jpj x jpk} domain actually computed by the process (although it may if {\tt jpni=1}). Instead each process will have collected and written out a number of complete longitudinal strips. If the ''one\_file'' option is chosen then all processes will collect their longitudinal strips and write (in parallel) to a single output file. 87 88 In detached mode and if the type of file is ''multiple\_file'', then each stand-alone XIOS process will collect data for a range of complete longitudinal strips and write to its own set of output files. If the ''one\_file'' option is chosen then all XIOS processes will collect their longitudinal strips and write (in parallel) to a single output file. Note running in detached mode requires launching a Multiple Process Multiple Data (MPMD) parallel job. The following subsection provides a typical example but the syntax will vary in different MPP environments. 89 90 \subsubsection{Number of cpu used by XIOS in detached mode} 91 92 The number of cores used by the XIOS is specified when launching the model. The number of cores dedicated to XIOS should be from ~1/10 to ~1/50 of the number or cores dedicated to NEMO. Some manufacturers suggest using O($\sqrt{N}$) dedicated IO processors for N processors but this is a general recommendation and not specific to NEMO. It is difficult to provide precise recommendations because the optimal choice will depend on the particular hardware properties of the target system (parallel filesystem performance, available memory, memory bandwidth etc.) and the volume and frequency of data to be created. Here is an example of 2 cpus for the io\_server and 62 cpu for nemo using mpirun: 93 94 \texttt{ mpirun -np 62 ./nemo.exe : -np 2 ./xios\_server.exe } 95 96 \subsubsection{Control of XIOS: the XIOS context in iodef.xml} 97 98 As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. See the XML basics section below for more details on XML syntax and rules. 99 100 \begin{tabular}{|p{4cm}|p{6.0cm}|p{2.0cm}|} 101 \hline 102 variable name & 103 description & 104 example \\ 105 \hline 106 \hline 107 buffer\_size & 108 buffer size used by XIOS to send data from NEMO to XIOS. Larger is more efficient. Note that needed/used buffer sizes are summarized at the end of the job & 109 25000000 \\ 110 \hline 111 buffer\_server\_factor\_size & 112 ratio between NEMO and XIOS buffer size. Should be 2. & 113 2 \\ 114 \hline 115 info\_level & 116 verbosity level (0 to 100) & 117 0 \\ 118 \hline 119 using\_server & 120 activate attached(false) or detached(true) mode & 121 true \\ 122 \hline 123 using\_oasis & 124 XIOS is used with OASIS(true) or not (false) & 125 false \\ 126 \hline 127 oasis\_codes\_id & 128 when using oasis, define the identifier of NEMO in the namcouple. Note that the identifier of XIOS is xios.x & 129 oceanx \\ 130 \hline 131 \end{tabular} 132 133 134 \subsection{Practical issues} 135 136 \subsubsection{Installation} 137 138 As mentioned, XIOS is supported separately and must be downloaded and compiled before it can be used with NEMO. See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance. NEMO will need to link to the compiled XIOS library. The 139 \href{http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/XIOS-IO-server-installation-and-use}{XIOS with NEMO} guide provides an example illustration of how this can be achieved. 140 141 \subsubsection{Add your own outputs} 142 143 It is very easy to add your own outputs with iomput. Many standard fields and diagnostics are already prepared (i.e., steps 1 to 3 below have been done) and simply need to be activated by including the required output in a file definition in iodef.xml (step 4). To add new output variables, all 4 of the following steps must be taken. 144 \begin{description} 145 \item[1.] in NEMO code, add a \\ 146 \texttt{ CALL iom\_put( 'identifier', array ) } \\ 147 where you want to output a 2D or 3D array. 148 149 \item[2.] If necessary, add \\ 150 \texttt{ USE iom\ \ \ \ \ \ \ \ \ \ \ \ ! I/O manager library } \\ 151 to the list of used modules in the upper part of your module. 152 153 \item[3.] in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code (see subsequent sections for a details of the XML syntax and rules). For example: 154 \vspace{-20pt} 155 \begin{alltt} {{\scriptsize 156 \begin{verbatim} 157 <field_definition> 158 <!-- T grid --> 159 160 <field_group id="grid_T" grid_ref="grid_T_3D"> 161 ... 162 <field id="identifier" long_name="blabla" ... /> 163 ... 164 </field_definition> 165 \end{verbatim} 166 }}\end{alltt} 167 Note your definition must be added to the field\_group whose reference grid is consistent with the size of the array passed to iomput. The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, reference grids and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90) or defined in the domain\_def.xml file. E.g.: 168 \vspace{-20pt} 169 \begin{alltt} {{\scriptsize 170 \begin{verbatim} 171 <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 172 \end{verbatim} 173 }}\end{alltt} 174 Note, if your array is computed within the surface module each nn\_fsbc time\_step, 175 add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$ which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90) 176 177 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) \\ 178 \vspace{-20pt} 179 \begin{alltt} {{\scriptsize 180 \begin{verbatim} 181 <file id="file1" .../> 182 ... 183 <field field_ref="identifier" /> 184 ... 185 </file> 186 \end{verbatim} 187 }}\end{alltt} 188 189 \end{description} 190 \subsection{XML fundamentals} 83 191 84 192 \subsubsection{ XML basic rules} … … 93 201 \subsubsection{Structure of the xml file used in NEMO} 94 202 95 The xml file is split into 3 parts: 96 \begin{description} 97 \item[field definition]: define all variables that can be output \\ 98 all lines in between the following two tags\\ 99 \verb? <field\_definition ...> ? \\ 100 \verb? </field\_definition ...> ? 101 \item[file definition]: define the netcdf files to be created and the variables they will contain \\ 102 all lines in between the following two tags \\ 103 \verb? <field\_definition> ? \\ 104 \verb? </field\_definition> ? 105 \item[axis and grid definitions]: define the horizontal and vertical grids \\ 106 all lines in between the following two set of two tags\\ 107 \verb? <axis\_definition ...> ? \\ 108 \verb? </axis\_definition ...> ? 109 and \\ 110 \verb? <grid\_definition ...> ? \\ 111 \verb? </grid\_definition ...> ? 112 \end{description} 113 114 \subsubsection{Inheritance and group } 115 116 Xml extensively uses the concept of inheritance. \\ 203 The XML file used in XIOS is structured by 7 families of tags: context, axis, domain, grid, field, file and variable. Each tag family has hierarchy of three flavors (except for context): 117 204 \\ 118 example 1: \\ 119 \vspace{-30pt} 205 \begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 206 \hline 207 flavor & 208 description & 209 example \\ 210 \hline 211 \hline 212 root & 213 declaration of the root element that can contain element groups or elements & 214 {\scriptsize \verb? < file_definition ... >?} \\ 215 \hline 216 group & 217 declaration of a group element that can contain element groups or elements & 218 {\scriptsize \verb? < file_group ... >?} \\ 219 \hline 220 element & 221 declaration of an element that can contain elements & 222 {\scriptsize \verb? < file ... >?} \\ 223 \hline 224 \end{tabular} 225 \\ 226 227 Each element may have several attributes. Some attributes are mandatory, other are optional but have a default value and other are are completely optional. Id is a special attribute used to identify an element or a group of elements. It must be unique for a kind of element. It is optional, but no reference to the corresponding element can be done if it is not defined. 228 229 The XML file is split into context tags that are used to isolate IO definition from different codes or different parts of a code. No interference is possible between 2 different contexts. Each context has its own calendar and an associated timestep. In NEMO, we used the following contexts (that can be defined in any order):\\ 230 \\ 231 \begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 232 \hline 233 context & 234 description & 235 example \\ 236 \hline 237 \hline 238 context xios & 239 context containing information for XIOS & 240 {\scriptsize \verb? <context id="xios" ... ?} \\ 241 \hline 242 context nemo & 243 context containing IO information for NEMO (mother grid when using AGRIF) & 244 {\scriptsize \verb? <context id="nemo" ... ?} \\ 245 \hline 246 context 1\_nemo & 247 context containing IO information for NEMO child grid 1 (when using AGRIF) & 248 {\scriptsize \verb? <context id="1_nemo" ... ?} \\ 249 \hline 250 context n\_nemo & 251 context containing IO information for NEMO child grid n (when using AGRIF) & 252 {\scriptsize \verb? <context id="n_nemo" ... ?} \\ 253 \hline 254 \end{tabular} 255 \\ 256 257 \noindent The xios context contains only 1 tag: 258 \\ 259 \begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 260 \hline 261 context tag & 262 description & 263 example \\ 264 \hline 265 \hline 266 variable\_definition & 267 define variables needed by XIOS. This can be seen as a kind of namelist for XIOS. & 268 {\scriptsize \verb? <variable_definition ... ?} \\ 269 \hline 270 \end{tabular} 271 \\ 272 273 \noindent Each context tag related to NEMO (mother or child grids) is divided into 5 parts (that can be defined in any order):\\ 274 \\ 275 \begin{tabular}{|p{3.0cm}|p{4.5cm}|p{4.5cm}|} 276 \hline 277 context tag & 278 description & 279 example \\ 280 \hline 281 \hline 282 field\_definition & 283 define all variables that can potentially be outputted & 284 {\scriptsize \verb? <field_definition ... ?} \\ 285 \hline 286 file\_definition & 287 define the netcdf files to be created and the variables they will contain & 288 {\scriptsize \verb? <file_definition ... ?} \\ 289 \hline 290 axis\_definition & 291 define vertical axis & 292 {\scriptsize \verb? <axis_definition ... ?} \\ 293 \hline 294 domain\_definition & 295 define the horizontal grids & 296 {\scriptsize \verb? <domain_definition ... ?} \\ 297 \hline 298 grid\_definition & 299 define the 2D and 3D grids (association of an axis and a domain) & 300 {\scriptsize \verb? <grid_definition ... ?} \\ 301 \hline 302 \end{tabular} 303 \\ 304 305 \subsubsection{Nesting XML files} 306 307 The XML file can be split in different parts to improve its readability and facilitate its use. The inclusion of XML files into the main XML file can be done through the attribute src: \\ 308 {\scriptsize \verb? <context src="./nemo_def.xml" /> ?}\\ 309 310 \noindent In NEMO, by default, the field and domain definition is done in 2 separate files: 311 {\scriptsize \tt 312 \begin{verbatim} 313 NEMOGCM/CONFIG/SHARED/field_def.xml 314 and 315 NEMOGCM/CONFIG/SHARED/domain_def.xml 316 \end{verbatim} 317 } 318 \noindent that are included in the main iodef.xml file through the following commands: \\ 319 {\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\ 320 \verb? <domain_definition src="./domain_def.xml" /> ? } 321 322 323 \subsubsection{Use of inheritance} 324 325 XML extensively uses the concept of inheritance. XML has a tree based structure with a parent-child oriented relation: all children inherit attributes from parent, but an attribute defined in a child replace the inherited attribute value. Note that the special attribute ''id'' is never inherited. \\ 326 \\ 327 example 1: Direct inheritance. 328 \vspace{-20pt} 120 329 \begin{alltt} {{\scriptsize 121 330 \begin{verbatim} 122 <field_definition operation="ave (X)" >123 124 <field id="sss" operation="inst(X)"/> <!-- instantaneous sss -->331 <field_definition operation="average" > 332 <field id="sst" /> <!-- averaged sst --> 333 <field id="sss" operation="instant"/> <!-- instantaneous sss --> 125 334 </field_definition> 126 335 \end{verbatim} 127 336 }}\end{alltt} 128 337 129 The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''ave (X)''130 of the attribute ''operation'' from its parent ''field definition''. Note that a child can overwrite338 The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average'' 339 of the attribute ''operation'' from its parent. Note that a child can overwrite 131 340 the attribute definition inherited from its parents. In the example above, the field ''sss'' will 132 therefore output instantaneous values instead of average values. 133 134 example 2: Use (or overwrite) attributes value of a field when listing the variables included in a file341 for example output instantaneous values instead of average values. \\ 342 \\ 343 example 2: Inheritance by reference. 135 344 \vspace{-20pt} 136 345 \begin{alltt} {{\scriptsize 137 346 \begin{verbatim} 138 347 <field_definition> 139 <field id="sst" description="sea surface temperature" />140 <field id="sss" description="sea surface salinity" />348 <field id="sst" long_name="sea surface temperature" /> 349 <field id="sss" long_name="sea surface salinity" /> 141 350 </field_definition> 142 351 143 352 <file_definition> 144 <file id="file_1" />145 <field ref="sst"/> <!-- default def -->146 <field ref="sss" description="my description" /> <!-- overwrite -->147 353 <file id="myfile" output_freq="1d" /> 354 <field field_ref="sst" /> <!-- default def --> 355 <field field_ref="sss" long_name="my description" /> <!-- overwrite --> 356 </file> 148 357 </file_definition> 149 358 \end{verbatim} 150 359 }}\end{alltt} 151 152 With the help of the inheritance, the concept of group allow to define a set of attributes 153 for several fields or files. 154 155 example 3, group of fields: define a group ''T\_grid\_variables'' identified with the name 156 ''grid\_T''. By default variables of this group have no vertical axis but, following inheritance 157 rules, ''axis\_ref'' can be redefined for the field ''toce'' that is a 3D variable. 158 \vspace{-30pt} 360 Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 361 362 \subsubsection{Use of Groups} 363 364 Groups can be used for 2 purposes. Firstly, the group can be used to define common attributes to be shared by the elements of the group through inheritance. In the following example, we define a group of field that will share a common grid ''grid\_T\_2D''. Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 365 \vspace{-20pt} 159 366 \begin{alltt} {{\scriptsize 160 367 \begin{verbatim} 161 <field_definition> 162 <group id="grid_T" axis_ref="none" grid_ref="T_grid_variables"> 163 <field id="sst"/> 164 <field id="sss"/> 165 <field id="toce" axis_ref="deptht"/> <!-- overwrite axis def --> 166 </group> 167 </field_definition> 368 <field_group id="grid_T" grid_ref="grid_T_2D"> 369 <field id="toce" long_name="temperature" unit="degC" grid_ref="grid_T_3D"/> 370 <field id="sst" long_name="sea surface temperature" unit="degC" /> 371 <field id="sss" long_name="sea surface salinity" unit="psu" /> 372 <field id="ssh" long_name="sea surface height" unit="m" /> 373 ... 168 374 \end{verbatim} 169 375 }}\end{alltt} 170 376 171 example 4, group of files: define a group of file with the attribute output\_freq equal to 432000 (5 days) 172 \vspace{- 30pt}377 Secondly, the group can be used to replace a list of elements. Several examples of groups of fields are proposed at the end of the file {\tt CONFIG/SHARED/field\_def.xml}. For example, a short list of the usual variables related to the U grid: 378 \vspace{-20pt} 173 379 \begin{alltt} {{\scriptsize 174 380 \begin{verbatim} 175 <file_definition> 176 <group id="5d" output_freq="432000"> <!-- 5d files --> 177 <file id="5d_grid_T" name="auto"> <!-- T grid file --> 381 <field_group id="groupU" > 382 <field field_ref="uoce" /> 383 <field field_ref="suoce" /> 384 <field field_ref="utau" /> 385 </field_group> 386 \end{verbatim} 387 }}\end{alltt} 388 that can be directly included in a file through the following syntax: 389 \vspace{-20pt} 390 \begin{alltt} {{\scriptsize 391 \begin{verbatim} 392 <file id="myfile_U" output_freq="1d" /> 393 <field_group group_ref="groupU"/> 394 <field field_ref="uocetr_eff" /> <!-- add another field --> 395 </file> 396 \end{verbatim} 397 }}\end{alltt} 398 399 \subsection{Detailed functionalities } 400 401 The file {\tt NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml} provides several examples of the use of the new functionalities offered by the XML interface of XIOS. 402 403 \subsubsection{Define horizontal subdomains} 404 Horizontal subdomains are defined through the attributs zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj of the tag family domain. It must therefore be done in the domain part of the XML file. For example, in {\tt CONFIG/SHARED/domain\_def.xml}, we provide the following example of a definition of a 5 by 5 box with the bottom left corner at point (10,10). 405 \vspace{-20pt} 406 \begin{alltt} {{\scriptsize 407 \begin{verbatim} 408 <domain_group id="grid_T"> 409 <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> 410 \end{verbatim} 411 }}\end{alltt} 412 The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example: 413 \vspace{-20pt} 414 \begin{alltt} {{\scriptsize 415 \begin{verbatim} 416 <file id="myfile_vzoom" output_freq="1d" > 417 <field field_ref="toce" domain_ref="myzoom"/> 418 </file> 419 \end{verbatim} 420 }}\end{alltt} 421 Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain. The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code and can therefore be outputted without taking care of their (i,j) position in the grid. These predefined domains can be activated by the use of specific domain\_ref: ''EqT'', ''EqU'' or ''EqW'' for the equatorial sections and the mooring position for TAO, RAMA and PIRATA followed by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) 422 \vspace{-20pt} 423 \begin{alltt} {{\scriptsize 424 \begin{verbatim} 425 <file id="myfile_vzoom" output_freq="1d" > 426 <field field_ref="toce" domain_ref="0n180wT"/> 427 </file> 428 \end{verbatim} 429 }}\end{alltt} 430 Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if you use the ''multiple\_file'' type for your output files, you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). We are therefore advising to use the ''one\_file'' type in this case. 431 432 \subsubsection{Define vertical zooms} 433 Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. It must therefore be done in the axis part of the XML file. For example, in NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml, we provide the following example: 434 \vspace{-20pt} 435 \begin{alltt} {{\scriptsize 436 \begin{verbatim} 437 <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" > 438 <axis id="deptht" /> 439 <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" /> 440 \end{verbatim} 441 }}\end{alltt} 442 The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example: 443 \vspace{-20pt} 444 \begin{alltt} {{\scriptsize 445 \begin{verbatim} 446 <file id="myfile_hzoom" output_freq="1d" > 447 <field field_ref="toce" axis_ref="deptht_myzoom"/> 448 </file> 449 \end{verbatim} 450 }}\end{alltt} 451 452 \subsubsection{Control of the output file names} 453 454 The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example: 455 \vspace{-20pt} 456 \begin{alltt} {{\scriptsize 457 \begin{verbatim} 458 <file_group id="1d" output_freq="1d" name="myfile_1d" > 459 <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA" --> 178 460 ... 179 180 <file id="5d_grid_U" name="auto"> <!-- U grid file-->461 </file> 462 <file id="myfileB" name_suffix="_BBB" > <!-- will create file "myfile_1d_BBB" --> 181 463 ... 182 </file> 183 </group> 184 </file_definition> 464 </file> 465 </file_group> 185 466 \end{verbatim} 186 467 }}\end{alltt} 187 188 \subsubsection{Control of the xml attributes from NEMO} 189 190 The values of some attributes are automatically defined by NEMO (and any definition 191 given in the xml file is overwritten). By convention, these attributes are defined to ''auto'' 192 (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). 193 194 Here is the list of these attributes: \\ 468 However it is often very convienent to define the file name with the name of the experiment, the output file frequency and the date of the beginning and the end of the simulation (which are informations stored either in the namelist or in the XML file). To do so, we added the following rule: if the id of the tag file is ''fileN''(where N = 1 to 99) or one of the predefined sections or moorings (see next subsection), the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:\\ 469 \\ 470 \begin{tabular}{|p{4cm}|p{8cm}|} 471 \hline 472 \centering placeholder string & automatically replaced by \\ 473 \hline 474 \hline 475 \centering @expname@ & 476 the experiment name (from cn\_exp in the namelist) \\ 477 \hline 478 \centering @freq@ & 479 output frequency (from attribute output\_freq) \\ 480 \hline 481 \centering @startdate@ & 482 starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd? format \\ 483 \hline 484 \centering @startdatefull@ & 485 starting date of the simulation (from nn\_date0 in the restart or the namelist). \verb?yyyymmdd_hh:mm:ss? format \\ 486 \hline 487 \centering @enddate@ & 488 ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd? format \\ 489 \hline 490 \centering @enddatefull@ & 491 ending date of the simulation (from nn\_date0 and nn\_itend in the namelist). \verb?yyyymmdd_hh:mm:ss? format \\ 492 \hline 493 \end{tabular}\\ 494 \\ 495 496 \noindent For example, 497 {{\scriptsize 498 \begin{verbatim} 499 <file id="myfile_hzoom" name="myfile_@expname@_@startdate@_freq@freq@" output_freq="1d" > 500 \end{verbatim} 501 }} 502 \noindent with the namelist: 503 {{\scriptsize 504 \begin{verbatim} 505 cn_exp = "ORCA2" 506 nn_date0 = 19891231 507 ln_rstart = .false. 508 \end{verbatim} 509 }} 510 \noindent will give the following file name radical: 511 {{\scriptsize 512 \begin{verbatim} 513 myfile_ORCA2_19891231_freq1d 514 \end{verbatim} 515 }} 516 517 \subsubsection{Other controls of the xml attributes from NEMO} 518 519 The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary). 520 521 Here is the list of these attributes:\\ 195 522 \\ 196 523 \begin{tabular}{|l|c|c|c|} … … 202 529 \multicolumn{2}{|c|}{field\_definition} & freq\_op & \np{rn\_rdt} \\ 203 530 \hline 204 \multicolumn{2}{|c|}{SBC} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\ 205 \hline 206 1h, 2h, 3h, 4h, 6h, 12h & \_grid\_T, \_grid\_U, & name & filename defined by \\ 207 1d, 3d, 5d & \_grid\_V, \_grid\_W, & & a call to rou{dia\_nam} \\ 208 1m, 2m, 3m, 4m, 6m & \_icemod, \_ptrc\_T, & & following NEMO \\ 209 1y, 2y, 5y, 10y & \_diad\_T, \_scalar & & nomenclature \\ 531 \multicolumn{2}{|c|}{SBC} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_fsbc} \\ 532 \hline 533 \multicolumn{2}{|c|}{ptrc\_T} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 534 \hline 535 \multicolumn{2}{|c|}{diad\_T} & freq\_op & \np{rn\_rdt} $\times$ \np{nn\_dttrc} \\ 210 536 \hline 211 537 \multicolumn{2}{|c|}{EqT, EqU, EqW} & jbegin, ni, & according to the grid \\ 212 538 \multicolumn{2}{|c|}{ } & name\_suffix & \\ 213 539 \hline 214 \multicolumn{2}{|c|}{TAO, RAMA and PIRATA moorings} & ibegin, jbegin,& according to the grid \\540 \multicolumn{2}{|c|}{TAO, RAMA and PIRATA moorings} & zoom\_ibegin, zoom\_jbegin, & according to the grid \\ 215 541 \multicolumn{2}{|c|}{ } & name\_suffix & \\ 216 542 \hline … … 218 544 219 545 220 \subsection{ Detailed functionalities}546 \subsection{XML reference tables} 221 547 222 548 \subsubsection{Tag list} 223 549 224 \begin{description} 225 226 \item[context]: define the model using the xml file. Id is the only attribute accepted. 227 Its value must be ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom. Child of simulation tag. 228 229 \item[field]: define the field to be output. Accepted attributes are axis\_ref, description, enable, 230 freq\_op, grid\_ref, id (if child of field\_definition), level, operation, name, ref (if child of file), 231 unit, zoom\_ref. Child of field\_definition, file or group of fields tag. 232 233 \item[field\_definition]: definition of the part of the xml file corresponding to the field definition. 234 Accept the same attributes as field tag. Child of context tag. 235 236 \item[group]: define a group of file or field. Accept the same attributes as file or field. 237 238 \item[file]: define the output file's characteristics. Accepted attributes are description, enable, 239 output\_freq, output\_level, id, name, name\_suffix. Child of file\_definition or group of files tag. 240 241 \item[file\_definition]: definition of the part of the xml file corresponding to the file definition. 242 Accept the same attributes as file tag. Child of context tag. 243 244 \item[axis]: definition of the vertical axis. Accepted attributes are description, id, positive, size, unit. 245 Child of axis\_definition tag. 246 247 \item[axis\_definition]: definition of the part of the xml file corresponding to the vertical axis definition. 248 Accept the same attributes as axis tag. Child of context tag 249 250 \item[grid]: definition of the horizontal grid. Accepted attributes are description and id. 251 Child of axis\_definition tag. 252 253 \item[grid\_definition]: definition of the part of the xml file corresponding to the horizontal grid definition. 254 Accept the same attributes as grid tag. Child of context tag 255 256 \item[zoom]: definition of a subdomain of an horizontal grid. Accepted attributes are description, id, 257 i/jbegin, ni/j. Child of grid tag. 258 259 \end{description} 550 \begin{longtable}{|p{2.2cm}|p{2.5cm}|p{3.5cm}|p{2.2cm}|p{1.6cm}|} 551 \hline 552 tag name & 553 description & 554 accepted attribute & 555 child of & 556 parent of \endhead 557 \hline 558 simulation & 559 this tag is the root tag which encapsulates all the content of the xml file & 560 none & 561 none & 562 context \\ 563 \hline 564 context & 565 encapsulates parts of the xml file dedicated to different codes or different parts of a code & 566 id (''xios'', ''nemo'' or ''n\_nemo'' for the nth AGRIF zoom), src, time\_origin & 567 simulation & 568 all root tags: ... \_definition \\ 569 \hline 570 \hline 571 field\_definition & 572 encapsulates the definition of all the fields that can potentially be outputted & 573 axis\_ref, default\_value, domain\_ref, enabled, grid\_ref, level, operation, prec, src & 574 context & 575 field or field\_group \\ 576 \hline 577 field\_group & 578 encapsulates a group of fields & 579 axis\_ref, default\_value, domain\_ref, enabled, group\_ref, grid\_ref, id, level, operation, prec, src & 580 field\_definition, field\_group, file & 581 field or field\_group \\ 582 \hline 583 field & 584 define a specific field & 585 axis\_ref, default\_value, domain\_ref, enabled, field\_ref, grid\_ref, id, level, long\_name, name, operation, prec, standard\_name, unit & 586 field\_definition, field\_group, file & 587 none \\ 588 \hline 589 \hline 590 file\_definition & 591 encapsulates the definition of all the files that will be outputted & 592 enabled, min\_digits, name, name\_suffix, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 593 context & 594 file or file\_group \\ 595 \hline 596 file\_group & 597 encapsulates a group of files that will be outputted & 598 enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 599 file\_definition, file\_group & 600 file or file\_group \\ 601 \hline 602 file & 603 define the contents of a file to be outputted & 604 enabled, description, id, min\_digits, name, name\_suffix, output\_freq, output\_level, split\_freq\_format, split\_freq, sync\_freq, type, src & 605 file\_definition, file\_group & 606 field \\ 607 \hline 608 axis\_definition & 609 define all the vertical axis potentially used by the variables & 610 src & 611 context & 612 axis\_group, axis \\ 613 \hline 614 axis\_group & 615 encapsulates a group of vertical axis & 616 id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & 617 axis\_definition, axis\_group & 618 axis\_group, axis \\ 619 \hline 620 axis & 621 define a vertical axis & 622 id, lon\_name, positive, src, standard\_name, unit, zoom\_begin, zoom\_end, zoom\_size & 623 axis\_definition, axis\_group & 624 none \\ 625 \hline 626 \hline 627 domain\_\-definition & 628 define all the horizontal domains potentially used by the variables & 629 src & 630 context & 631 domain\_\-group, domain \\ 632 \hline 633 domain\_group & 634 encapsulates a group of horizontal domains & 635 id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 636 domain\_\-definition, domain\_group & 637 domain\_\-group, domain \\ 638 \hline 639 domain & 640 define an horizontal domain & 641 id, lon\_name, src, zoom\_ibegin, zoom\_jbegin, zoom\_ni, zoom\_nj & 642 domain\_\-definition, domain\_group & 643 none \\ 644 \hline 645 \hline 646 grid\_definition & 647 define all the grid (association of a domain and/or an axis) potentially used by the variables & 648 src & 649 context & 650 grid\_group, grid \\ 651 \hline 652 grid\_group & 653 encapsulates a group of grids & 654 id, domain\_ref, axis\_ref & 655 grid\_definition, grid\_group & 656 grid\_group, grid \\ 657 \hline 658 grid & 659 define a grid & 660 id, domain\_ref, axis\_ref & 661 grid\_definition, grid\_group & 662 none \\ 663 \hline 664 \end{longtable} 260 665 261 666 262 667 \subsubsection{Attributes list} 263 668 264 Applied to a tag or a group of tags. 265 266 % table to be added ? 267 Another table, perhaps? 268 269 %%%% 270 271 Attribute 272 Applied to? 273 Definition 274 Comment 275 axis\_ref 276 field 277 String defining the vertical axis of the variable. It refers to the id of the vertical axis defined in the axis tag. 278 Use ''non'' if the variable has no vertical axis 279 280 %%%%%% 281 282 \begin{description} 283 284 \item[axis\_ref]: field attribute. String defining the vertical axis of the variable. 285 It refers to the id of the vertical axis defined in the axis tag. 286 Use ''none'' if the variable has no vertical axis 287 288 \item[description]: this attribute can be applied to all tags but it is used only with the field tag. 289 In this case, the value of description will be used to define, in the output netcdf file, 290 the attributes long\_name and standard\_name of the variable. 291 292 \item[enabled]: field and file attribute. Logical to switch on/off the output of a field or a file. 293 294 \item[freq\_op]: field attribute (automatically defined, see part 1.4 (''control of the xml attributes'')). 295 An integer defining the frequency in seconds at which NEMO is calling iom\_put for this variable. 296 It corresponds to the model time step (rn\_rdt in the namelist) except for the variables computed 297 at the frequency of the surface boundary condition (rn\_rdt ? nn\_fsbc in the namelist). 298 299 \item[grid\_ref]: field attribute. String defining the horizontal grid of the variable. 300 It refers to the id of the grid tag. 301 302 \item[ibegin]: zoom attribute. Integer defining the zoom starting point along x direction. 303 Automatically defined for TAO/RAMA/PIRATA moorings (see part 1.4). 304 305 \item[id]: exists for all tag. This is a string defining the name to a specific tag that will be used 306 later to refer to this tag. Tags of the same category must have different ids. 307 308 \item[jbegin]: zoom attribute. Integer defining the zoom starting point along y direction. 309 Automatically defined for TAO/RAMA/PIRATA moorings and equatorial section (see part 1.4). 310 311 \item[level]: field attribute. Integer from 0 to 10 defining the output priority of a field. 312 See output\_level attribute definition 313 314 \item[operation]: field attribute. String defining the type of temporal operation to perform on a variable. 315 Possible choices are ''ave(X)'' for temporal mean, ''inst(X)'' for instantaneous, ''t\_min(X)'' for temporal min 316 and ''t\_max(X)'' for temporal max. 317 318 \item[output\_freq]: file attribute. Integer defining the operation frequency in seconds. 319 For example 86400 for daily mean. 320 321 \item[output\_level]: file attribute. Integer from 0 to 10 defining the output priority of variables in a file: 322 all variables listed in the file with a level smaller or equal to output\_level will be output. 323 Other variables won't be output even if they are listed in the file. 324 325 \item[positive]: axis attribute (always .FALSE.). Logical defining the vertical axis convention used 326 in \NEMO (positive downward). Define the attribute positive of the variable in the netcdf output file. 327 328 \item[prec]: field attribute. Integer defining the output precision. 329 Not implemented, we always output real4 arrays. 330 331 \item[name]: field or file attribute. String defining the name of a variable or a file. 332 If the name of a file is undefined, its id is used as a name. 2 files must have different names. 333 Files with specific ids will have their name automatically defined (see part 1.4). 334 Note that is name will be automatically completed by the cpu number (if needed) and ''.nc'' 335 336 \item[name\_suffix]: file attribute. String defining a suffix to be inserted after the name 337 and before the cpu number and the ''.nc'' termination. Files with specific ids have an 338 automatic definition of their suffix (see part 1.4). 339 340 \item[ni]: zoom attribute. Integer defining the zoom extent along x direction. 341 Automatically defined for equatorial sections (see part 1.4). 342 343 \item[nj]: zoom attribute. Integer defining the zoom extent along x direction. 344 345 \item[ref]: field attribute. String referring to the id of the field we want to add in a file. 346 347 \item[size]: axis attribute. use unknown... 348 349 \item[unit]: field attribute. String defining the unit of a variable and the associated 350 attribute in the netcdf output file. 351 352 \item[zoom\_ref]: field attribute. String defining the subdomain of data on which 353 the file should be written (to ouput data only in a limited area). 354 It refers to the id of a zoom defined in the zoom tag. 355 \end{description} 356 357 358 \subsection{IO\_SERVER} 359 360 \subsubsection{Attached or detached mode?} 361 362 Iom\_put is based on the io\_server developed by Yann Meurdesoif from IPSL 363 (see \href{http://forge.ipsl.jussieu.fr/ioserver/browser}{here} for the source code or 364 see its copy in NEMOGCM/EXTERNAL directory). 365 This server can be used in ''attached mode'' (as a library) or in ''detached mode'' 366 (as an external executable on n cpus). In attached mode, each cpu of NEMO will output 367 its own subdomain. In detached mode, the io\_server will gather data from NEMO 368 and output them split over n files with n the number of cpu dedicated to the io\_server. 369 370 \subsubsection{Control the io\_server: the namelist file xmlio\_server.def} 371 372 % 373 %Again, a small table might be more readable? 374 %Name 375 %Type 376 %Description 377 %Comment 378 %Using_server 379 %Logical 380 %Switch to use the server in attached or detached mode 381 %(.TRUE. corresponding to detached mode). 382 383 The control of the use of the io\_server is done through the namelist file of the io\_server 384 called xmlio\_server.def. 385 386 \textbf{using\_server}: logical, switch to use the server in attached or detached mode 387 (.TRUE. corresponding to detached mode). 388 389 \textbf{using\_oasis}: logical, set to .TRUE. if NEMO is used in coupled mode. 390 391 \textbf{client\_id} = ''oceanx'' : character, used only in coupled mode. 392 Specify the id used in OASIS to refer to NEMO. The same id must be used to refer to NEMO 393 in the \$NBMODEL part of OASIS namcouple in the call of prim\_init\_comp\_proto in cpl\_oasis3f90 394 395 \textbf{server\_id} = ''ionemo'' : character, used only in coupled mode. 396 Specify the id used in OASIS to refer to the IO\_SERVER when used in detached mode. 397 Use the same id to refer to the io\_server in the \$NBMODEL part of OASIS namcouple. 398 399 \textbf{global\_mpi\_buffer\_size}: integer; define the size in Mb of the MPI buffer used by the io\_server. 400 401 \subsubsection{Number of cpu used by the io\_server in detached mode} 402 403 The number of cpu used by the io\_server is specified only when launching the model. 404 Here is an example of 2 cpus for the io\_server and 6 cpu for opa using mpirun: 405 406 \texttt{ -p 2 -e ./ioserver} 407 408 \texttt{ -p 6 -e ./opa } 409 410 411 \subsection{Practical issues} 412 413 \subsubsection{Add your own outputs} 414 415 It is very easy to add you own outputs with iom\_put. 4 points must be followed. 416 \begin{description} 417 \item[1-] in NEMO code, add a \\ 418 \texttt{ CALL iom\_put( 'identifier', array ) } \\ 419 where you want to output a 2D or 3D array. 420 421 \item[2-] don't forget to add \\ 422 \texttt{ USE iom ! I/O manager library } \\ 423 in the list of used modules in the upper part of your module. 424 425 \item[3-] in the file\_definition part of the xml file, add the definition of your variable using the same identifier you used in the f90 code. 426 \vspace{-20pt} 427 \begin{alltt} {{\scriptsize 428 \begin{verbatim} 429 <field_definition> 430 ... 431 <field id="identifier" description="blabla" /> 432 ... 433 </field_definition> 434 \end{verbatim} 435 }}\end{alltt} 436 attributes axis\_ref and grid\_ref must be consistent with the size of the array to pass to iom\_put. 437 if your array is computed within the surface module each nn\_fsbc time\_step, 438 add the field definition within the group defined with the id ''SBC'': $<$group id=''SBC''...$>$ 439 440 \item[4-] add your field in one of the output files \\ 441 \vspace{-20pt} 442 \begin{alltt} {{\scriptsize 443 \begin{verbatim} 444 <file id="file_1" .../> 445 ... 446 <field ref="identifier" /> 447 ... 448 </file> 449 \end{verbatim} 450 }}\end{alltt} 451 452 \end{description} 453 454 \subsubsection{Several time axes in the output file} 455 456 If your output file contains variables with different operations (see operation definition), 457 IOIPSL will create one specific time axis for each operation. Note that inst(X) will have 458 a time axis corresponding to the end each output period whereas all other operators 459 will have a time axis centred in the middle of the output periods. 460 461 \subsubsection{Error/bug messages from IOIPSL} 462 463 If you get the following error in the standard output file: 464 \vspace{-20pt} 465 \begin{alltt} {{\scriptsize 466 \begin{verbatim} 467 FATAL ERROR FROM ROUTINE flio_dom_set 468 --> too many domains simultaneously defined 469 --> please unset useless domains 470 --> by calling flio_dom_unset 471 \end{verbatim} 472 }}\end{alltt} 473 474 You must increase the value of dom\_max\_nb in fliocom.f90 (multiply it by 10 for example). 475 476 If you mix, in the same file, variables with different freq\_op (see definition above), 477 like for example variables from the surface module with other variables, 478 IOIPSL will print in the standard output file warning messages saying there may be a bug. 479 \vspace{-20pt} 480 \begin{alltt} {{\scriptsize 481 \begin{verbatim} 482 WARNING FROM ROUTINE histvar_seq 483 --> There were 10 errors in the learned sequence of variables 484 --> for file 4 485 --> This looks like a bug, please report it. 486 \end{verbatim} 487 }}\end{alltt} 488 489 Don't worry, there is no bug, everything is properly working! 490 491 % } %end \gmcomment 669 \begin{longtable}{|p{2.2cm}|p{4cm}|p{3.8cm}|p{2cm}|} 670 \hline 671 attribute name & 672 description & 673 example & 674 accepted by \endhead 675 \hline 676 axis\_ref & 677 refers to the id of a vertical axis & 678 axis\_ref="deptht" & 679 field, grid families \\ 680 \hline 681 enabled & 682 switch on/off the output of a field or a file & 683 enabled=".TRUE." & 684 field, file families \\ 685 \hline 686 default\_value & 687 missing\_value definition & 688 default\_value="1.e20" & 689 field family \\ 690 \hline 691 description & 692 just for information, not used & 693 description="ocean T grid variables" & 694 all tags \\ 695 \hline 696 domain\_ref & 697 refers to the id of a domain & 698 domain\_ref="grid\_T" & 699 field or grid families \\ 700 \hline 701 field\_ref & 702 id of the field we want to add in a file & 703 field\_ref="toce" & 704 field \\ 705 \hline 706 grid\_ref & 707 refers to the id of a grid & 708 grid\_ref="grid\_T\_2D" & 709 field family \\ 710 \hline 711 group\_ref & 712 refer to a group of variables & 713 group\_ref="mooring" & 714 field\_group \\ 715 \hline 716 id & 717 allow to identify a tag & 718 id="nemo" & 719 accepted by all tags except simulation \\ 720 \hline 721 level & 722 output priority of a field: 0 (high) to 10 (low)& 723 level="1" & 724 field family \\ 725 \hline 726 long\_name & 727 define the long\_name attribute in the NetCDF file & 728 long\_name="Vertical T levels" & 729 field \\ 730 \hline 731 min\_digits & 732 specify the minimum of digits used in the core number in the name of the NetCDF file & 733 min\_digits="4" & 734 file family \\ 735 \hline 736 name & 737 name of a variable or a file. If the name of a file is undefined, its id is used as a name & 738 name="tos" & 739 field or file families \\ 740 \hline 741 name\_suffix & 742 suffix to be inserted after the name and before the cpu number and the ''.nc'' termination of a file & 743 name\_suffix="\_myzoom" & 744 file family \\ 745 \hline 746 attribute name & 747 description & 748 example & 749 accepted by \\ 750 \hline 751 \hline 752 operation & 753 type of temporal operation: average, accumulate, instantaneous, min, max and once & 754 operation="average" & 755 field family \\ 756 \hline 757 output\_freq & 758 operation frequency. units can be ts (timestep), y, mo, d, h, mi, s. & 759 output\_freq="1d12h" & 760 field family \\ 761 \hline 762 output\_level & 763 output priority of variables in a file: 0 (high) to 10 (low). All variables listed in the file with a level smaller or equal to output\_level will be output. Other variables won't be output even if they are listed in the file. & 764 output\_level="10"& 765 file family \\ 766 \hline 767 positive & 768 convention used for the orientation of vertival axis (positive downward in \NEMO). & 769 positive="down" & 770 axis family \\ 771 \hline 772 prec & 773 output precision: real 4 or real 8 & 774 prec="4" & 775 field family \\ 776 \hline 777 split\_freq & 778 frequency at which to temporally split output files. Units can be ts (timestep), y, mo, d, h, mi, s. Useful for long runs to prevent over-sized output files.& 779 split\_freq="1mo" & 780 file family \\ 781 \hline 782 split\_freq\-\_format & 783 date format used in the name of temporally split output files. Can be specified 784 using the following syntaxes: \%y, \%mo, \%d, \%h \%mi and \%s & 785 split\_freq\_format= "\%y\%mo\%d" & 786 file family \\ 787 \hline 788 src & 789 allow to include a file & 790 src="./field\_def.xml" & 791 accepted by all tags except simulation \\ 792 \hline 793 standard\_name & 794 define the standard\_name attribute in the NetCDF file & 795 standard\_name= "Eastward\_Sea\_Ice\_Transport" & 796 field \\ 797 \hline 798 sync\_freq & 799 NetCDF file synchronization frequency (update of the time\_counter). units can be ts (timestep), y, mo, d, h, mi, s. & 800 sync\_freq="10d" & 801 file family \\ 802 \hline 803 attribute name & 804 description & 805 example & 806 accepted by \\ 807 \hline 808 \hline 809 time\_origin & 810 specify the origin of the time counter & 811 time\_origin="1900-01-01 00:00:00"& 812 context \\ 813 \hline 814 type (1)& 815 specify if the output files are to be split spatially (multiple\_file) or not (one\_file) & 816 type="multiple\_file" & 817 file familly \\ 818 \hline 819 type (2)& 820 define the type of a variable tag & 821 type="boolean" & 822 variable \\ 823 \hline 824 unit & 825 unit of a variable or the vertical axis & 826 unit="m" & 827 field and axis families \\ 828 \hline 829 zoom\_ibegin & 830 starting point along x direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings & 831 zoom\_ibegin="1" & 832 domain family \\ 833 \hline 834 zoom\_jbegin & 835 starting point along y direction of the zoom. Automatically defined for TAO/RAMA/PIRATA moorings & 836 zoom\_jbegin="1" & 837 domain family \\ 838 \hline 839 zoom\_ni & 840 zoom extent along x direction & 841 zoom\_ni="1" & 842 domain family \\ 843 \hline 844 zoom\_nj & 845 zoom extent along y direction & 846 zoom\_nj="1" & 847 domain family \\ 848 \hline 849 \end{longtable} 850 492 851 493 852 … … 544 903 domain size in any dimension. The algorithm used is: 545 904 905 \vspace{-20pt} 546 906 \begin{alltt} {{\scriptsize 547 907 \begin{verbatim}
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