MANUAL DEL SWAN - JOSÉ CONTRERAS Call
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1. Carry out the following steps for setting up SWAN on your computer 1 An include file containing some machine dependent macros must be created first This file is called macros inc and can be created by typing 2 make config 3 Now SWAN can be built for serial or parallel mode as follows mode instruction serial make ser parallel shared make omp parallel distributed make mpi 4 IMPORTANT NOTES e To Windows users o To execute the above instructions just open a command prompt o To build SWAN on Windows platforms by means of a Makefile you need a make program However such a program is usually not available in MS Windows environment There are two alternatives to get a make program 1 You can download the Visual Studio 2005 2008 2010 Express for free http www microsoft com express This contains tools for building applications It also contains a make program called NMAKE EXE 2 You can download Nmake 1 5 for Win32 that is freely available see http support microsoft com default aspx scid kb en us 0132084 Run the downloaded file Nmake1 5 exe to extract it Copy both the NMAKE EXE and the NMAKE ERR file to SWAN directory o This setup does support OpenMP for Windows dual core systems 1f Intel Fortran compiler is provided o This installation currently supports MPICH2 for Windows XP Vista 7 older versions are probably not supported See Section 3 4 for further information o Itis assumed that both the2. corresponding operating system e g VAX systems If necessary change to e To insert TAB in the initialisation file just use the TAB key on your keyboard e Depending on the operating system the first directory separation character in swaninit as used in the input file may be replaced by the second one if appropriate e Date and time can be read and written according to various options The following options are available 1 19870530 153000 ISO notation 30 May 87 15 30 00 05 30 87 15 30 00 15 30 00 87 05 30 15 30 00 8705301530 WAM equivalence AA gin UN Note that the ISO notation has no millenium problem therefore the ISO notation is recommended In case of other options the range of valid dates is in between January 1 1911 and December 31 2010 both inclusive e Incase of a parallel MPI run at the machine having a number of independent processors it is important to assign subdomains representing appropriate amounts of work to each processor Usually this refers to an equal number of grid points per subdomain However if the computer has processors which are not all equally fast a so called heterogeneous machine then the sizes of the subdomains depend on the speed of the processors Faster processors should deal with more grid points than slower ones Therefore if necessary a list of non default processor speeds is provided The given speeds are in of default 100 As an illustrating example we hav
3. different PE sub directories So in principle in case of restarting the same number of processors must be employed Instead a MANUAL DEL SWAN 2013 single hotfile can be created from the existing local PE hotfiles using the program unhcat exe as available from SWAN version 40 91 This executable is generated from the Fortran program HottifySWAN ftn90 To concatenate the multiple hotfiles into a single hotfile globalization just execute unhcat exe With this program it is also possible to create a set of local PE hotfiles from an existing global hotfile localization over a different number of processors MANUAL DEL SWAN 2013 Testing the system The SWAN system consists of one executable file swan exe a command file swan edt and a run procedure swanrun bat Or swanrun Depending on your system you may use 32 bit or 64 bit executable These executables for Windows XP Vista 7 can be obtained from the SWAN web site The input and output to a number of test problems is provided on the SWAN web page The files with extension swn are the command files for these tests the files with extension bot are the bottom files for these tests etc This input can be used to make a configuration test of SWAN on your computer Compare the results with those in the provided output files Note that the results need not to be identical up to the last digit To run the SWAN program for the test cases at least 50 MBytes of free internal mem
4. hcat nml HottifySWAN ftn90 edit file swan edt Matlab scripts for unstructured grids plotunswan m plotgrid m documentations swanuse tex swanuse pdf swanimp tex swanimp pdf swantech tex swantech pdf swanpgr tex swanpgr pdf latexfordummies tex latexfordummies pdf conc st eps The Latex files tex can be read and written by any editor and can be compiled with LATEX2 This compilation can also be done automatically see Section 3 5 On the SWAN web page you also find some test cases with some output files for making a MANUAL DEL SWAN 2013 configuration test of SWAN on your computer You may compare your results with those in the provided output files MANUAL DEL SWAN 2013 Use of patch files Between releases of authorised SWAN versions it is possible that bug fixes or new features are published on the SWAN web page These are provided by patch files that can be downloaded from the web site Typically a patch can be installed over the top of the existing source code Patches are indicated by a link to patchfile The names refer to the current version number supplemented with letter codes The first will be coded A i e 40 91 A the second will be coded B the third will be coded C etc The version number in the resulting output files will be updated to 40 91 ABC indicating the implemented patches To use a patch file follow the next instructions 1 download the file right click the f
5. installation command reading routines miscellaneous routines general modules modules for XNL modules for unstructured erids agioncmd ftn90 swn outnc ftn90 couple2adcirc ftn90 ocpids ftn ocpcre ftn ocpmikx ftn swmod1 ftn swmod2 ftn m constants ftn90 m fileto ftn90 serv_xnl4v5 ftn90 mod xn14v5 ftn90 SwanGriddata ftn90 SwanGridobjects ftn90 SwanCompdata ftn90 The source code is written in Fortran 90 Some routines are written in fixed form and depending on your system the extension may be for or f Other routines are written in free form and are indicated by extension 90 The conversion from ftn or ftn90 to one of these extensions can be done automatically or manually see Chapter 3 You are allow to make changes in the source code of SWAN but Delft University of Technology will not support modified versions of SWAN If you ever want your modifications to be implemented in the authorized version of SWAN the version on the SWAN web page you need to submit these changes to the SWAN team swan info citg tudelft nl The source code 1s being attended with the following files installation procedures INSTALL README Makefile Makefile latex macros inc which cmd platform pl MANUAL DEL SWAN 2013 switch pl adjlth pl run procedures SWANRUN README swanrun swanrun bat machinefile for parallel MPI runs machinefile for concatenation of multiple hotfiles swanhcat ftn
6. of subdomains and copy each of them into the corresponding local PE sub directories Finally it will copy the SWAN command file into the local PE sub directories If you decide later that you want to run on more or fewer cores you must perform this step again So more specifically run adcprep and indicate the number of processors First you need to do mesh partition using METIS by selecting 1 partmesh Next rerun adcprep and continue with full pre processing by selecting 2 prepall or 3 prepspec and specify the necessary ADCIRC files fort 14 and fort 15 you may skip the file fort 19 Be sure that the initialisation file swaninit has been created before running adcprep You may adapt this initialisation file by renaming INPUT to your own SWAN command file Otherwise you may copy your command file to INPUT After the mesh and input files have been prepared with adcprep the actual SWAN calculation is performed using swan exe This program performs the calculation on each subdomain and uses MPI to provide ongoing communication between the subdomains The command required for actually starting the SWAN job is highly dependent on the cluster software and queueing system Either way use the new executable to run this model in much the same way you would run the parallel SWAN see Chapter 5 After the simulation is finished the output data will be automatically merged With respect to the generation of hotfiles it is usually done in
7. MANUAL DEL SWAN 2013 SWAN IMPLEMENTATION MANUAL SWAN Cycle III version 40 91A by The SWAN team mail address Delft University of Technology Faculty of Civil Engineering and Geosciences Environmental Fluid Mechanics Section P O Box 5048 2600 GA Delft The Netherlands e mail swan info citg tudelft nl home page Attp www swan tudelft nl Copyright c 1993 2013 Delft University of Technology Permission 1s granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later version published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts A copy of the license is available at http www gnu org licenses fdl html TOC1 MANUAL DEL SWAN 2013 e Introduction o The material e Use of patch files e Installation of SWAN on your computer o Quick installation o Manual installation Modifications in the source code Compiling and linking SWAN source code o Building with netCDF support o Installation of MPICH2 on Windows XP Vista 7 o Make SWAN documentation e User dependent changes and the file swaninit e Usage of SWAN executable e Compiling and running unstructured mesh SWAN in parallel o Code compilation o Running the model e Testing the system MANUAL DEL SWAN 2013 About this manual The information about the SWAN package is distributed over four different do
8. al regions where the water depth varies greatly As a result this variable spatial meshing gives the highest resolution where it 1s most needed The use of unstructured grids facilitates to resolve the MANUAL DEL SWAN 2013 model area with a relative high accuracy but with a much fewer grid points than with regular grids It must be pointed out that the application of SWAN on ocean scales is not recommended from an efficiency point of view The WAM model and the WAVEWATCH III model which have been designed specifically for ocean applications are probably one order of magnitude more efficient than SWAN SWAN can be run on large scales much larger than coastal scales but this option is mainly intended for the transition from ocean scales to coastal scales transitions where nonstationarity is an issue and spherical coordinates are convenient for nesting A general suggestion 1s start simple SWAN helps in this with default options Furthermore suggestions are given that should help the user to choose among the many options conditions and in which mode to run SWAN first second or third generation mode stationary or nonstationary and ID or 2D MANUAL DEL SWAN 2013 The material The downloaded file swan4091 tar gz contains the SWAN source code You can unzip this file either with WinRAR in case of Windows or with the command tar xzf in case of UNIX or Linux The SWAN source code consists of the following files main p
9. are all optionally The meaning of these options are as follows S0085 Un1 Depending on the operating system both the TAB and directory separator character must have a proper value see also Chapter 4 This can be done by removing the switch DOS or IUNIX for Windows and UNIX Linux platforms respectively in the subroutines OCPINI in ocpids ftn and TXPBLA in swanser ftn For other operating system e g Macintosh you should change the values of the following variables manually pircH1 DIRCH2 in OCPINT TABc in OCPINT and irabu in TXPBLA SE If you have a Fortran 95 compiler or a Fortran 90 compiler that supports Fortran 95 features it might be useful to activate the CPU TIME statement in the subroutines SWTSTA and SWTSTO in swanser ftn by removing the switch F95 meant for the detailed timings of several parts of the SWAN calculation Note that this can be obtained with the command TEST by setting itest 1 in your command file mpa For the proper use of MPI you must remove the switch MPI at several places in the file swanparll ftn swancoml ftn and swmod1 ftn DUun To enable to do parallel unstructured mesh simulation the switch IPUN must be removed at several places in different files CES SOL If you use a Cray or SGI Fortran 90 compiler the subroutines OCPINI in ocpids ftn and FOR in ocpmix ftn should be adapted by removing the switch Cray or SGI since these compilers cannot read write
10. command file However it is assumed that the extension of this file is swn Note that contrary to UNIX Linux Windows does not distinguish between lowercase and uppercase characters in filenames Next the user may also indicate whether the run is serial or parallel In case of Windows use the run procedure swanrun bat from a command prompt Swanrun filename nprocs where filename is the name of your command file without extension assuming it is swn and nprocs indicates how many processes need to be launched for a parallel MPI run do not type the brackets they just indicate that nprocs is optional By default nprocs 1 You may also run on a dual quad core computer do not set nprocs The command line for the UNIX script swanrun 1s as follows swanrun input filename omp n mpi n where filename 1s the name of your command file without extension Note that the script swanrun need to be made executable first as follows chmod rx swanrun The parameter omp n specifies a parallel run on n cores using OpenMP Note that the UNIX script will set OMP NUM THREADS to n The parameter mpi n specifies a parallel run on n processors using MPI The parameter input is obliged whereas the parameters omp nand mpi n can be omitted default n 1 To redirect screen output to a file use the sign gt Use an ampersand to run SWAN in the background An example swanrun input f3lhar01 omp 4 gt swanout amp For a parallel MPI ru
11. cuments This User Manual describes the complete input and usage of the SWAN package The Implementation Manual explains the installation procedure of SWAN on a single or multi processor machine with shared or distributed memory The Programming rules is meant for programmers who want to develop SWAN The Scientific Technical documentation discusses the physical and mathematical details and the discretizations that are used in the SWAN program The mapping of these numerical techniques in SWAN code is also discussed In Chapter 2 general description of the model and some instructions concerning the usage of SWAN the treatment of grids boundary conditions etc is given It 1s advised to read this chapter before consulting the rest of the manual Chapter 3 gives some remarks concerning the input and output files of SWAN Chapter 4 describes the complete set of commands of the program SWAN It is strongly advised that users who are not so experienced in the use of SWAN first read Chapters 2 and 3 This Manual also contains some appendices In Appendix A definitions of several output parameters are given Appendix B outlines the syntax of the command file or input file A complete set of all the commands use in SWAN can be found in Appendix C Appendix D described the format of the files for spectral input and output by SWAN MANUAL DEL SWAN 2013 General description and instructions for use Subsections e Introduction e Limitation
12. directories include and lib are resided in C PROGRAM FILES MPICH2 If not the file macros inc should be adapted such that they can be found by the Makefile e One of the commands make ser make omp and make mpi must be preceded once by make config MANUAL DEL SWAN 2013 e If desirable you may clean up the generated object files and modules by typing make clean If you want to delete any stray files from a previous compilation just type make clobber e If you are unable to install SWAN using the Makefile and Perl scripts for whatever reason see Section 3 2 for instructions on manual installation MANUAL DEL SWAN 2013 Manual installation Subsections e Modifications in the source code e Compiling and linking SWAN source code MANUAL DEL SWAN 2013 Modifications in the source code To compile SWAN on your computer system properly some subroutines should be adapted first depending on the operating system use of compilers and the wish to use MPI for parallel runs This can be done by removing the switches started with followed by an indentifiable prefix in the first 3 or 4 columns of the subroutine A Perl script called switch pl is provided in the material that enables the user to quickly select the switches to be removed This script can be used as follows perl switch pl dos unix E4206 mpi oil creay 591 57 CV1S tamg mati impi adcirc netcdfi lt itn where the options
13. downloaded from the downloads page http www mcs anl gov research projects mpich2 downloads index php s downloa ds e During installation select MPICH to be installed for Everyone e Also make sure that you keep the default setting for passphrase usually behappy during the installation e After installing MPICH2 successfully you may add rules to your firewall to allow the programs mpiexec exe and smpd exe to communicate through firewall This process depends on your firewall e You need to add the bin folder of MPICH2 usually C PROGRAM FILES MPICH2 bin to your PATH e Next open an admin command prompt by right clicking on the command prompt icon and selecting run as administrator In the command prompt type the following commands in sequence smpd install mpiexec remove mpiexec register mpiexec validate it should return SUCCESS smpd status it should return smpd running on lt hostname gt If the last two commands are successfully then you are ready to run SWAN in parallel See Chapter 5 Note that when you register you should indicate your username and password as a user Moreover if your machine is not part of a domain do not specify any domain name MANUAL DEL SWAN 2013 Make SWAN documentation SWAN comes with 4 detailed documents which are provided as downloadable PDF files as well as browsable web pages e The User Manual describes the complete input and usage of the SWAN package e The Imp
14. e module MPI in swmod1 ftn must be included by removing the switch impi adcirc To enable to do coupled ADCIRC SWAN simulation the switch ADC must be removed at several places in different files However for a standalone SWAN simulation the switch INADC must be removed while the switch ADC should not be removed netcdf For the proper use of netCDF you must remove the switch NCF at several places in different files For example you work on a Linux cluster where MPI has been installed and use the Intel Fortran compiler that can handle Fortran 95 statements then type the following perl SGwitci pk Gnix ES MOL ie afta MANUAL DEL SWAN 2013 Note that due to the option unix the extension ftn is automatically changed into f and ftn90 into 90 MANUAL DEL SWAN 2013 After the necessary modifications are made as described in the previous section the source code is ready for compilation All source code is written in Fortran 90 so you must have a Fortran 90 compiler in order to compile SWAN The source code cannot be compiled with a Fortran 77 compiler If you intended to use MPI for parallel runs you must use the command mpif90 instead of the original compiler command or using the Integrated Development Environment e g for Visual Fortran see Installation and User s Guide for MPICH2 The SWAN source code complies with the ANSI Fortran 90 standard except for a few cases where the limit of 19 contin
15. e two PC s connected via an Ethernet switch of which the first one 1s 1 5 times faster than the second one The list would be LSU speed of processor 1 100 speed of processor 2 Based on this list SWAN will automatically distribute the total number of active grid points over two subdomains in an appropriate manner Referring to the above example with 1000 active points the first and second subdomains will contain 600 and 400 grid points respectively MANUAL DEL SWAN 2013 Usage of SWAN executable To help you in editing an command file for SWAN input the file swan edt 1s provided Two run procedures are provided among the source code one for the Windows platform called swanrun bat and one for the UNIX Linux platform called swanrun Basically the run procedure carries out the following actions e Copy the command file with extension swn to INPUT assuming INPUT is the standard file name for command input see Chapter 4 e Run SWAN e Copy the file PRINT assuming PRINT is the standard file name for print output see Chapter 4 to a file which name equals the command file with extension prt On other operating system a similar procedure can be followed For parallel MPI runs the program mpirun or mpiexec is needed and is provided in the MPICH2 distribution Before calling the run procedure the environment variable PATH need to be adapted by including the pathname of the directory where swan exe can be found In case o
16. ed which enables a considerable reduction in the turn around time for relatively large CPU demanding calculations Two parallelization strategies are available e The computational kernel of SWAN contains a number of OpenMP compiler directives so that users can optionally run SWAN on a dual core PC or multiprocessor systems e A message passing modelling is employed based on the Message Passing Interface MPI standard that enables communication between independent processors Hence users can optionally run SWAN on a Linux cluster The material on the SWAN web site provides a Makefile and two Perl scripts platform pl and switch p1 that enables the user to quickly install SWAN on the computer in a proper manner For this the following platforms operating systems and compilers are supported platform OS F90 compiler SGI Origin 3000 Silicon Graphics IRIX SGI IBM SP AIX IBM Compaq True 64 Alpha DEC ALFA OSF1 Compaq Sun SPARC Solaris Sun PA RISC HP 9000 series 700 800 HP UXvll HP IBM Power6 pSeries 575 Linux IBM Intel Pentium 32 bit PC Linux GNU g95 Intel Pentium 32 bit PC Linux GNU gfortran Intel Pentium 32 bit PC Linux Intel Intel Pentium 64 bit PC Linux Intel Intel Itanium 64 bit PC Linux Intel Intel Pentium 64 bit PC Linux Portland Group Intel Pentium 32 bit PC Linux Lahey MANUAL DEL SWAN 2013 Intel Pentium 32 bit PC MS Windows Intel Intel Pentium 64 bit PC MS Windows Intel Int
17. el Pentium 32 bit PC MS Windows Compaq Visual Power Mac G4 Mac OS X IBM If your computer and available compiler is mentioned in the table you may consult Section 3 1 for a quick installation of SWAN Otherwise read Section 3 2 for a detailed description of the manual installation of SWAN Note that for a successful installation a Perl package must be available on your computer In most cases it 1s available for Linux and a UNIX operating system Check it by typing perl v Otherwise you can download a free distribution for Windows called ActivePerl see http www activestate com activeperl downloads The Perl version should be at least 5 0 0 or higher Before installation the user may first decide how to run the SWAN program There are three possibilities e serial runs e parallel runs on shared memory systems or e parallel runs on distributed memory machines For stationary and small scale computations it may be sufficient to choose the serial mode 1 e one SWAN program running on one processor However for relatively large CPU demanding calculations e g instationary or nesting ones two ways of parallelism for reducing the turn around time are available e The SWAN code contains a number of so called OpenMP directives that enables the compiler to generate multithreaded code on a shared memory computer For this you need a Fortran 90 compiler supporting OpenMP 2 0 The performance is good for a restricted number of thread
18. f Windows this pathname can be specified through the category System of Control Panel on the Advanced tab click Environment Variables In case of UNIX or Linux running the bash shell sh or ksh the environment variable PATH may be changed as follows export PATH S PATH usr local swan if usr local swan is the directory where the executable swan exe is resided In case of the C shell csh use the following command setenv PATH S PATH usr local swan If appropriate you also need to add the directory path where the bin directory of MPICH2 is resided to PATH to have access to the command mpiexec You may also specify the number of threads to be used during execution of the multithreaded implementation of SWAN on multiprocessor systems The environment variable for this is OMP_NUM THREADS and can be set like export OMP NUM THREADS 4 or setenv OMP NUM THREADS 4 or in case of Windows OMP NUM THREADS 4 When dynamic adjustment of the number of threads is enabled the value given in OMP NUM THREADS represents the maximum number of threads allowed MANUAL DEL SWAN 2013 The provided run procedures enable the user to properly and easily run SWAN both serial as well as parallel MPI or OpenMP Note that for parallel MPI runs the executable swan exe Should be accessible by copying it to all the multiple machines or by placing it in a shared directory When running the SWAN program the user must specify the name of the
19. g option 100 speed of processor ik 100 speed of processor 2 100 speed of processor 3 100 speed of processor 4 Explanation e The version number of the initialisation file is included in the file so that SWAN can verify whether the file it reads is a valid initialisation file The current version 1s 4 e The initialisation file provides a character string containing the name of the institute that may carry out the computations or modifying the source code You may assign it to the name of your institute instead of DELFT UNIVERSITY OF TECHNOLOGY which is the present value e The standard input file and standard print file are usually named INPUT and PRINT respectively You may rename these files if appropriate e The unit reference numbers for the input and print files are set to 3 and 4 respectively If necessary you can change these numbers into the standard input and output unit numbers for your installation Another unit reference number is foreseen for output to screen and it set to 6 There is also a unit number for a separate test print file In the version that you downloaded from our web page this is equal to that of the print file so that test output will appear on the same file as the standard print output MANUAL DEL SWAN 2013 e The comment identifier to be used in the command file is usually but on some computer system this may be inappropriate because a line beginning with S is interpreted as a command for the
20. ile and choose save link as 2 place it in the directory where the source code of SWAN 1s located 3 execute patch p0 lt patchfile After applying a patch or patches you need to recompile the SWAN source code It is important to download the patch and not cut and paste it from the display of your web browser The reason for this is that some patches may contain tabs and most browsers will not preserve the tabs when they display the file Copying and pasting that text will cause the patch to fail because the tabs would not be found If you have trouble with patch you can look at the patch file itself Note to UNIX Linux users the downloaded patch files are MS DOS ASCII files and contain carriage return CR characters To convert these files to UNIX format use the command dos2unix Alternatively execute cat 40 91 A C tr d r patch that apply the patch files 40 91 A to 40 91 C to the SWAN source code at once after which the conversion is carried out Note to Windows users patch 1s a UNIX command Download the patch program from the SWAN web site which is appropriate for Windows operating system XP Vista 7 MANUAL DEL SWAN 2013 Installation of SWAN on your computer The portability of the SWAN code between different platforms 1s guaranteed by the use of standard ANSI FORTRAN 90 Hence virtually all Fortran compilers can be used for installing SWAN See also the manual Programming rules The SWAN code is paralleliz
21. ion of unstructured grids is far more optimal compared to structured grids Unstructured grids may contain triangles or a combination of triangles and quadrilaterals so called hybrid grids In the current version of SWAN however only triangular meshes can be employed Often the characteristic spatial scales of the wind waves propagating from deep to shallow waters are very diverse and would required to allow local refinement of the mesh near the coast without incurring overhead associated with grid adaptation at some distance offshore Traditionally this can be achieved by employing a nesting approach The idea of nesting is to first compute the waves on a coarse grid for a larger region and then on a finer grid for a smaller region The computation on the fine grid uses boundary conditions that are generated by the computation on the coarse grid Nesting can be repeated on ever decreasing scales using the same type of coordinates for the coarse computations and the nested computations Cartesian or spherical Note that curvi linear grids can be used for nested computations but the boundaries should always be rectangular The use of unstructured grids in SWAN offers a good alternative to nested models not only because of the ease of optimal adaption of mesh resolution but also the modest effort needed to generate grids about complicated geometries e g islands and irregular shorelines This type of flexible meshes is particularly useful in coast
22. istence of this file is an indication to study the results with more care e A file called ERRPTS or renamed by the run procedures as well as more than one file in case of parallel MPI runs containing the grid points where specific errors occured during the calculation such as non convergence of an iterative matrix solver Existence of this file is an indication to study the spectrum in that grid point with more care If indicated by the user a single or multiple hotfiles will be generated depending on the number of processors 1 e the number of hotfiles equals the number of processors see the User Manual Restarting a parallel MPI run can be either from a single concatenated hotfile or from multiple hotfiles In the latter case the number of processors must be equal to the number of generated hotfiles If appropriate the single hotfile can be created from a set of multiple hotfiles using the program hcat exe as available from SWAN version 40 51A This executable is generated from the Fortran program swanhcat ftn A self contained input file hcat nm1 is provided This file contains e g the basis name of the hotfile To concatenate the multiple hotfiles into a single hotfile just execute hcat exe MANUAL DEL SWAN 2013 Compiling and running unstructured mesh SWAN in parallel In order to efficiently carry out high resolution simulations with the unstructured mesh version of SWAN a parallel code is build using message pas
23. lementation Manual explains the installation procedure of SWAN on a single or multi processor machine with shared or distributed memory e The Programming rules is meant for programmers who want to develop SWAN e The Technical documentation discusses the mathematical details and the discretizations that are used in the SWAN program These documents are written in L TEX format If you are new to L TEX we recommend to read first the manual L TEX for dummies that is available in the SWAN material The PDF files are very easy to generate by just typing MANUAL DEL SWAN 2013 User dependent changes and the file swanini SWAN allows you to customize the input and the output to the wishes of your department company or institute This can be done by changing the settings in the initialisation file swaninit which is created during the first time SWAN is executed on your computer system The changes in swaninit only affect the runs executed in the directory that contains that file A typical initialisation file swaninit may look like 4 version of initialisation file Delft University of Technology name of institute 3 command file ref number INPUT command file name 4 print file ref number PRINT print file name 4 test file ref number test file name 6 screen ref number 99 highest file ref number comment identifier TAB TAB character dir sep char in input file 2 dir sep char replacing previous one 1 default time codin
24. lines longer than 256 characters by default By means MANUAL DEL SWAN 2013 of the option rect in the OPEN statement sufficiently long lines can be read write by these compilers cvis The same subroutines OCPINI and FOR need also to be adapted when the Compag Visual Fortran compiler is used in case of a parallel MPI run Windows systems have a well known problem of the inability of opening a file by multiple SWAN executables This can be remedied by using the option sHarep in the OPEN statement for shared access For this just remove the switch CVIS i LING If the user want to print the timings both wall clock and CPU times in seconds of different processes within SWAN then remove the switch TIMG Otherwise no timings will be keeped up and subsequently printed in the PRINT file matl4 By default the created binary Matlab files are of Level 5 MAT File format and are thus compatible with MATLAB version 5 and up In this case the switch MatL5 must be removed However some machines do not support a 1 byte unit for the record length e g IBM Power6 At those computers the binary Matlab files must be formatted of Level 4 In this case the switch MatL4 must be removed while the switch MatL5 should not be removed Level 4 MAT files are compatible with MATLAB versions 4 and earlier However they can be read with the later versions of MATLAB impi Some Fortran compilers do not support USE MPI statement and therefore th
25. n you may also need a machinefile that contains the names of the nodes in your parallel environment Put one node per line in the file Lines starting with the character are comment lines You can specify a number after the node name to indicate how many cores to launch on the node This is useful e g for multi core processors The run procedure will cycle through this list until all the requested processes are launched Example of such a file may look like here eight processes will be launched nodel node2 2 node4 node7 4 Note that for Windows platforms a space should be used instead of a colon as the separation character in the machinefile SWAN will generate a number of output files MANUAL DEL SWAN 2013 e A print file with the name PRINT that can be renamed by the user with a batch DOS or script UNIX file e g with the provided run procedures For parallel MPI runs however a sequence of PRINT files will be generated PRINT 001 PRINT 002 etc depending on the number of processors The print file s contain s the echo of the input information concerning the iteration process possible errors timings etc e Numerical output such as table spectra and block output appearing in files with user provided names e A file called Errfile or renamed by the run procedures as well as more than one file in case of parallel MPI runs containing the error messages is created only when SWAN produces error messages Ex
26. ory is recommended For more realistic cases 100 to 500 MBytes may be needed whereas for more simple stationary or 1D cases significant less memory is needed less than 5 MBytes for 1D cases
27. probably first need to remove the files that were created during the compilation of the commonly used SWAN model You can do this by typing make clobber to remove the stray files If necessary type make config to have SWAN attempt to create a file macros inc with compiler flags for your system Be sure to complete the line O DIR work odir4 where the abovementioned object files are resided Then type make punswan to make the parallel unstructured mesh version of SWAN It will follow the SWAN convention of assigning the name swan exe to the executable MANUAL DEL SWAN 2013 Running the model The main difference between running commonly used SWAN in parallel and running the unstructured mesh version of SWAN in parallel on a multi core cluster is the need to explicitly decompose the unstructured mesh and input files e g fort 14 and fort 15 into smaller pieces so that each piece can run on its own core on the cluster The program adcprep 1S used to perform the decomposition The actual mesh partitioning is done by the well known METIS package http glaros dtc umn edu gkhome views metis In order to break up the original input files which describe the full domain into smaller pieces called subdomains go to the directory where the input files are located and execute adcprep You need to specify the number of cores that you plan to use for the simulation The program will decompose your input files into that number
28. rogram swanmain ftn pre processing routines swanpre 1 ftn swanpre2 ftn SwanBndStruc ftn90 computational routines swancoml ftn swancom2 ftn swancom3 ftn swancom4 ftn swancom5S ftn post processing routines swanoutl ftn swanout2 ftn service routines swanser ftn SwanIntgratSpc ftn90 routines for support parallel MPI runs swanparll ftn routines for unstructured grids SwanReadGrid ftn90 SwanReadADCGrid ftn90 SwanReadTriangleGrid ftn90 SwanReadEasymeshGrid ftn90 SwanInitCompGrid ftn90 SwanCheckGrid ftn90 SwanCreateEdges ftn90 SwanGridTopology ftn90 SwanGridVert ftn90 SwanGridCell ftn90 SwanGridFace ftn90 MANUAL DEL SWAN 2013 SwanPrintGridInfo ftn90 SwanFindPoint ftn90 SwanPointinMesh ftn90 SwanBpntlist ftn90 SwanPrepComp ftn90 SwanVertlist ftn90 SwanCompUnstruc ftn90 SwanDispParm ftn90 SwanPropvelX ftn90 SwanSweepSel ftn90 SwanPropvelS ftn90 SwanTranspAc ftn90 SwanTranspX ftn90 SwanDiffPar ftn90 SwanGSECorr ftn90 SwanInterpolatePoint ftn90 SwanlInterpolate Ac ftn90 SwanInterpolateOutput ftn90 SwanConvAccur ftn90 SwanConvStopc ftn90 Swan ThreadBounds ftn90 SwanFindObstacles ftn90 SwanCrossObstacle ftn90 SwanComputeForce ftn90 routines for parallel unstructured grids SwanReadfort18 ftn90 SwanSumOverNodes ftn90 SwanMinOverNodes ftn90 SwanMaxOverNodes ftn90 SwanPunCollect ftn90 modules and subroutines for netCDF nctablemd ftn90 MANUAL DEL SWAN 2013 couplers routines for
29. s lt 8 This type of parallelism can be used e g on Symmetric multiprocessors and PC s with dual core or quad core processors e Ifthe user want to run SWAN on a relative large number of processors a message passing model is a good alternative It is based on independent processors which do not share any memory but are connected via an interconnection network e g cluster of Linux PC s connected via fast Ethernet switches The implementation is based on the Message Passing Interface MPI standard e g MPICH2 distribution freely available for several platforms such as Linux and Windows at http www unix mcs anl gov mpi mpich The SWAN code contains a set of generic subroutines MANUAL DEL SWAN 2013 that call a number of MPI routines meant for local data exchange gathering data global reductions etc This technique is beneficial for larger simulations only such that the communication times are relatively small compared to the computing times e Fora proper installation of MPICH2 on Windows XP Vista 7 please consult Section 3 4 e Consult Chapter 6 for parallel unstructured mesh simulations on distributed memory machines Subsections e Quick installation e Manual installation o Modifications in the source code o Compiling and linking SWAN source code e Building with netCDF support e Installation of MPICH2 on Windows XP Vista 7 e Make SWAN documentation MANUAL DEL SWAN 2013 Quick installation
30. s e Internal scenarios limiters shortcomings and coding bugs e Relation to WAM WAVEWATCH III and others e Units and coordinate systems e Choice of grids time windows and boundary initial first guess conditions o Introduction o Input grid s and time window s o Computational grids and boundary initial first guess conditions o Output grids e Activation of physical processes e Time and date notation MANUAL DEL SWAN 2013 Introduction The purpose of this chapter is to give some general advice in choosing the basic input for SWAN computations SWAN 1s a third generation wave model for obtaining realistic estimates of wave parameters in coastal areas lakes and estuaries from given wind bottom and current conditions However SWAN can be used on any scale relevant for wind generated surface gravity waves The model is based on the wave action balance equation with sources and sinks An important question addressed 1s how to choose various grids in SWAN resolution orientation etc including nesting In general we consider two types of grids structured and unstructured Structured grids may be recti linear and uniform or curvi linear They always consist of quadrilaterals in which the number of grid cells that meet each other in an internal grid point is 4 In unstructured grids this number can be arbitrarily usually between 4 and 10 For this reason the level of flexibility with respect to the grid point distribut
31. sing paradigm and tested on a commodity computer cluster In parallelizing unstructured mesh version of SWAN we employ the same paradigm as applied in the circulation model ADCIRC http www adcirc org and so the parallel version of the unstructured mesh SWAN model uses the same domain decomposition and localized communication as the parallel version of ADCIRC For a proper use version 50 of ADCIRC must be employed For details on the implementation and use of the coupled ADCIRC SWAN model go to http www caseydietrich com swanadcirc It is assumed that the unstructured mesh is stored in the file fort 14 and the associated model domain information is stored in fort 15 and that these files are yet available Subsections e Code compilation e Running the model MANUAL DEL SWAN 2013 Code compilation The parallel version of the unstructured SWAN model utilizes the parallel infrastructure from parallel ADCIRC Specifically it needs the MKDIR SIZES GLOBAL and MESSENGER object files So those need to be compiled before the parallel unstructured mesh SWAN model is compiled Also for mesh partition a program called adcprep need to be compiled as well These compilations are performed typically by navigating to the directory work and typing make adcprep padcirc Make sure that the DADcsWAN flag has been added to the DPRE line in the cmplrflags mk file To compile the parallel version of the unstructured mesh SWAN model you
32. swan exe after linking Referring to the previous example compilation and linking may be done as follows Mmp3f90 swnodl f swmod2 f m constants 90 m Ti11eT10 T190 serv xn1l4v5 T90 mod xnl4v5 f90 SwanGriddata f90 SwanGridobjects f90 SwanCompdata 90 ocp f swan f Swan f90 o swan exe MANUAL DEL SWAN 2013 Building with netCDF support SWAN 40 91A contains extensions that provide netCDF output of spectra and maps of several wave parameters Carry out the following steps 1 Make sure that netCDF 4 1 x is compiled and available on your system For details consult htfp www unidata ucar edu software netcdf docs netcdf install The Fortran interface must have been enabled when netCDF was bullt 2 Define the variable NETCDFROOT in file macros inc to point to the netCDF root directory e g NETCDFROOT usr local netcdf 4 1 3 in case of Linux or NETCDFROOT C PROGRAM FILES netcdf in case of Windows This enables to compile netCDF I O into SWAN 3 Build SWAN as usual e g make mpi see Section 3 1 MANUAL DEL SWAN 2013 Installation of MPICH2 on Windows XP Vista 7 SWAN can be built with support for MPI It is assumed that MPI has been installed already in the Linux environment However this is probably not the case for Windows This section instructs you how to install MPI in the Windows environment It is assumed that your OS is either Windows XP Vista or 7 e Install MPICH2 on your machine using the installer
33. uation lines is violated We are currently not aware of any compiler that cannot deal with this violation of the ANSI standard When compiling SWAN you should check that the compiler allocates the same amount of memory for all INTEGERS REAL and LoGicaALs Usually for these variables 4 bytes are allocated on supercomputers vector or parallel however this sometimes is 8 bytes When a compiler allocates 8 bytes for a reaL and 4 bytes for an InTEGER for example SWAN will not run correctly Furthermore SWAN can generate binary MATLAB files on request which are unformatted Some compilers e g Compaq Visual Fortran and Intel Fortran version 9 x or higher measured record length in 4 byte or longword units and as a consequence these unformatted files cannot be loaded in MATLAB Hence in such as case a compiler option is needed to request I byte units e g for Compaq Visual Fortran this is assume byterecl and for Intel Fortran version 9 x or higher this is assume byterecl The modules in files swmod1 ftn swmod2 ftn m constants ftn90 m fileio ftn90 Serv xnl4v5 ftn90 mod _ xnl4v5 ftn90 SwanGriddata ftn90 SwanGridobjects ftn90 and SwanCompdata ftn90 must be compiled first Several subroutines use these modules These subroutines need the compiled versions of the modules before they can be compiled Linking should be done without any options nor using shared libraries e g math or NAG It 1s recommended to rename the executable to
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