Compiling SA_MESH (r965)

Transcription

1 Compiling SA_MESH (r965) Instructions: Code availability: Copy code from giws_research : Modelling_Code/SA_MESH/MESH_Code r965 is the most recent version of the code

2 Compiling SA_MESH (r965) cd to your local copy of the code: cd /cygdrive/c/data/temp/mesh_code/trunk/r965

3 Compiling SA_MESH (r965) Run make (serial) or make -f makefile_mpi (parallelized) Running make will create sa_mesh Running make -f makefile_mpi will create mpi_sa_mesh

4 Compiling SA_MESH (r965) Run make clean (serial) or make -f makefile_mpi clean (parallelized) to remove intermediate files (e.g., *.o and *.mod files created during the build process) Always clean the folder when switching between computer architectures and compilers (e.g., between gfortran, ifort, and mpifort)

5 Running SA_MESH (r965) Copy sa_mesh or mpi_sa_mesh to a folder containing input files for SA_MESH

6 Running SA_MESH (r965) cd to the folder containing MESH input files

7 Running SA_MESH (r965) - sa_mesh in serial Run./sa_mesh

8 Running SA_MESH (r965) - mpi_sa_mesh in parallel Run mpirun -np 3./mpi_sa_mesh mpirun cannot be run from cmd.exe without calling mintty.exe Consider running mpi_sa_mesh from a single, central location to avoid adding exceptions to Windows Firewall rules

9 Running SA_MESH (r965) - mpi_sa_mesh in parallel Run mpirun -np 3./mpi_sa_mesh

10 Running SA_MESH (r965) - mpi_sa_mesh in Serial Run./mpi_sa_mesh This will run mpi_sa_mesh in serial Only one version of the code needs to be compiled, mpi_sa_mesh, which can be run in serial or in parallel, and is compiled using mpifort

11 Working in Eclipse (for Parallel Application Developers) Instructions: If this is the first time using Eclipse: Download and extract "Eclipse for Parallel Application Developers": Start Eclipse by running "eclipse.exe Close the Welcome page Open the Fortran perspective by clicking from the menu bar: Window > Open Perspective > Other... > Fortran

12 Working in Eclipse (Eclipse for Parallel Application Developers) Create a new project: File > New > Fortran Project Name the project and select the project type: Others > Executable (Gnu Fortran on Windows) Click Finish

13 Working in Eclipse (Eclipse for Parallel Application Developers) Open the properties of the project: Uncheck Generate Makefiles automatically (it s best to use the makefile and makefile.def provided with the code) Take note of the Build directory

14 Working in Eclipse (Eclipse for Parallel Application Developers) Make sure the Build directory exists in the project folder makefile and makefile.def will be imported to this folder

15 Working in Eclipse (Eclipse for Parallel Application Developers) Import a copy of makefile and makefile.def : Right-click on the Build directory > Import > File System > Select the files Click Finish

16 Working in Eclipse (Eclipse for Parallel Application Developers) Update the DIR_REPO variable in makefile.def If the file doesn t open because of its extension: Right-click > Open With > Other > Makefile Editor Comment all other DIR_REPO declarations in the file (using the number sign)

17 Working in Eclipse (Eclipse for Parallel Application Developers) Create targets to connect Eclipse to the build commands in makefile : all: Compile all code clean: Clean intermediate objects (e.g., *.o and *.mod files) veryclean: Clean intermediate objects as well as sa_mesh or mpi_sa_mesh

18 Working in Eclipse (Eclipse for Parallel Application Developers) Double-click the target to execute the build command The status of the build command shows up in the Console pane The Binaries group is added to the project, which contains sa_mesh or mpi_sa_mesh

19 Working in Eclipse (Eclipse for Parallel Application Developers) Linking to Source files (Soft-links) This is good practice for working with the repository DIR_REPO in makefile.def can point directly to the repository Soft-links are created to the source files No source files are copied to the project If soft-links are created to the repository, code is automatically updated in the Eclipse project by SVN Update Soft-links should not be used to link makefile or makefile.def Copies of these files are imported to the Build directory

20 Working in Eclipse (Eclipse for Parallel Application Developers) Create soft-links to the files: Right-click on the project > Import > File System Browse to the local copy of the code or of the repository Expand the tree-view, select a folder, and select the desired files Do not click Finish

21 Working in Eclipse (Eclipse for Parallel Application Developers) To create soft-links to files (Continued): Expand >> Advanced Check Create links in workspace Check Create link locations relative to to preserve the folder structure Click Finish

22 Working in Eclipse (Eclipse for Parallel Application Developers) Files that are symbolically linked are marked with a shortcut arrow Not all files have to be imported (e.g., if only CLASS files or for a particular module) The DIR_REPO variable in makefile.def is used to find the rest of the code In this scenario, all code should be soft-linked makefile and makefile.def are the only files copied into the Eclipse project

23 Working in Eclipse (Eclipse for Parallel Application Developers) Changes made to linked files are saved in the original file Do not make symbolic links directly to giws_research, make symbolic links to a local copy of this code or to a local copy of the repository

24 Working with the Repository The current URL: svn://watflood.uwaterloo.ca/mesh You don t have access right now, but I ve put in a request for user credentials NEVER EVER commit non-text/binary files to the repository This includes: Word documents, Excel spreadsheets, Zip files, files in binary sequential format, compiled code ONLY commit text files (e.g., source code) to the repository If you do not want or need to edit code, you can copy code or binaries from giws_research : Modelling_Code/SA_MESH/MESH_Code

25 Working with the Repository On Windows, TortoiseSVN can be used to interact with the repository:

26 Working with the Repository Once you have credentials, you can update your existing local copy of the repository: Rightclick on the folder > SVN Tortoise > Relocate A valid username and password are required to access and browse the repository

27 Working with the Repository Alternatively, a new local copy of the repository can be created: Right-click in a folder > SVN Checkout Update the Checkout directory Click Choose items

28 Working with the Repository Select the most recent tag from the tree-view: Tags > SA_MESH > SA_MESH_ Select: TRUNK Click OK to close the window

29 Working with the Repository Select HEAD Revision to get the latest revision of code Optionally, select Revision and enter a revision in the textbox (e.g., 965) to checkout a specific revision of the code Optionally, click Show log to show the commit history (i.e., to show a list of revisions) Click OK

30 Working with the Repository TortoiseSVN will download files and create a local copy of the repository

31 Working with the Repository More details on the repository will be discussed at next week s developer meeting: Thursday, June 30, 2 PM?

32 Interacting with the Standalone MESH Wiki GIWS members have access to privileges on the Standalone MESH Wiki Old user IDs and password should still work too, but login is required via the guest login page (and not via PAWS CAS):

33 Interacting with the Standalone MESH Wiki Log in via PAWS CAS or using the guest login page

34 Interacting with the Standalone MESH Wiki Once logged in, you can contribute to Wiki articles You can also Watch an article to receive notifications when that article has been changed

35 Interacting with the Standalone MESH Wiki You can use the search box to search for tags, content, and articles

36 Some extra resources on the Wiki Running Python in Cygwin: l Compiling and running on Plato: nd+parallel+mpi Forcing data sources (2011):