Getting Started in Linux/Unix

2018-08-13T18:31:00Z

Bblanton: /* Running the Serial Quarter Annular Harbor Test Case */

== Getting Started in Linux/Unix ==

As with most useful and complex models, just getting started is the main initial barrier. This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. <strong> If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. </strong> And although the general process of running ADCIRC on a Windoze computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windoze computer. See "Compiling and Running ADCIRC on Windoze" instead.

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described.

This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit files (using an editor such as vi/vim, emacs (really?), or a GUI editor)
* is familiar with working on computers via the "command line" (i.e., not clicking around with the mouse as in Windoze)
* has the source code (which is not freely available)
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran (the best language eva') and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: [https://en.wikipedia.org/wiki/Fortran Fortran-Wikipedia] and this: [https://en.wikipedia.org/wiki/Compiler Compilers-Wikipedia].

==== Which Compiler Do I Use? ====
If you are working on a desktop machine, you probably know if a compiler is available. If one is not available and you have administrative access to the computer, install the GNU fortran compiler. Otherwise, have an administrative user install it. The compiler is available here: https://gcc.gnu.org/wiki/GFortranBinaries

If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are high that a Fortran compiler exists on that machine. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them.

Regardless, let's assume that you have a compiler identified. The mechanics of compiling ADCIRC are independent of the specific compiler.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders" in Windoze parlance). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. Assuming that you have the gfortran compiler available somewhere on your environment's PATH, edit the cmplrflags.mk file by uncommenting the line that says "compiler=gnu". This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type "make adcirc" to compile the serial ADCIRC model.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail here: [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/].
The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. It looks like this:

[[File:testcase_grid2.png|Quarter Annular Harbor Test Case Grid]]

Get the test case, if you have not already done so. The serial case is here: [http://www.unc.edu/ims/adcirc/test_cases/quarter_annular/serial_quarter_annular_v51_52_20.zip] Unzip/untar the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and uncompress the contents.

There are 16 files in this directory. The fort.14 and fort.15 files are <strong>input</strong> files. The rest are output by ADCIRC and contain various parts of the solution.

File:Testcase grid2.png

2018-08-13T18:30:02Z

Bblanton:

2018-08-10T13:54:42Z

Bblanton:

Getting Started with Running ADCIRC in Linux/Unix

2018-08-10T13:53:21Z

Bblanton:

== Getting Started in Linux/Unix ==

As with most useful and complex models, just getting started is the main initial barrier. This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. <strong> If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. </strong> And although the general process of running ADCIRC on a Windoze computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windoze computer. See "Compiling and Running ADCIRC on Windoze" instead.

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described.

This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit files (using an editor such as vi/vim, emacs (really?), or a GUI editor)
* is familiar with working on computers via the "command line" (i.e., not clicking around with the mouse as in Windoze)
* has the source code (which is not freely available)
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran (the best language eva') and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: https://en.wikipedia.org/wiki/Compiler

==== Which Compiler Do I Use? ====
If you are working on a desktop machine, you probably know if a compiler is available. If one is not available and you have administrative access to the computer, install the GNU fortran compiler. Otherwise, have an administrative user install it. The compiler is available here: https://gcc.gnu.org/wiki/GFortranBinaries

If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are high that a Fortran compiler exists on that machine. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them.

Regardless, let's assume that you have a compiler identified. The mechanics of compiling ADCIRC are independent of the specific compiler.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders" in Windoze parlance). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. Assuming that you have the gfortran compiler available somewhere on your environment's PATH, edit the cmplrflags.mk file by uncommenting the line that says "compiler=gnu". This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type "make adcirc" to compile the serial ADCIRC model.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail here: [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/].
The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. It looks like this:

[[File:Example.jpg|thumb|Quarter Annular Harbor Test Case Grid]]

Get the test case, if you have not already done so. The serial case is here: [http://www.unc.edu/ims/adcirc/test_cases/quarter_annular/serial_quarter_annular_v51_52_20.zip] Unzip/untar the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and uncompress the contents.

There are 16 files in this directory. The fort.14 and fort.15 files are <strong>input</strong> files. The rest are output by ADCIRC and contain various parts of the solution.

Getting Started with Running ADCIRC in Linux/Unix

2018-08-10T13:48:09Z

Bblanton: Created page with "== Getting Started with Running ADCIRC in Linux/Unix == As with most useful and complex models, just getting started is the main initial barrier. This section of the wiki de..."

== Getting Started with Running ADCIRC in Linux/Unix ==

As with most useful and complex models, just getting started is the main initial barrier. This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. <strong> If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. </strong> And although the general process of running ADCIRC on a Windoze computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windoze computer. See "Compiling and Running ADCIRC on Windoze" instead.

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described.

This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit files (using an editor such as vi/vim, emacs (really?), or a GUI editor)
* is familiar with working on computers via the "command line" (i.e., not clicking around with the mouse as in Windoze)
* has the source code (which is not freely available)
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran (the best language eva') and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: https://en.wikipedia.org/wiki/Compiler

==== Which Compiler Do I Use? ====
If you are working on a desktop machine, you probably know if a compiler is available. If one is not available and you have administrative access to the computer, install the GNU fortran compiler. Otherwise, have an administrative user install it. The compiler is available here: https://gcc.gnu.org/wiki/GFortranBinaries

If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are high that a Fortran compiler exists on that machine. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them.

Regardless, let's assume that you have a compiler identified. The mechanics of compiling ADCIRC are independent of the specific compiler.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders" in Windoze parlance). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. Assuming that you have the gfortran compiler available somewhere on your environment's PATH, edit the cmplrflags.mk file by uncommenting the line that says "compiler=gnu". This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type "make adcirc" to compile the serial ADCIRC model.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail here: [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/].
The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. It looks like this:

[[File:Example.jpg|thumb|Quarter Annular Harbor Test Case Grid]]

Get the test case, if you have not already done so. The serial case is here: [http://www.unc.edu/ims/adcirc/test_cases/quarter_annular/serial_quarter_annular_v51_52_20.zip] Unzip/untar the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and uncompress the contents.

There are 16 files in this directory. The fort.14 and fort.15 files are <strong>input</strong> files. The rest are output by ADCIRC and contain various parts of the solution.

2018-08-08T18:01:30Z

Bblanton: