ROMS Mac - Revision history

Robertson at 15:22, 28 January 2021

2021-01-28T15:22:44Z

← Older revision		Revision as of 15:22, 28 January 2021
Line 3:		Line 3:
	Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his website. The particular system this is tested on is a MacBook Pro running Mac OS X 10.5.4, Darwin 9.4.0.		Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his website. The particular system this is tested on is a MacBook Pro running Mac OS X 10.5.4, Darwin 9.4.0.

	{{note}}<span class="red">'''Note:''' This tutorial is quite outdated ~~with~~ but we hope to update it soon.</span>		{{note}}<span class="red">'''Note:''' This tutorial is quite outdated but we hope to update it soon.</span>

	==Install Supporting Software==		==Install Supporting Software==

Robertson at 15:14, 28 January 2021

2021-01-28T15:14:11Z

← Older revision		Revision as of 15:14, 28 January 2021
Line 2:		Line 2:

	Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his website. The particular system this is tested on is a MacBook Pro running Mac OS X 10.5.4, Darwin 9.4.0.		Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his website. The particular system this is tested on is a MacBook Pro running Mac OS X 10.5.4, Darwin 9.4.0.

			{{note}}<span class="red">'''Note:''' This tutorial is quite outdated with but we hope to update it soon.</span>

	==Install Supporting Software==		==Install Supporting Software==

Robertson at 16:19, 8 January 2021

2021-01-08T16:19:38Z

← Older revision		Revision as of 16:19, 8 January 2021
Line 64:		Line 64:
	::<div class="box"><span class="forestGreen">mkdir Upwelling<br />cd Upwelling</span></div>		::<div class="box"><span class="forestGreen">mkdir Upwelling<br />cd Upwelling</span></div>

	:*Copy the <span class="red">roms_upwelling\.in</span> file into the <span class="red">Upwelling</span> directory you just created.		:*Copy the <span class="red">roms_upwelling.in</span> file into the <span class="red">Upwelling</span> directory you just created.
	::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/External/roms_upwelling\.in .</span></div>		::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/External/roms_upwelling.in .</span></div>

	:*Copy the <span class="red">upwelling.h</span> file into the <span class="red">Upwelling</span> directory in the same way.		:*Copy the <span class="red">upwelling.h</span> file into the <span class="red">Upwelling</span> directory in the same way.
Line 119:		Line 119:
	==Run ROMS==		==Run ROMS==

	:*We need to make one change to our <span class="red">roms_upwelling\.in</span> file so open it with your favorite editor and find the following line:<div class="box"> <span class="blue">VARNAME</span> = ROMS/External/varinfo.dat</div>and change it to (again replacing 'joeroms' with your Mac user name):<div class="box"> <span class="blue">VARNAME</span> = /home/joeroms/ROMS/trunk/ROMS/External/varinfo.dat</div>		:*We need to make one change to our <span class="red">roms_upwelling.in</span> file so open it with your favorite editor and find the following line:<div class="box"> <span class="blue">VARNAME</span> = ROMS/External/varinfo.dat</div>and change it to (again replacing 'joeroms' with your Mac user name):<div class="box"> <span class="blue">VARNAME</span> = /home/joeroms/ROMS/trunk/ROMS/External/varinfo.dat</div>
	:*Save and close the <span class="red">roms_upwelling\.in</span> file		:*Save and close the <span class="red">roms_upwelling.in</span> file
	:*In cygwin, within the <span class="red">Upwelling</span> directory where your <span class="forestGreen">oceanS</span> and <span class="red">roms_upwelling\.in</span> files live, type:		:*In cygwin, within the <span class="red">Upwelling</span> directory where your <span class="forestGreen">oceanS</span> and <span class="red">roms_upwelling.in</span> files live, type:
	::<div class="box"><span class="forestGreen">./oceanS < roms_upwelling\.in</span></div>		::<div class="box"><span class="forestGreen">./oceanS < roms_upwelling.in</span></div>

	If lots of numbers are displayed on the screen ROMS is running! Out of the box, ROMS comes programmed to run the Upwelling test case, which is what you are running now. When it finishes, the following output files are created:		If lots of numbers are displayed on the screen ROMS is running! Out of the box, ROMS comes programmed to run the Upwelling test case, which is what you are running now. When it finishes, the following output files are created:

Robertson: Text replacement - "ocean_(.*)\.in" to "roms_$1\.in"

2020-07-21T18:42:41Z

Text replacement - "ocean_(.*)\.in" to "roms_$1\.in"

← Older revision		Revision as of 18:42, 21 July 2020
Line 64:		Line 64:
	::<div class="box"><span class="forestGreen">mkdir Upwelling<br />cd Upwelling</span></div>		::<div class="box"><span class="forestGreen">mkdir Upwelling<br />cd Upwelling</span></div>

	:*Copy the <span class="red">~~ocean_upwelling~~.in</span> file into the <span class="red">Upwelling</span> directory you just created.		:*Copy the <span class="red">roms_upwelling\.in</span> file into the <span class="red">Upwelling</span> directory you just created.
	::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/External/~~ocean_upwelling~~.in .</span></div>		::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/External/roms_upwelling\.in .</span></div>

	:*Copy the <span class="red">upwelling.h</span> file into the <span class="red">Upwelling</span> directory in the same way.		:*Copy the <span class="red">upwelling.h</span> file into the <span class="red">Upwelling</span> directory in the same way.
Line 119:		Line 119:
	==Run ROMS==		==Run ROMS==

	:*We need to make one change to our <span class="red">~~ocean_upwelling~~.in</span> file so open it with your favorite editor and find the following line:<div class="box"> <span class="blue">VARNAME</span> = ROMS/External/varinfo.dat</div>and change it to (again replacing 'joeroms' with your Mac user name):<div class="box"> <span class="blue">VARNAME</span> = /home/joeroms/ROMS/trunk/ROMS/External/varinfo.dat</div>		:*We need to make one change to our <span class="red">roms_upwelling\.in</span> file so open it with your favorite editor and find the following line:<div class="box"> <span class="blue">VARNAME</span> = ROMS/External/varinfo.dat</div>and change it to (again replacing 'joeroms' with your Mac user name):<div class="box"> <span class="blue">VARNAME</span> = /home/joeroms/ROMS/trunk/ROMS/External/varinfo.dat</div>
	:*Save and close the <span class="red">~~ocean_upwelling~~.in</span> file		:*Save and close the <span class="red">roms_upwelling\.in</span> file
	:*In cygwin, within the <span class="red">Upwelling</span> directory where your <span class="forestGreen">oceanS</span> and <span class="red">~~ocean_upwelling~~.in</span> files live, type:		:*In cygwin, within the <span class="red">Upwelling</span> directory where your <span class="forestGreen">oceanS</span> and <span class="red">roms_upwelling\.in</span> files live, type:
	::<div class="box"><span class="forestGreen">./oceanS < ~~ocean_upwelling~~.in</span></div>		::<div class="box"><span class="forestGreen">./oceanS < roms_upwelling\.in</span></div>

	If lots of numbers are displayed on the screen ROMS is running! Out of the box, ROMS comes programmed to run the Upwelling test case, which is what you are running now. When it finishes, the following output files are created:		If lots of numbers are displayed on the screen ROMS is running! Out of the box, ROMS comes programmed to run the Upwelling test case, which is what you are running now. When it finishes, the following output files are created:

Robertson: New page:
Tutorial: Installing ROMS on a Macintosh
Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his webs...

2009-04-30T15:05:55Z

New page: <div class="title">Tutorial: Installing ROMS on a Macintosh</div> Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his webs...

New page

<div class="title">Tutorial: Installing ROMS on a Macintosh</div>

Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his website. The particular system this is tested on is a MacBook Pro running Mac OS X 10.5.4, Darwin 9.4.0.

==Install Supporting Software==

{{note}}<span class="red">Note:</span> most of this software needs to be installed in the order given (e.g. you need Xcode to have the installation of gfortran be right, and you need gfortran to make NetCDF).

===Xcode===

Download the Apple Developers Tools Xcode, from [http://developer.apple.com/technology/tools.html developer.apple.com/technology/tools.html], click the Xcode 3: free download link. Follow the standard installation (this means that it will install itself when you click on it, and you just need to click to accept a few defaults). To download this you need to sign up as an ADC member, but if you already have an Apple account (e.g. for iTunes) you can use that. It is free. {{warning}}<span class="red">Caution:</span> the download is about 1 GB.

===GNU Fortran Compiler===

Get <span class="red">gfortran-4.2.3.dmg</span> (the GNU Fortran compiler) from [http://r.research.att.com/tools r.research.att.com/tools/] and follow the standard installation. If the install is successful, executing <span class="forestGreen">which gfortran</span> in the Mac Terminal should give you the full path to the gfortran compiler:

:<div class="box"><span class="forestGreen">which gfortran</span><br>/usr/local/bin/gfortran</div>

===GNU Make===

{{note}}<span class="red">Note:</span> if you already have version '''3.8.1''' you can skip this step.

Get <span class="red">make-3.8.1.tar.gz</span> [http://ftp.gnu.org/pub/gnu/ from ftp.gnu.org/pub/gnu/]. Create the directory <span class="red">~/src</span> (<span class="red">~</span> is your home directory, normally a sub-directory of <span class="red">/Users</span>). Put the tar file into <span class="red">~/src</span> (note that the Mac download tool already gets rid of the ".gz"), and then extract it by executing:

:<div class="box"><span class="forestGreen">tar xvf make-3.8.1.tar</span></div>

Next, go into the new directory make-3.8.1 and execute the following three commands:

:<div class="box"><span class="forestGreen">./configure<br>make<br>sudo make install</span></div>

===Perl===

Perl is most likely already installed. However, if executing <span class="forestGreen">which perl</span> from a Mac Terminal tells you perl isn't found, you will need to install it.

===NetCDF===

Download <span class="red">netcdf-3.6.3.tar.gz</span> from [http://www.unidata.ucar.edu/software/netcdf www.unidata.ucar.edu/software/netcdf] (down on the lower right part of the page). This is the source code for '''NetCDF 3''', which you are going to compile on your machine using <span class="forestGreen">gfortran</span>, the same compiler you will use for compiling ROMS. You could also move up to '''NetCDF 4''', but this requires installing '''HDF5'''. Perhaps those instructions will be added later. Put the tar file in <span class="red">~/src</span>, extract it, and go into the directory <span class="forestGreen">netcdf-3.6.3</span> that is created. Also, make sure that the directory <span class="red">/opt</span> exists on your machine. Then execute (the second command has a capital "o" not a zero):

:<div class="box"><span class="forestGreen">export FC=gfortran<br>export FFLAGS='-O3'<br>./configure --prefix=/opt/gfortran/serial/netcdf3<br>make<br>make check<br>sudo make install</span></div>

===Subversion (SVN)===

Get subversion 1.5.2-2 from [http://www.collab.net/downloads/community www.collab.net/downloads/community] and follow the standard installation.

==Download ROMS==
This section assumes that you have registered and obtained your ROMS username/password.

Create the directory <span class="red">~/ROMS</span> and checkout the ROMS source code replacing 'joeroms' with your ROMS user name:

:<div class="box"><span class="forestGreen">cd ~<br>mkdir ROMS<br>cd ROMS<br>svn checkout --username joeroms <nowiki>https://www.myroms.org/svn/src/trunk</nowiki></span></div>

You will see many lines stream by. When it finishes, type <span class="forestGreen">ls</span>. You have a folder named <span class="red">trunk</span> that contains the ROMS source code.

{{note}}<span class="red">Note:</span> The first time you run the '''svn''' command you will be asked for your ROMS password and store it for future use.

==Customizing the [[build Script|Build Script]]==

The ROMS source code comes with a [[build Script|build script]] in the <span class="red">ROMS/Bin</span> directory. Examples written with <span class="forestGreen">bash</span> (<span class="red">build.bash</span>) and <span class="forestGreen">csh</span> (<span class="red">build.sh</span>) are provided. For convenience, we will work with <span class="red">build.bash</span> since <span class="forestGreen">bash</span> is the default shell on a Mac. A full description of the build script can be found [[build Script|here]].

:*At the same level as your new <span class="red">trunk</span> directory create a new folder named <span class="red">Projects</span> and change into it.
::<div class="box"><span class="forestGreen">mkdir Projects<br />cd Projects</span></div>

:*Create a folder named <span class="red">Upwelling</span> and change into it. 'Upwelling' is the name of the [[Test Cases|ROMS test case]] we are going to compile and run.
::<div class="box"><span class="forestGreen">mkdir Upwelling<br />cd Upwelling</span></div>

:*Copy the <span class="red">ocean_upwelling.in</span> file into the <span class="red">Upwelling</span> directory you just created.
::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/External/ocean_upwelling.in .</span></div>

:*Copy the <span class="red">upwelling.h</span> file into the <span class="red">Upwelling</span> directory in the same way.
::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/Include/upwelling.h .</span></div>

:*Copy the <span class="red">build.bash</span> file into the <span class="red">Upwelling</span> directory.
::<div class="box"><span class="forestGreen">cp ../../trunk/ROMS/Bin/build.bash .</span></div>

:*Open the <span class="red">build.bash</span> script you just copied into your <span class="red">Upwelling</span> directory using your favorite text editor.

:*Scroll down until you find <span class="orange">MY_ROOT_DIR</span> and <span class="orange">MY_ROOT_DIR</span>. Set them as follows (replacing 'joeroms' with your Mac user name).
::<div class="box"><span class="blue"> export</span> <span class="red">MY_ROOT_DIR</span>=/Users/joeroms/ROMS<br /><span class="blue"> export</span> <span class="red">MY_PROJECT_DIR</span>=${<span class="red">MY_ROOT_DIR</span>}/Projects/Upwelling</div>

:*Now set <span class="orange">MY_ROMS_SRC</span> to:
::<div class="box"><span class="blue"> export</span> <span class="red">MY_ROMS_SRC</span>=${<span class="red">MY_ROOT_DIR</span>}/trunk</div>

:*Make sure that <span class="orange">MY_CPP_FLAGS</span> is '''not''' set. I had to comment out one line with the # symbol like so:
::<div class="box">#<span class="blue">export</span> <span class="red">MY_CPP_FLAGS</span>="-DNPZD_POWELL"</div>

:*We are compiling in serial using the <span class="red">gfortran</span> compiler so make your <span class="red">build.bash</span> match the following:
::<div class="box"><span class="blue"> export</span> <span class="red">USE_MPI</span>=<br /><span class="blue"> export</span> <span class="red">USE_MPIF90</span>=<br /><span class="blue"> export</span> <span class="red">FORT</span>=gfortran</div>

:*Uncomment the line:
::<div class="box"><span class="blue">#export</span> <span class="red">USE_MY_LIBS</span>=on</div>to look like:<div class="box"><span class="blue"> export</span> <span class="red">USE_MY_LIBS</span>=on</div>

:*Find the <span class="forestGreen">gfortran</span> ''')''' section inside the '''<span class="blue">if</span> [ -n "${<span class="red">USE_MY_LIBS</span>:+1}" ]''' block.

:*Near the bottom of the <span class="forestGreen">gfortran</span> ''')''' section you will find the following lines:
::<div class="box">      '''else'''<br />          <span class="blue">export</span> <span class="red">NETCDF_INCDIR</span>=/opt/gfortransoft/serial/netcdf3/include<br />          <span class="blue">export</span> <span class="red">NETCDF_LIBDIR</span>=/opt/gfortransoft/serial/netcdf3/lib<br />      '''fi'''</div>change them to:<div class="box">      '''else'''<br />          <span class="blue">export</span> <span class="red">NETCDF_INCDIR</span>=/usr/local/include<br />          <span class="blue">export</span> <span class="red">NETCDF_LIBDIR</span>=/usr/local/lib<br />      '''fi'''</div>

:*Save and close the <span class="red">build.bash</span> file.

==Create the <span class="red">Darwin-gfortran.mk</span> file==

ROMS does not have a Mac-gfortran make module so you will need to create one. Luckily, the <span class="red">Linux-gfortran.mk</span> can be used without modification:

:<div class="box"><span class="forestGreen">cd ~/ROMS/trunk/Compilers<br>cp Linux-gfortran.mk Darwin-gfortran.mk<br>cd ~/ROMS/Projects/Upwelling</span></div>

==Compile ROMS==

Before you run ROMS, you need to compile it to create an executable <span class="red">oceanS</span> file. ROMS Source-Code files are readable by humans while executable files are readable by computers. The compilation process translates the source files into executables. Here are the instructions:

:*In cygwin, if you're not there already, go to the Upwelling directory:
::<div class="box"><span class="forestGreen">cd ~/roms/Projects/Upwelling</span></div>

:*Then type:
::<div class="box"><span class="forestGreen">./build.bash</span></div>

:*If lots of stuff comes on the screen then you are good. This will take ~15 min.
:*When it finishes type <span class="forestGreen">ls</span>; if you can see <span class="red">oceanS</span> (your executable file), then the compilation was successful.

==Run ROMS==

:*We need to make one change to our <span class="red">ocean_upwelling.in</span> file so open it with your favorite editor and find the following line:<div class="box"> <span class="blue">VARNAME</span> = ROMS/External/varinfo.dat</div>and change it to (again replacing 'joeroms' with your Mac user name):<div class="box"> <span class="blue">VARNAME</span> = /home/joeroms/ROMS/trunk/ROMS/External/varinfo.dat</div>
:*Save and close the <span class="red">ocean_upwelling.in</span> file
:*In cygwin, within the <span class="red">Upwelling</span> directory where your <span class="forestGreen">oceanS</span> and <span class="red">ocean_upwelling.in</span> files live, type:
::<div class="box"><span class="forestGreen">./oceanS < ocean_upwelling.in</span></div>

If lots of numbers are displayed on the screen ROMS is running! Out of the box, ROMS comes programmed to run the Upwelling test case, which is what you are running now. When it finishes, the following output files are created:

:<span class="red">ocean_avg.nc</span><br><span class="red">ocean_dia.nc</span><br><span class="red">ocean_his.nc</span><br><span class="red">ocean_rst.nc</span>

To learn one way to visualize them, [[Plotting Package Installation|click here]].

Thats it! You got ROMS running!

Now comes the hard part: Learn how to use ROMS. But by now you are probably all coffeed-up and ready learn more. [http://www.myroms.org/index.php?page=RomsPackages Click here] for a good place to start.

Good luck!

ROMS Mac - Revision history

Robertson at 15:22, 28 January 2021

Robertson at 15:14, 28 January 2021

Robertson at 16:19, 8 January 2021

Robertson: Text replacement - "ocean_(.*)\.in" to "roms_$1\.in"

Robertson: New page: Tutorial: Installing ROMS on a Macintosh Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his webs...

Robertson: New page:
Tutorial: Installing ROMS on a Macintosh
Special thanks to Parker MacCready at the University of Washington. Most of this tutorial is taken verbatim from his webs...