Talk:build roms - Revision history

Arango at 17:43, 2 June 2021

2021-06-02T17:43:51Z

← Older revision		Revision as of 17:43, 2 June 2021
Line 8:		Line 8:
	# Compile. Run the <span class="red">build_roms.csh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build_roms.csh -j 2</span></div>		# Compile. Run the <span class="red">build_roms.csh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build_roms.csh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build_roms.csh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build_roms.csh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./romsS''' < roms_lake_signell.in > & log & (Serial)<br />'''./romsO''' < roms_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./~~oceanM~~''' roms_lake_signell.in & log & (MPI)</div>		# Run <div class="box">'''./romsS''' < roms_lake_signell.in > & log & (Serial)<br />'''./romsO''' < roms_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./romsM''' roms_lake_signell.in >& log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''~~ocean_his~~.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''roms_his.nc'''</div>

Arango at 17:11, 2 June 2021

2021-06-02T17:11:43Z

← Older revision		Revision as of 17:11, 2 June 2021
Line 1:		Line 1:
	[[User:Rsignell\|Rsignell]] 17:31, 18 June 2007 (UTC)<br />		[[User:Rsignell\|Rsignell]] 17:31, 18 June 2007 (UTC)<br />
	----		----
	Here is an example of using the <span class="red">~~build~~.sh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!		Here is an example of using the <span class="red">build_roms.csh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!

	# Make a project directory. On our Opteron cluster, I have one directory where I keep the source code: <div class="box"><span class="twilightBlue">/home/rsignell/models/roms_rutgers/trunk</span></div>and another where I actually do model runs<div class="box"><span class="twilightBlue">/home/rsignell/projects</span></div>So on my system, for a new test, I make a directory called<div class="box"><span class="twilightBlue">/home/rsignell/projects/test1</span></div>		# Make a project directory. On our Opteron cluster, I have one directory where I keep the source code: <div class="box"><span class="twilightBlue">/home/rsignell/models/roms_rutgers/trunk</span></div>and another where I actually do model runs<div class="box"><span class="twilightBlue">/home/rsignell/projects</span></div>So on my system, for a new test, I make a directory called<div class="box"><span class="twilightBlue">/home/rsignell/projects/test1</span></div>
	# Checkout the source code using '''svn''' (or unpack the source code if you got a tarfile or zipfile somewhere) and copy the <span class="red">~~build~~.sh</span> script (which you will find in '''ROMS/Bin''' sub-directory) to your project directory.		# Checkout the source code using '''svn''' (or unpack the source code if you got a tarfile or zipfile somewhere) and copy the <span class="red">build_roms.csh</span> script (which you will find in '''ROMS/Bin''' sub-directory) to your project directory.
	# Edit <span class="red">~~build~~.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''~~pgi~~''', '''~~ifort~~''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build_roms.csh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''ifort''', '''gfortran''', '''pgi''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">~~build~~.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./~~build~~.sh -j 2</span></div>		# Compile. Run the <span class="red">build_roms.csh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build_roms.csh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">~~build~~.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build_roms.csh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./~~oceanS~~''' < roms_lake_signell.in > & log & (Serial)<br />'''./~~oceanO~~''' < roms_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' roms_lake_signell.in & log & (MPI)</div>		# Run <div class="box">'''./romsS''' < roms_lake_signell.in > & log & (Serial)<br />'''./romsO''' < roms_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' roms_lake_signell.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>

Robertson: Robertson moved page Talk:build Script to Talk:build roms: Script changed names

2021-05-24T13:53:06Z

Robertson moved page Talk:build Script to Talk:build roms: Script changed names

← Older revision	Revision as of 13:53, 24 May 2021
(No difference)

Robertson: Text replacement - "\.in" to ".in"

2021-01-08T17:35:19Z

Text replacement - "\.in" to ".in"

← Older revision		Revision as of 17:35, 8 January 2021
Line 7:		Line 7:
	# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>		# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell\.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell\.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./oceanS''' < roms_lake_signell\.in > & log & (Serial)<br />'''./oceanO''' < roms_lake_signell\.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' roms_lake_signell\.in & log & (MPI)</div>		# Run <div class="box">'''./oceanS''' < roms_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < roms_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' roms_lake_signell.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>

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

2020-07-21T18:47:37Z

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

← Older revision		Revision as of 18:47, 21 July 2020
Line 7:		Line 7:
	# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>		# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">~~ocean_lake_signell~~.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">~~ocean_lake_signell~~.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">roms_lake_signell\.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">roms_lake_signell\.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./oceanS''' < ~~ocean_lake_signell~~.in > & log & (Serial)<br />'''./oceanO''' < ~~ocean_lake_signell~~.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ~~ocean_lake_signell~~.in & log & (MPI)</div>		# Run <div class="box">'''./oceanS''' < roms_lake_signell\.in > & log & (Serial)<br />'''./oceanO''' < roms_lake_signell\.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' roms_lake_signell\.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>

Arango at 16:51, 6 March 2008

2008-03-06T16:51:44Z

← Older revision		Revision as of 16:51, 6 March 2008
Line 7:		Line 7:
	# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>		# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk~~</span>~~<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>		# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>

Arango at 17:34, 18 June 2007

2007-06-18T17:34:08Z

← Older revision		Revision as of 17:34, 18 June 2007
Line 1:		Line 1:
	[[User:~~Arango~~\|~~Arango~~]] 17:31, 18 June 2007 (UTC)<br />		[[User:Rsignell\|Rsignell]] 17:31, 18 June 2007 (UTC)<br />
			----
	Here is an example of using the <span class="red">build.sh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!		Here is an example of using the <span class="red">build.sh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!

Arango at 17:31, 18 June 2007

2007-06-18T17:31:15Z

← Older revision		Revision as of 17:31, 18 June 2007
Line 1:		Line 1:
			[[User:Arango\|Arango]] 17:31, 18 June 2007 (UTC)<br />
	Here is an example of using the <span class="red">build.sh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!		Here is an example of using the <span class="red">build.sh</span> script to build the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] test case, one of my favorites!

Arango at 16:04, 18 June 2007

2007-06-18T16:04:57Z

← Older revision		Revision as of 16:04, 18 June 2007
Line 5:		Line 5:
	# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>		# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>
	# Set up the input files for the run. ROMS uses several ASCII input ~~file~~ to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the ROMS/External directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk</span><br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input files to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the '''ROMS/External''' directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF metadata parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles ('''NtileI''', '''NtileJ''') I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk</span><br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>		# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>

Arango at 16:41, 16 June 2007

2007-06-16T16:41:34Z

← Older revision		Revision as of 16:41, 16 June 2007
Line 3:		Line 3:
	# Make a project directory. On our Opteron cluster, I have one directory where I keep the source code: <div class="box"><span class="twilightBlue">/home/rsignell/models/roms_rutgers/trunk</span></div>and another where I actually do model runs<div class="box"><span class="twilightBlue">/home/rsignell/projects</span></div>So on my system, for a new test, I make a directory called<div class="box"><span class="twilightBlue">/home/rsignell/projects/test1</span></div>		# Make a project directory. On our Opteron cluster, I have one directory where I keep the source code: <div class="box"><span class="twilightBlue">/home/rsignell/models/roms_rutgers/trunk</span></div>and another where I actually do model runs<div class="box"><span class="twilightBlue">/home/rsignell/projects</span></div>So on my system, for a new test, I make a directory called<div class="box"><span class="twilightBlue">/home/rsignell/projects/test1</span></div>
	# Checkout the source code using '''svn''' (or unpack the source code if you got a tarfile or zipfile somewhere) and copy the <span class="red">build.sh</span> script (which you will find in '''ROMS/Bin''' sub-directory) to your project directory.		# Checkout the source code using '''svn''' (or unpack the source code if you got a tarfile or zipfile somewhere) and copy the <span class="red">build.sh</span> script (which you will find in '''ROMS/Bin''' sub-directory) to your project directory.
	# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', ifort) and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the pgi compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.		# Edit <span class="red">build.sh</span> to specify: <div class="box"><span class="red">MY_ROMS_APPLICATION</span> [[LAKE_SIGNELL]]<br /><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk<br/><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>and set which compiler I want to use (e.g. '''pgi''', '''ifort''') and what type of executable I want (MPI, OpenMP, or Serial). Even though I use the '''pgi''' compiler on our cluster, I actually build MPI code using the [[mpif90]] script, so I set <span class="red">USE_MPIF90</span> '''on''' as well as '''pgi'''.
	# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs: <div class="box"><<span class="red">./build.sh -j 2</span></div>		# Compile. Run the <span class="red">build.sh</span> script. If you have more than one processor on the machine you are compiling on you can use the -j option to build faster. For example, to use 2 CPUs use: <div class="box"><span class="red">./build.sh -j 2</span></div>
	# Set up the input files for the run. ROMS uses an ASCII input file to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the ROMS/External directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk</span><br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>		# Set up the input files for the run. ROMS uses several ASCII input file to specify some of the run parameters, and we use the '''.in''' extension by convention to indicate these files. For the test cases, these are found in the ROMS/External directory. So to run ROMS from our project directory, we need to copy over the right input files for the [[LAKE_SIGNELL_CASE \| LAKE_SIGNELL]] case. We also want a copy of [[varinfo.dat]], which defines NetCDF parameters. <div class="box">'''cp''' <span class="twilightBlue">~/models/roms_rutgers/trunk/ROMS/External/{lake_signell.in,varinfo.dat} ~/projects/test1</span></div>I then need to modify <span class="twilightBlue">ocean_lake_signell.in</span> to point to the local directory to find [[varinfo.dat]], <span class="twilightBlue">floats_lake_signell.in</span> and <span class="twilightBlue">sediment_lake_signell.in</span>.<br />I can also edit <span class="twilightBlue">ocean_lake_signell.in</span> to specify how many tiles I want to have. If I want to run with Serial or OpenMP, I can specify the tiling however I want, but I want to run on 4 CPUs with MPI, the CPUs and number of tiles has to be the same. I want to run on 4 CPUS with MPI, so I leave the default 2x2 tiling. <br /><br />If you are lazy and don't want to make all these edits and just want to try it out, you can get<div class="box">http://stellwagen.er.usgs.gov/rps/share/lake_signell.tar.gz</div>and just edit these two lines (and perhaps the compiler options) in the <span class="red">build.sh</span> script<div class="box"><span class="red">MY_ROMS_SRC</span> /home/rsignell/models/roms_rutgers/trunk</span><br /><span class="red">MY_PROJECT_DIR</span> /home/rsignell/projects/test1</div>
	# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>		# Run <div class="box">'''./oceanS''' < ocean_lake_signell.in > & log & (Serial)<br />'''./oceanO''' < ocean_lake_signell.in > & log & (OpenMP)<br />'''mpirun''' -n 4 -hostfile node_file '''./oceanM''' ocean_lake_signell.in & log & (MPI)</div>
	# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>		# Check out the results<div class"box">[[ncview]] '''ocean_his.nc'''</div>