Tutorial - Revision history

Apwillis: /* Start the run */

2020-07-15T09:52:15Z

Start the run

← Older revision		Revision as of 02:52, 15 July 2020
Line 97:		Line 97:
	Here we see that the state used as the initial condition was saved at simulation time 200, and that the time has been reset to 0. We also see the increase in Reynolds number Re and a slight increase in the radial resolution, N.		Here we see that the state used as the initial condition was saved at simulation time 200, and that the time has been reset to 0. We also see the increase in Reynolds number Re and a slight increase in the radial resolution, N.

	If a message like the following appears in the terminal window		If a message like the following appears almost immediately in the terminal window
	'[1]+ Done nohup ./main.out ...'		'[1]+ Done nohup ./main.out ...'
	then it is likely that there was an error. In that case, try		then it is likely that there was an error. In that case, try
Line 105:		Line 105:
	running instead with		running instead with
	> mpirun -np 1 ./main.out > OUT 2> OUT.err &		> mpirun -np 1 ./main.out > OUT 2> OUT.err &
	You might need to include a path to mpirun; ~~search~~ your <tt>Makefile</tt> ~~for the mpirun command~~.		You might need to include a path to mpirun; copy the path from that to the mpif90 command in your <tt>Makefile</tt>.

	=== Monitor the run ===		=== Monitor the run ===

Apwillis: /* Where to start - initial conditions and the main.info file */

2020-07-15T09:44:30Z

Where to start - initial conditions and the main.info file

← Older revision		Revision as of 02:44, 15 July 2020
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	-rw-rw-r-- 1 758 Jul 16 2014 main.info		-rw-rw-r-- 1 758 Jul 16 2014 main.info
	-rw-rw-r-- 1 3177740 Jun 10 2013 state0010.cdf.dat		-rw-rw-r-- 1 3177740 Jun 10 2013 state0010.cdf.dat
	The directory <tt>Re2400a1.25/</tt> contains an output state file <tt>state0010.cdf.dat</tt> and a <tt>main.info</tt> file. The [[main.info]] file is a record of parameter settings that were used when compiling the executable that produced the state file.		The directory <tt>Re2400a1.25/</tt> contains an output state file <tt>state0010.cdf.dat</tt> and a <tt>main.info</tt> file. The [[main.info]] file is a plain text record of parameter settings that were used when compiling the executable that produced the state file.

	'''A more computationally demanding example:''' You may wish to start from [[File:Re5300.Retau180.5D.tgz]] and compare data with Eggels et al. (1994) JFM. To run at a reasonable pace, try running on 5-10 cores.		'''A more computationally demanding example:''' You may wish to start from [[File:Re5300.Retau180.5D.tgz]] and compare data with Eggels et al. (1994) JFM. To run at a reasonable pace, try running on 5-10 cores.

Apwillis: /* Monitor the run */

2018-07-16T14:22:08Z

Monitor the run

← Older revision		Revision as of 07:22, 16 July 2018
Line 181:		Line 181:
	> quit		> quit
	</pre>		</pre>
	This is a rough plot indicating the drop-off in amplitude of coefficients ~~(the drop-off in energies will be the square of these values)~~, defined by E_k = max_{nm} a_{nkm}, E_m = max_{nk} a_{nkm}, E_n = max_{km} a_{nkm}, where n is the index of axial resolution, k for axial and m for azimuthal.		This is a rough plot indicating the drop-off in amplitude of coefficients, defined by E_k = max_{nm} a_{nkm}, E_m = max_{nk} a_{nkm}, E_n = max_{km} a_{nkm}, where n is the index of axial resolution, k for axial and m for azimuthal.

	Ideally, the lines should all drop by around 3-4 orders of magnitude or more. If there is an upward spike at the end of one of the lines, then this is usually the signature of a timestep that is too large.		Ideally, the lines should all drop by around 3-4 orders of magnitude or more. If there is an upward spike at the end of one of the lines, then this is usually the signature of a timestep that is too large.

Apwillis: /* Make a util */

2018-07-03T10:08:32Z

Make a util

← Older revision		Revision as of 03:08, 3 July 2018
Line 216:		Line 216:
	Let's return to the code,		Let's return to the code,
	cd <path>/openpipeflow-x.xx/		cd <path>/openpipeflow-x.xx/
			Let's compile the utility
			utils/prim2matlab.f90
	In <tt>Makefile</tt>, ensure that it is set to make the <tt>prim2matlab</tt> utility,		In <tt>Makefile</tt>, ensure that it is set to make the <tt>prim2matlab</tt> utility,
	UTIL = prim2matlab [~~ommitting~~ the .f90 extension]		UTIL = prim2matlab [ommit the .f90 extension]
	~~In the <tt>utils/</tt> directory there is a corresponding file <tt>prim2matlab.f90</tt>.~~		Now,
	> make		> make
	> make install		> make install

Apwillis: /* Start the run */

2018-01-03T12:22:52Z

Start the run

← Older revision		Revision as of 05:22, 3 January 2018
Line 95:		Line 95:
	initialising output files...		initialising output files...
	timestepping.....		timestepping.....
	Here we see that the state used as the initial condition was saved at simulation time 200, and that the time has been reset to 0. We also see the increase in Reynolds number $Re$ and a slight increase in the radial resolution, $N$.		Here we see that the state used as the initial condition was saved at simulation time 200, and that the time has been reset to 0. We also see the increase in Reynolds number Re and a slight increase in the radial resolution, N.

	If a message like the following appears in the terminal window		If a message like the following appears in the terminal window

Apwillis: /* Start the run */

2018-01-03T12:22:09Z

Start the run

← Older revision		Revision as of 05:22, 3 January 2018
Line 86:		Line 86:
	Output and errors normally sent to the terminal window are redirected to the OUT files.		Output and errors normally sent to the terminal window are redirected to the OUT files.

	~~A few seconds after starting~~ the job, ~~press enter again~~.		To check the job started as expected, try
	If ~~there is~~ a message like		> head OUT
			precomputing function requisites...
			loading state...
			t : 199.999999999963 --> 0.000000000000000E+000
			Re : 2400.00000000000 --> 2500.00000000000
			N : 60 --> 64
			initialising output files...
			timestepping.....
			Here we see that the state used as the initial condition was saved at simulation time 200, and that the time has been reset to 0. We also see the increase in Reynolds number $Re$ and a slight increase in the radial resolution, $N$.

			If a message like the following appears in the terminal window
	'[1]+ Done nohup ./main.out ...'		'[1]+ Done nohup ./main.out ...'
	then it is likely that there was an error. In that case, try		then it is likely that there was an error. In that case, try

Apwillis: /* Monitor the run */

2017-12-20T11:40:09Z

Monitor the run

← Older revision		Revision as of 04:40, 20 December 2017
Line 121:		Line 121:
	-rw-rw-r-- 1 2901 Dec 20 11:21 vel_spec0002.dat		-rw-rw-r-- 1 2901 Dec 20 11:21 vel_spec0002.dat
	-rw-rw-r-- 1 33615 Dec 20 11:22 vel_totEID.dat		-rw-rw-r-- 1 33615 Dec 20 11:22 vel_totEID.dat
	The code outputs snapshot data, which includes a 4-digit number e.g. <tt>vel_spec0003.dat</tt> and <tt>state0012.cdf.dat</tt>,		The code outputs
	~~and~~ time-series data, e.g. the energy as a function of time <tt>vel_energy.dat</tt>.		* '''snapshot data''', which includes a 4-digit number e.g. <tt>vel_spec0003.dat</tt> and <tt>state0012.cdf.dat</tt>, saved every <tt>i_save_rate1</tt> (typically 2000) timesteps, and
	~~Snapshot data is saved every <tt>i_save_rate1</tt> (typically 2000) timesteps~~, ~~and time-series data is~~ saved every <tt>i_save_rate2</tt> (typically 10) timesteps .		* '''time-series data''', e.g. the energy as a function of time <tt>vel_energy.dat</tt>, saved every <tt>i_save_rate2</tt> (typically 10) timesteps .
	~~Sometimes the time-series files are buffered, i.e. no output is written until the buffer is filled. The OUT file is less likely to be buffered.~~

	To see how far it has run, try		To see how far it has run, try
Line 142:		Line 141:
	0.409000000000E+02 0.245084886492E+00 0.219972040124E+00 0.183121641848E+00		0.409000000000E+02 0.245084886492E+00 0.219972040124E+00 0.183121641848E+00
	0.410000000000E+02 0.245043352978E+00 0.219956948128E+00 0.183132588846E+00		0.410000000000E+02 0.245043352978E+00 0.219956948128E+00 0.183132588846E+00
			Sometimes the time-series files are buffered, i.e. no output is written until the buffer is filled, so don't panic if it doesn't seem to be updating. The OUT file is less likely to be buffered.

	Column 1 of <tt>vel_energy.dat</tt> is the time, column 2 is the energy in the perturbation to the mean flow. Columns 3 and 4 are the energies in the axial mean (k=0) and azimuthal mean (m=0) components respectively.		Column 1 of <tt>vel_energy.dat</tt> is the time, column 2 is the energy in the perturbation to the mean flow. Columns 3 and 4 are the energies in the axial mean (k=0) and azimuthal mean (m=0) components respectively.

	Let the code run for a few minutes, give it a chance to save a few state files.		Let the code run for a few minutes, give it a chance to save a few state files.
	To see the simulation times when ~~the~~ state were saved,		To see the simulation times '''when state were saved''',
	> grep state OUT \| less		> grep state OUT \| less
	loading state...		loading state...
Line 153:		Line 154:

	[[File:Tut_E3d.png\|thumb\|right\|Energy vs time]]		[[File:Tut_E3d.png\|thumb\|right\|Energy vs time]]
	Let's plot the energy as a function of time:		Let's plot the '''energy as a function of time''':
	<!-- need pre to preserve dollar symbol -->		<!-- need pre to preserve dollar symbol -->
	<pre>		<pre>
Line 163:		Line 164:

	[[File:Tut_spec0001.png\|thumb\|right\|Spectrum]]		[[File:Tut_spec0001.png\|thumb\|right\|Spectrum]]
	It is a good idea to keep track of the resolution. Still in <tt>gnuplot</tt>		It is a good idea to keep track of the '''resolution'''. Still in <tt>gnuplot</tt>
	<pre>		<pre>
	> set log		> set log

Apwillis: /* Monitor the run */

2017-12-20T11:22:08Z

Monitor the run

← Older revision		Revision as of 04:22, 20 December 2017
Line 124:		Line 124:
	and time-series data, e.g. the energy as a function of time <tt>vel_energy.dat</tt>.		and time-series data, e.g. the energy as a function of time <tt>vel_energy.dat</tt>.
	Snapshot data is saved every <tt>i_save_rate1</tt> (typically 2000) timesteps, and time-series data is saved every <tt>i_save_rate2</tt> (typically 10) timesteps .		Snapshot data is saved every <tt>i_save_rate1</tt> (typically 2000) timesteps, and time-series data is saved every <tt>i_save_rate2</tt> (typically 10) timesteps .
			Sometimes the time-series files are buffered, i.e. no output is written until the buffer is filled. The OUT file is less likely to be buffered.

	To see how far it has run, try		To see how far it has run, try
Line 141:		Line 142:
	0.409000000000E+02 0.245084886492E+00 0.219972040124E+00 0.183121641848E+00		0.409000000000E+02 0.245084886492E+00 0.219972040124E+00 0.183121641848E+00
	0.410000000000E+02 0.245043352978E+00 0.219956948128E+00 0.183132588846E+00		0.410000000000E+02 0.245043352978E+00 0.219956948128E+00 0.183132588846E+00
	Column 1 of <tt>vel_energy.dat</tt> is the time, column 2 is the energy in the perturbation to the mean flow. Columns 3 and 4 are the energies in the ~~axially averaged~~ (k=0) and ~~azimuthally averaged~~ (m=0) components respectively.		Column 1 of <tt>vel_energy.dat</tt> is the time, column 2 is the energy in the perturbation to the mean flow. Columns 3 and 4 are the energies in the axial mean (k=0) and azimuthal mean (m=0) components respectively.
	~~Sometimes the time-series files are buffered, i.e. no output is written until the buffer is filled. The OUT file is less likely to be buffered~~.

	Let the code run for a few minutes, give it a chance to save a few state files.		Let the code run for a few minutes, give it a chance to save a few state files.

Apwillis: /* Compile and setup a job directory */

2017-12-20T11:17:48Z

Compile and setup a job directory

← Older revision		Revision as of 04:17, 20 December 2017
Line 65:		Line 65:
	any differences in parameters between jobs:		any differences in parameters between jobs:
	> diff install/main.info Re2400a1.25/main.info		> diff install/main.info Re2400a1.25/main.info
	In this case the ~~main~~ difference is Re=2400 increased to Re=2500.		In this case the important difference is Re=2400 increased to Re=2500.

	We'll create a new job directory with an initial condition in there ready for the new run		We'll create a new job directory with an initial condition in there ready for the new run

Apwillis: /* Monitor the run */

2017-12-20T10:56:08Z

Monitor the run

← Older revision		Revision as of 03:56, 20 December 2017
Line 99:		Line 99:
	=== Monitor the run ===		=== Monitor the run ===

	Let the code run until new files are produced:		Let the code run until new files are produced (~10mins):
	> ls -l		> ls -l
	-rw-rw-r-- 1 20 Dec 20 11:11 HOST		-rw-rw-r-- 1 20 Dec 20 11:11 HOST