Running Mars mesoscale model - Revision history

Jorge: /* Restarting simulations */

2025-04-02T14:43:27Z

‎Restarting simulations

Jorge at 15:31, 20 March 2025

2025-03-20T15:31:27Z

Jorge: /* Troubleshooting restart files in big simulations */

2025-03-16T21:43:36Z

‎Troubleshooting restart files in big simulations

Jorge at 16:52, 24 February 2025

2025-02-24T16:52:09Z

Jorge: /* Troubleshooting restart files in big simulations (ONGOING) */

2025-02-24T16:46:18Z

‎Troubleshooting restart files in big simulations (ONGOING)

Jorge at 12:08, 24 February 2025

2025-02-24T12:08:00Z

Jorge at 11:49, 24 February 2025

2025-02-24T11:49:11Z

Jorge at 14:11, 13 February 2025

2025-02-13T14:11:11Z

Jorge at 14:00, 13 February 2025

2025-02-13T14:00:23Z

Jorge at 13:59, 13 February 2025

2025-02-13T13:59:44Z

← Older revision		Revision as of 14:43, 2 April 2025
Line 15:		Line 15:

	===namelist.input===		===namelist.input===
		+
		+	==Changing vertical resolution==
		+	Before running real.exe, a new levels file needs to be generated. The script to do this is in SIMU/RUN/vert_level_python.
		+
		+	==Smoothing topography in the borders==
		+	This might help sometimes when simulations are breaking, but it didn't work for me so far. This script can smooth the topography in the borders of a wrfinput file.
		+
		+	<syntaxhighlight>
		+	import numpy as np
		+	import xarray as xr
		+	import sys
		+	import os
		+
		+	from scipy.ndimage import gaussian_filter
		+
		+	def smooth_borders(a,margin):
		+	out=np.zeros(a.shape)
		+	for i in range(margin):
		+	if i>0:
		+	b=a[i:-i,i:-i]
		+	else:
		+	b=a[:]
		+	c=gaussian_filter(b, sigma=margin-i)
		+	if i>0:
		+	out[i:-i,i:-i]=c
		+	else:
		+	out=c[:]
		+
		+	return out
		+
		+	margin=int(sys.argv[1])
		+	input_file=sys.argv[2]
		+
		+
		+	#Open file
		+	ds=xr.open_dataset(input_file)
		+
		+	a=ds.HGT.values[0]
		+	a=smooth_borders(a,margin)
		+	ds.HGT.values[0]=a
		+
		+	os.system('mv %s %s_presmooth'%(input_file,input_file))
		+	ds.to_netcdf(input_file)
		+
		+	</syntaxhighlight>

	==Restarting simulations==		==Restarting simulations==

@@ Line 22: / Line 22: @@
 To restart from an existing restart file, we must change the "restart" option to .true., and the start_month,start_day, and start_hour need to be updated to coincide with the time of the restart file. Since we can tune the starting of the simulation with a resolution of hours (and not minutes), this means that the restart files need to be saved at integer hours, and therefore the restart_interval option should have values 37*N, with N the number of hours of interval between restart files.
-==Troubleshooting restart files in big simulations==
+===Troubleshooting restart files in big simulations===
 In big simulations restart files fail to be saved. This does not cause any problem, and the simulation keeps running. When increasing verbosity to one, the rsl.error file contains this error messages (Note that for this debug execution we set restart_interval to 1 to obtain the error quickly):
@@ Line 79: / Line 79: @@
 This is documented in https://docs.unidata.ucar.edu/netcdf-fortran/current/nc_f77_interface_guide.html

@@ Line 49: / Line 49: @@
 </syntaxhighlight>
-The problem is in the file wrf_io.F90. When we execute a search for this file, there are various copies of it (only files with a number before deserve our attention, others are flags)
+The problem is in the file wrf_io.F90. We have to update two files
 <syntaxhighlight>
-NO./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/inc/wrf_io_flags.h
+code/MESOSCALE/LMD_MM_MARS/SRC/WRFV2/external/io_netcdf/wrf_io.F90: line 1188
-./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_netcdf/wrf_io.F90
+code/MESOSCALE/LMD_MM_MARS/SRC/WRFV2/external/io_pnetcdf/wrf_io.F90: line 1195
 </syntaxhighlight>
-The problem is caused by the big size of the restart files, it will happen when files are bigger than 2gb. In line 1188 of wrf_io.*(1195 in some versions of the file we find:
+The problem is caused by the big size of the restart files, it will happen when files are bigger than 2gb.
 <syntaxhighlight>
-stat = NF_CREATE(FileName, NF_CLOBBER, DH%NCID)
+IOR(NF_CLOBBER,NF_64BIT_OFFSET)
 </syntaxhighlight>
-Apparently, these parameters only work when writing files smaller than 2gb. We can fix that be replacing this line by:
+Then the resulting line looks like
 <syntaxhighlight>
 stat = NF_CREATE(FileName, IOR(NF_CLOBBER,NF_64BIT_OFFSET), DH%NCID)
 </syntaxhighlight>
-IMPORTANT NOTES.
+This is documented in https://docs.unidata.ucar.edu/netcdf-fortran/current/nc_f77_interface_guide.html

← Older revision		Revision as of 16:52, 24 February 2025
Line 9:		Line 9:

	Increasing the output frequency in parallel runs doesn't work. Even with a frequency of 1 doesn't work.		Increasing the output frequency in parallel runs doesn't work. Even with a frequency of 1 doesn't work.
		+
		+	==Notes on clear input and output files (TBD)==
		+
		+	==Notes on configuration files (TBD)==
		+
		+	===namelist.input===

	==Restarting simulations==		==Restarting simulations==

@@ Line 16: / Line 16: @@
 To restart from an existing restart file, we must change the "restart" option to .true., and the start_month,start_day, and start_hour need to be updated to coincide with the time of the restart file. Since we can tune the starting of the simulation with a resolution of hours (and not minutes), this means that the restart files need to be saved at integer hours, and therefore the restart_interval option should have values 37*N, with N the number of hours of interval between restart files.
-==Troubleshooting restart files in big simulations (ONGOING)==
+==Troubleshooting restart files in big simulations==
 In big simulations restart files fail to be saved. This does not cause any problem, and the simulation keeps running. When increasing verbosity to one, the rsl.error file contains this error messages (Note that for this debug execution we set restart_interval to 1 to obtain the error quickly):
@@ Line 43: / Line 43: @@
 </syntaxhighlight>
-The problem is in the file wrf_io.F90. When we execute a search for this file, there are 4 different copies of it:
+The problem is in the file wrf_io.F90. When we execute a search for this file, there are various copies of it (only files with a number before deserve our attention, others are flags)
 <syntaxhighlight>
-./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_netcdf/wrf_io.F90
+NO./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/inc/wrf_io_flags.h
-./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_pnetcdf/wrf_io.F90
+./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_netcdf/wrf_io.F90
-./code/MESOSCALE/LMD_MM_MARS/SRC/WRFV2/external/io_netcdf/wrf_io.F90
+NO./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_netcdf/wrf_io.o
-./code/MESOSCALE/LMD_MM_MARS/SRC/WRFV2/external/io_pnetcdf/wrf_io.F90
+./code/MESOSCALE/LMD_MM_MARS/mars_lmd_new_real_mpifort_64/WRFV2/external/io_netcdf/wrf_io.f
 </syntaxhighlight>
-Apparently, the problem is related to the big size of the restart files. In line 1188 (1195 in some versions of the file we find:
+The problem is caused by the big size of the restart files, it will happen when files are bigger than 2gb. In line 1188 of wrf_io.*(1195 in some versions of the file we find:
 <syntaxhighlight>
 stat = NF_CREATE(FileName, NF_CLOBBER, DH%NCID)
@@ Line 62: / Line 72: @@
 stat = NF_CREATE(FileName, IOR(NF_CLOBBER,NF_64BIT_OFFSET), DH%NCID)
 </syntaxhighlight>

← Older revision		Revision as of 11:49, 24 February 2025
Line 9:		Line 9:

	Increasing the output frequency in parallel runs doesn't work. Even with a frequency of 1 doesn't work.		Increasing the output frequency in parallel runs doesn't work. Even with a frequency of 1 doesn't work.
		+
		+	==Restarting simulations==
		+	In the file namelist.input there is the option "restart". The comment for this option says "Output restart files?" but actually it refers to whether or not the simulation should try to start from a previous simulation.
		+	Restart files are periodically saved, this can be configured with restart_interval. The value is an integer number corresponding to the number of "minutes" (with a Martian hour having 37 minutes) between restart files. By default this is very long (8880, corresponding to 10 sols). If we write 37 it will be every hour. If we write 37*6 it will be every 6 hours, etc.
		+
		+	To restart from an existing restart file, we must change the "restart" option to .true., and the start_month,start_day, and start_hour need to be updated to coincide with the time of the restart file. Since we can tune the starting of the simulation with a resolution of hours (and not minutes), this means that the restart files need to be saved at integer hours, and therefore the restart_interval option should have values 37*N, with N the number of hours of interval between restart files.
		+
		+	==Troubleshooting restart files in big simulations==
		+	Restart files

← Older revision		Revision as of 14:11, 13 February 2025
Line 7:		Line 7:

	When running in a single core, in my case at least it produces NaNs with low output frequency (37) but by increasing the output frequency (6 works for me) it is solved. This is weird but seem to be right.		When running in a single core, in my case at least it produces NaNs with low output frequency (37) but by increasing the output frequency (6 works for me) it is solved. This is weird but seem to be right.
		+
		+	Increasing the output frequency in parallel runs doesn't work. Even with a frequency of 1 doesn't work.

← Older revision		Revision as of 14:00, 13 February 2025
Line 6:		Line 6:
	The mesoscale model cannot run in parallel in spirit at the moment, it runs but it outputs NaNs everywhere.		The mesoscale model cannot run in parallel in spirit at the moment, it runs but it outputs NaNs everywhere.

−	When running in a single core, in my case at least it produces NaNs with low output frequency (37) but by ~~reducing~~ the output frequency to 6 it is solved. This is weird but seem to be right.	+	When running in a single core, in my case at least it produces NaNs with low output frequency (37) but by increasing the output frequency (6 works for me) it is solved. This is weird but seem to be right.

@@ Line 3: / Line 3: @@
 The user manual can be found at https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/blob/master/MESOSCALE/MANUAL/SRC/user_manual.pdf?ref_type=heads
 The mesoscale model cannot run in parallel in spirit at the moment, it runs but it outputs NaNs everywhere.
 When running in a single core, in my case at least it produces NaNs with low output frequency (37) but by reducing the output frequency to 6 it is solved. This is weird but seem to be right.