Planets - User contributions [en]

Hgardfou reports NaNs in temperature field

2024-10-18T07:43:18Z

Maureenjcohen:

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of '''n''' causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values can cause a slow crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = y
</pre>
Or both can be set to '''n'''. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

=== Compiler optimisation too high ===
(October 2024): The compiler optimisation flag is set in the arch-[***].fcm files in PROD_FFLAGS for normal runs (and DEBUG_FFLAGS for debug runs). The level should be "-O2" as "-O3" may lead to instability in chemistry runs. The penalty is the simulation will run more slowly.

[[Category:Errors]]
[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Hgardfou reports NaNs in temperature field

2024-10-10T12:22:08Z

Maureenjcohen: /* Age of air tracer included in chemistry array */

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of '''n''' causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values can cause a slow crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = y
</pre>
Or both can be set to '''n'''. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

[[Category:Errors]]
[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Hgardfou reports NaNs in temperature field

2024-10-10T10:10:54Z

Maureenjcohen: /* Wrong value of nbapp_chem */

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of '''n''' causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values can cause a slow crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = n
</pre>
Or both can be set to '''n'''. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

[[Category:Errors]]
[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Hgardfou reports NaNs in temperature field

2024-10-10T10:09:50Z

Maureenjcohen:

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of '''n''' causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values cause a crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = n
</pre>
Or both can be set to '''n'''. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

[[Category:Errors]]
[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Hgardfou reports NaNs in temperature field

2024-10-10T10:08:19Z

Maureenjcohen:

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of '''n''' causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values cause a crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = n
</pre>
Or both can be set to '''n'''. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

Hgardfou reports NaNs in temperature field

2024-10-10T10:06:07Z

Maureenjcohen: Created page with "== The symptoms == The log gcm.out reads: <pre> i,k,temperature = 1 1 NaN i,k,temperature = 2 1..."

== The symptoms ==
The log gcm.out reads:
<pre>
i,k,temperature = 1 1 NaN
i,k,temperature = 2 1 NaN
i,k,temperature = 3 1 NaN
etc.
</pre>
At the end of a long report of NaNs, there is a message like:
<pre>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
STOP 1
</pre>
and
<pre>Stopping in hgardfou
Reason = hgardfou stops debutphy
Houston, we have a problem, ierr = 1
</pre>

== Known causes ==
The message indicates numerical instability in the temperature field, which can be caused by different things. It may happen quickly when the simulation starts or more slowly after significant runtime. Note: even though the reported NaNs started at gridbox i,k 1,1, this doesn't mean the instability began there - the hgardfou subroutine checks the temperature field starting from level 1, so it will report bad values in this order.

=== Wrong value of callthermos ===
(October 2024): In physiq.def, the flag callthermos must be:
<pre>
callthermos = y
</pre>
when running a chemistry simulation with 78 levels. A value of **n** causes an immediate crash.

=== Wrong value of nbapp_chem ===
(October 2024): In physiq.def, the flag nbapp_chem must be:
<pre>
nbapp_chem = 24000
</pre>
Other values cause a crash after 0.1-0.2 Venus days.

=== Age of air tracer included in chemistry array ===
(October 2024): The age of air cannot be included in chemistry runs. The flags in physiq.def should be:
<pre>
ok_chem = y
ok_aoa = n
</pre>
or
<pre>
ok_chem = n
ok_aoa = n
</pre>
Or both can be set to **n**. This also causes a crash after 0.1-0.2 Venus days. There is a check in conf_phys which should warn the user if the settings are incoherent and stop the simulation.

Running the Venus PCM with age of air

2024-10-10T09:24:21Z

Maureenjcohen:

The age of air expresses the time since an air parcel has been in a user-specified source region, such as an altitude level. It is based on a passive tracer that circulates through the atmosphere. The calculation uses the ratio of the abundance of the tracer in each gridbox to the abundance in the source region to determine how long it has been since the air in the gridbox has been in the source region. It is a useful way to find transport timescales between regions and reveal teleconnections.

== Basic settings in defs files ==

In gcm.def: iflag_trac = 1

In physiq.def: ok_aoa = y

In traceur.def: 10 10 aoa

These three settings are necessary to include age of air in the simulation. Currently, the age of air tracer cannot be included in a chemistry simulation, i.e. chemistry and age of air must be computed in separate simulations. This is because the increasing age of air tracer abundance appears to cause numerical instability when included in the tracer array sent to the photochemistry scheme.

== Customisation ==

In physiq.def, the flag

reinit_aoa = y/n

controls whether the age of air is reinitialised (set to 0) at the start of the simulation. The default is '''y''', so that each simulation starts fresh. If you change the setting to '''n''', the simulation will read the existing value of age of air from restartphy and add it to the calculation in the new simulation as an offset. This makes it possible to chain together multiple restarts without losing track of the age.

In physiq.def, the flag

lev_aoa = 1

controls the source level where the age of air tracer is released. It can be set to any model level. Default is '''1''', the surface.

== Output ==

Turning on ok_aoa adds two 3-D fields to the output: the tracer abundance ("aoa" or "aoaVL1") and the age of air in seconds ("age").

== Bibliography ==
Maureen Cohen, James Holmes, Stephen Lewis, Manish Patel. '''Planetary Waves Drive Horizontal Variations in Trace Species in the Venus Deep Atmosphere''', The Planetary Science Journal, 5 (219) (2024). DOI: https://doi.org/10.3847/PSJ/ad76a8

Maarten Krol, Marco de Bruine, Lars Killaars, Huug Ouwersloot, Andrea Pozzer, Yi Yin, Frederic Chevallier, Philippe Bousquet, Prabir Patra, Dmitry Belikov, Shamil Maksyutov, Sandip Dhomse, Wuhu Feng, and Martyn P. Chipperfield, '''Age of air as a diagnostic for transport timescales in global models''', Geoscientific Model Development, 11 (8), 3109–3130 (2018). DOI: https://doi.org/10.5194/gmd-11-3109-2018

[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Running the Venus PCM with age of air

2024-10-10T09:24:00Z

Maureenjcohen:

The age of air expresses the time since an air parcel has been in a user-specified source region, such as an altitude level. It is based on a passive tracer that circulates through the atmosphere. The calculation uses the ratio of the abundance of the tracer in each gridbox to the abundance in the source region to determine how long it has been since the air in the gridbox has been in the source region. It is a useful way to find transport timescales between regions and reveal teleconnections.

== Basic settings in defs files ==

In gcm.def: iflag_trac = 1

In physiq.def: ok_aoa = y

In traceur.def: 10 10 aoa

These three settings are necessary to include age of air in the simulation. Currently, the age of air tracer cannot be included in a chemistry simulation, i.e. chemistry and age of air must be computed in separate siulations. This is because the increasing age of air tracer abundance appears to cause numerical instability when included in the tracer array in the photochemistry scheme.

== Customisation ==

In physiq.def, the flag

reinit_aoa = y/n

controls whether the age of air is reinitialised (set to 0) at the start of the simulation. The default is '''y''', so that each simulation starts fresh. If you change the setting to '''n''', the simulation will read the existing value of age of air from restartphy and add it to the calculation in the new simulation as an offset. This makes it possible to chain together multiple restarts without losing track of the age.

In physiq.def, the flag

lev_aoa = 1

controls the source level where the age of air tracer is released. It can be set to any model level. Default is '''1''', the surface.

== Output ==

Turning on ok_aoa adds two 3-D fields to the output: the tracer abundance ("aoa" or "aoaVL1") and the age of air in seconds ("age").

== Bibliography ==
Maureen Cohen, James Holmes, Stephen Lewis, Manish Patel. '''Planetary Waves Drive Horizontal Variations in Trace Species in the Venus Deep Atmosphere''', The Planetary Science Journal, 5 (219) (2024). DOI: https://doi.org/10.3847/PSJ/ad76a8

Maarten Krol, Marco de Bruine, Lars Killaars, Huug Ouwersloot, Andrea Pozzer, Yi Yin, Frederic Chevallier, Philippe Bousquet, Prabir Patra, Dmitry Belikov, Shamil Maksyutov, Sandip Dhomse, Wuhu Feng, and Martyn P. Chipperfield, '''Age of air as a diagnostic for transport timescales in global models''', Geoscientific Model Development, 11 (8), 3109–3130 (2018). DOI: https://doi.org/10.5194/gmd-11-3109-2018

[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]

Running the Venus PCM with age of air

2024-08-23T17:02:46Z

Maureenjcohen: Created page with "The age of air expresses the time since an air parcel has been in a user-specified source region, such as an altitude level. It is based on a passive tracer that circulates th..."

The age of air expresses the time since an air parcel has been in a user-specified source region, such as an altitude level. It is based on a passive tracer that circulates through the atmosphere. The calculation uses the ratio of the abundance of the tracer in each gridbox to the abundance in the source region to determine how long it has been since the air in the gridbox has been in the source region. It is a useful way to find transport timescales between regions and reveal teleconnections.

== Basic settings in defs files ==

In gcm.def: iflag_trac = 1

In physiq.def: ok_aoa = y

In traceur.def: 10 10 aoa

These three settings are necessary to include age of air in the simulation.

== Customisation ==

In physiq.def, the flag

reinit_aoa = y/n

controls whether the age of air is reinitialised (set to 0) at the start of the simulation. The default is '''y''', so that each simulation starts fresh. If you change the setting to '''n''', the simulation will read the existing value of age of air from restartphy and add it to the calculation in the new simulation as an offset. This makes it possible to chain together multiple restarts without losing track of the age.

In physiq.def, the flag

lev_aoa = 1

controls the source level where the age of air tracer is released. It can be set to any model level. Default is '''1''', the surface.

== Output ==

Turning on ok_aoa adds two 3-D fields to the output: the tracer abundance ("aoa" or "aoaVL1") and the age of air in seconds ("age").

== Bibliography ==

Maarten Krol, Marco de Bruine, Lars Killaars, Huug Ouwersloot, Andrea Pozzer, Yi Yin, Frederic Chevallier, Philippe Bousquet, Prabir Patra, Dmitry Belikov, Shamil Maksyutov, Sandip Dhomse, Wuhu Feng, and Martyn P. Chipperfield, '''Age of air as a diagnostic for transport timescales in global models''', Geoscientific Model Development, 11 (8), 3109–3130 (2018). DOI: https://doi.org/10.5194/gmd-11-3109-2018

[[Category:Venus-Model]]
[[Category:Venus-LMDZ]]