From knarf at cct.lsu.edu  Tue Jan  5 12:59:21 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Tue, 5 Jan 2010 12:59:21 -0600
Subject: [Developers] General EOS interface
In-Reply-To: <20091207202529.GT9360@numrel07.cct.lsu.edu>
References: <20091207202529.GT9360@numrel07.cct.lsu.edu>
Message-ID: <20100105185920.GG14498@numrel07.cct.lsu.edu>

Hi,

On Mon, Dec 07, 2009 at 02:25:29PM -0600, Frank Loeffler wrote:
> as agreed by the authors of the general EOS interface, the development
> of the new interface has now been moved to the Cactus server inside the
> CactusEOS arrangement. You can get it by adding the following to your
> thornlist:

I think it would make sense to move EOS_Polytrope and EOS_Hybrid to
CactusEOS as well (the non-general EOS versions). The general EOS
versions are now already there and EOS_Ideal_Fluid is also there.

Are there objections?

Frank

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From baiotti at yukawa.kyoto-u.ac.jp  Thu Jan  7 01:45:26 2010
From: baiotti at yukawa.kyoto-u.ac.jp (Baiotti Luca)
Date: Thu, 07 Jan 2010 16:45:26 +0900
Subject: [Developers] [Patches] ADMConstraints: Recompute constraints
 after regridding and restricting
In-Reply-To: <42C1EED3-9A88-4270-83F9-A89AB27464F9@cct.lsu.edu>
References: <FEC7E664-250D-4982-85F3-5158DE3AE098@aei.mpg.de>
	<42C1EED3-9A88-4270-83F9-A89AB27464F9@cct.lsu.edu>
Message-ID: <4B459116.8020109@yukawa.kyoto-u.ac.jp>

Hello,

since this patch breaks the testsuites, I would like to be sure that it will 
remain as is now in the repository before updating the testsuites.

Could you confirm?

Luca


Erik Schnetter wrote:
> On Dec 5, 2009, at 10:27 , Ian Hinder wrote:
> 
>> Schedule the computation of the constraints in the
>> CactusEinstein/ADMConstraints thorn in CCTK_POSTREGRID and CCTK_POSTRESTRICT.
>> Previously, the constraints would have contained undefined (or poison) values
>> after regridding.
> 
> 
> These changes only modify the behaviour if constraints_persist is set to true.
> In this case, the constraints are supposed to be treated like an evolved
> variable, and are supposed to be either evaluated after each substep (in
> MoL_PostStep) or in EVOL after MoL_Evolution.  In particular, the coarse-grid
> constraints are then supposed to be restricted from finer grids, same as an
> evolved variable.
> 
> I don't see why it should be necessary to re-evaluate them in the postrestrict
> bin; this would be equivalent to re-setting the BSSN variables there.  Under
> what circumstances do you see this problem?  Where are the constraints
> undefined?  Re-applying the boundary conditions, including interpolating from
> the next coarser level, should be good enough, but apparently isn't for you.
> Evaluating the constraints again undoes the restriction operation.
> 
> Another difference is the value of the constraints on the buffer zones.  If the
> constraints are evaluated there, they have a large error, since the constraints
> calculate derivatives of interpolated values (which is not a good idea).  It is
> better the interpolate the constraints there from the coarser grid, since this
> leads to a smooth solution there.
> 
> -erik
> 

From schnetter at cct.lsu.edu  Sun Jan 10 13:29:44 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Sun, 10 Jan 2010 13:29:44 -0600
Subject: [Developers] Run MoL_PostStep after recovery
Message-ID: <446AA32C-695C-4CA2-875E-DAC2DF5B3073@cct.lsu.edu>

I suggest to run MoL_PostStep after recovery.  This will ensure that all 
dependent variables are calculated, and boundary conditions are applied 
correctly.  (Dependent variables are e.g. the ADMBase variables which 
may not be checkpointed.)  MoL_PostStep is already run after initial 
data have been set up, after restriction, and after regridding.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   
http://www.cct.lsu.edu/~eschnett/




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From knarf at cct.lsu.edu  Sun Jan 10 14:23:54 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Sun, 10 Jan 2010 14:23:54 -0600
Subject: [Developers] [Patches] Run MoL_PostStep after recovery
In-Reply-To: <446AA32C-695C-4CA2-875E-DAC2DF5B3073@cct.lsu.edu>
References: <446AA32C-695C-4CA2-875E-DAC2DF5B3073@cct.lsu.edu>
Message-ID: <20100110202354.GC6469@numrel07.cct.lsu.edu>

On Sun, Jan 10, 2010 at 01:29:44PM -0600, Erik Schnetter wrote:
> I suggest to run MoL_PostStep after recovery.  This will ensure that all dependent variables are calculated, and boundary conditions are applied correctly.  (Dependent variables are e.g. the ADMBase variables which may not be checkpointed.)  MoL_PostStep is already run after initial data have been set up, after restriction, and after regridding.

I think this is a good idea. It will make recovery (just) a bit slower,
but since that is only run once that should not be a problem and should
be out-weighted by the advantages.

Frank

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From cott at tapir.caltech.edu  Sun Jan 10 14:30:14 2010
From: cott at tapir.caltech.edu (Christian D. Ott)
Date: Sun, 10 Jan 2010 12:30:14 -0800
Subject: [Developers] [Patches] Run MoL_PostStep after recovery
In-Reply-To: <20100110202354.GC6469@numrel07.cct.lsu.edu>
References: <446AA32C-695C-4CA2-875E-DAC2DF5B3073@cct.lsu.edu>
	<20100110202354.GC6469@numrel07.cct.lsu.edu>
Message-ID: <20100110203014.GB17787@wilson.tapir.caltech.edu>



On Sun, Jan 10, 2010 at 02:23:54PM -0600, Frank Loeffler wrote:
> On Sun, Jan 10, 2010 at 01:29:44PM -0600, Erik Schnetter wrote:
> > I suggest to run MoL_PostStep after recovery.  This will ensure that all dependent variables are calculated, and boundary conditions are applied correctly.  (Dependent variables are e.g. the ADMBase variables which may not be checkpointed.)  MoL_PostStep is already run after initial data have been set up, after restriction, and after regridding.
> 
> I think this is a good idea. It will make recovery (just) a bit slower,
> but since that is only run once that should not be a problem and should
> be out-weighted by the advantages.

Me too. In fact, we need this to recover form runs using McLachlan as those don't
checkpoint ADMBase variables. These are recomputed in MoL_PostStep. Other thorns
requiring ADMBase variables in Post_Recover_Variables can just schedule their routines
independent of the spacetime thorn AFTER MoL_PostStep in Post_Recover_Variables.

 - Christian 

From ian.hinder at aei.mpg.de  Mon Jan 11 03:43:28 2010
From: ian.hinder at aei.mpg.de (Ian Hinder)
Date: Mon, 11 Jan 2010 10:43:28 +0100
Subject: [Developers] [Patches] ADMConstraints: Recompute constraints
	after regridding and restricting
In-Reply-To: <4B459116.8020109@yukawa.kyoto-u.ac.jp>
References: <FEC7E664-250D-4982-85F3-5158DE3AE098@aei.mpg.de>
	<42C1EED3-9A88-4270-83F9-A89AB27464F9@cct.lsu.edu>
	<4B459116.8020109@yukawa.kyoto-u.ac.jp>
Message-ID: <B9573CFA-3BD3-4742-9F3B-4448DD906191@aei.mpg.de>


On 7 Jan 2010, at 08:45, Baiotti Luca wrote:

> Hello,
>
> since this patch breaks the testsuites, I would like to be sure that  
> it will remain as is now in the repository before updating the  
> testsuites.
>
> Could you confirm?

Erik's comment suggests that this is not the correct fix, so until I  
investigate my problem further, I suggest that the patch is  
withdrawn.  My symptoms were that I saw poison in the constraint norms  
which went away when I made this change. I was under the impression  
that analysis quantities needed to be recomputed after restriction and  
regridding, but as Erik points out, the constraints_persist parameter  
implies different semantics for the constraints which should make this  
unnecessary.

I should have said in the patch email that this was a proposed/ 
tentative patch; apologies for any trouble this has caused.

> Erik Schnetter wrote:
>> On Dec 5, 2009, at 10:27 , Ian Hinder wrote:
>>> Schedule the computation of the constraints in the
>>> CactusEinstein/ADMConstraints thorn in CCTK_POSTREGRID and  
>>> CCTK_POSTRESTRICT.
>>> Previously, the constraints would have contained undefined (or  
>>> poison) values
>>> after regridding.
>> These changes only modify the behaviour if constraints_persist is  
>> set to true.
>> In this case, the constraints are supposed to be treated like an  
>> evolved
>> variable, and are supposed to be either evaluated after each  
>> substep (in
>> MoL_PostStep) or in EVOL after MoL_Evolution.  In particular, the  
>> coarse-grid
>> constraints are then supposed to be restricted from finer grids,  
>> same as an
>> evolved variable.
>> I don't see why it should be necessary to re-evaluate them in the  
>> postrestrict
>> bin; this would be equivalent to re-setting the BSSN variables  
>> there.  Under
>> what circumstances do you see this problem?  Where are the  
>> constraints
>> undefined?  Re-applying the boundary conditions, including  
>> interpolating from
>> the next coarser level, should be good enough, but apparently isn't  
>> for you.
>> Evaluating the constraints again undoes the restriction operation.
>> Another difference is the value of the constraints on the buffer  
>> zones.  If the
>> constraints are evaluated there, they have a large error, since the  
>> constraints
>> calculate derivatives of interpolated values (which is not a good  
>> idea).  It is
>> better the interpolate the constraints there from the coarser grid,  
>> since this
>> leads to a smooth solution there.
>> -erik

-- 
Ian Hinder
ian.hinder at aei.mpg.de


From schnetter at cct.lsu.edu  Mon Jan 11 11:31:39 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Mon, 11 Jan 2010 11:31:39 -0600
Subject: [Developers] [Patches] ADMConstraints: Recompute constraints
	after regridding and restricting
In-Reply-To: <B9573CFA-3BD3-4742-9F3B-4448DD906191@aei.mpg.de>
References: <FEC7E664-250D-4982-85F3-5158DE3AE098@aei.mpg.de>
	<42C1EED3-9A88-4270-83F9-A89AB27464F9@cct.lsu.edu>
	<4B459116.8020109@yukawa.kyoto-u.ac.jp>
	<B9573CFA-3BD3-4742-9F3B-4448DD906191@aei.mpg.de>
Message-ID: <C10C1F37-E593-415D-9F4A-B39A7923E758@cct.lsu.edu>

On Jan 11, 2010, at 3:43 , Ian Hinder wrote:

> On 7 Jan 2010, at 08:45, Baiotti Luca wrote:
> 
>> Hello,
>> 
>> since this patch breaks the testsuites, I would like to be sure that  
>> it will remain as is now in the repository before updating the  
>> testsuites.
>> 
>> Could you confirm?
> 
> Erik's comment suggests that this is not the correct fix, so until I  
> investigate my problem further, I suggest that the patch is  
> withdrawn.  My symptoms were that I saw poison in the constraint norms  
> which went away when I made this change. I was under the impression  
> that analysis quantities needed to be recomputed after restriction and  
> regridding, but as Erik points out, the constraints_persist parameter  
> implies different semantics for the constraints which should make this  
> unnecessary.

Is this patch in cvs at the moment?

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/




From knarf at cct.lsu.edu  Mon Jan 11 11:41:32 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Mon, 11 Jan 2010 11:41:32 -0600
Subject: [Developers] [Patches] ADMConstraints: Recompute constraints
 after regridding and restricting
In-Reply-To: <C10C1F37-E593-415D-9F4A-B39A7923E758@cct.lsu.edu>
References: <FEC7E664-250D-4982-85F3-5158DE3AE098@aei.mpg.de>
	<42C1EED3-9A88-4270-83F9-A89AB27464F9@cct.lsu.edu>
	<4B459116.8020109@yukawa.kyoto-u.ac.jp>
	<B9573CFA-3BD3-4742-9F3B-4448DD906191@aei.mpg.de>
	<C10C1F37-E593-415D-9F4A-B39A7923E758@cct.lsu.edu>
Message-ID: <20100111174128.GH16133@numrel07.cct.lsu.edu>

On Mon, Jan 11, 2010 at 11:31:39AM -0600, Erik Schnetter wrote:
> Is this patch in cvs at the moment?

Not anyore.

Frank

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From schnetter at cct.lsu.edu  Mon Jan 11 14:02:51 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Mon, 11 Jan 2010 14:02:51 -0600
Subject: [Developers] CactusUtils/TerminationTrigger
Message-ID: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>

I suggest to add a new thorn to CactusUtils: TerminationTrigger.

This thorn watches the elapsed walltime.  If only n minutes are left 
before the some limit set by the user, it triggers termination of the 
simulation.  Termination is also triggered if a special file with a 
special content exists.

This thorn was written by Christian Ott based on an original idea by 
Steve White.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   
http://www.cct.lsu.edu/~eschnett/




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From bgiacoma at astro.umd.edu  Mon Jan 11 14:12:39 2010
From: bgiacoma at astro.umd.edu (Bruno Giacomazzo)
Date: Mon, 11 Jan 2010 15:12:39 -0500
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
Message-ID: <6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>

Hi Erik,
	why you don't use AEIThorns/ManualTermination (svn co https:// 
svn.aei.mpg.de:/numrel/AEIThorns/ManualTermination/trunk  
ManualTermination)?

	It does the same identical thing and, being under AEIThorns, it  
should be also public available. I use it regularly to stop jobs some  
minutes before the walltime limit or when I want to force a job to  
write a checkpoint file and then quit (by editing the content of a  
file that is checked regularly). This seems to be the same thing that  
is done by TerminationTrigger.

Cheers,
Bruno


On Jan 11, 2010, at 3:02 PM, Erik Schnetter wrote:

> I suggest to add a new thorn to CactusUtils: TerminationTrigger.
>
> This thorn watches the elapsed walltime.  If only n minutes are left
> before the some limit set by the user, it triggers termination of the
> simulation.  Termination is also triggered if a special file with a
> special content exists.
>
> This thorn was written by Christian Ott based on an original idea by
> Steve White.
>
> -erik
>
> -- 
> Erik Schnetter <schnetter at cct.lsu.edu>
> http://www.cct.lsu.edu/~eschnett/
>
>
>
>
> --- StripMime Report -- processed MIME parts ---
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> ---
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers

Dr. Bruno Giacomazzo
Department of Astronomy
University of Maryland
College Park
MD 20742-2421
USA

Tel.  : +1 301 405 0676
Fax  : +1 301 314 9067
Cell. : +1 443 535 5846
email : bgiacoma at astro.umd.edu

----------------------------------------------------------------------
There are only 10 types of people in the world:
Those who understand binary, and those who don't
----------------------------------------------------------------------

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From bgiacoma at astro.umd.edu  Mon Jan 11 14:12:39 2010
From: bgiacoma at astro.umd.edu (Bruno Giacomazzo)
Date: Mon, 11 Jan 2010 15:12:39 -0500
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
Message-ID: <6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>

Hi Erik,
	why you don't use AEIThorns/ManualTermination (svn co https:// 
svn.aei.mpg.de:/numrel/AEIThorns/ManualTermination/trunk  
ManualTermination)?

	It does the same identical thing and, being under AEIThorns, it  
should be also public available. I use it regularly to stop jobs some  
minutes before the walltime limit or when I want to force a job to  
write a checkpoint file and then quit (by editing the content of a  
file that is checked regularly). This seems to be the same thing that  
is done by TerminationTrigger.

Cheers,
Bruno


On Jan 11, 2010, at 3:02 PM, Erik Schnetter wrote:

> I suggest to add a new thorn to CactusUtils: TerminationTrigger.
>
> This thorn watches the elapsed walltime.  If only n minutes are left
> before the some limit set by the user, it triggers termination of the
> simulation.  Termination is also triggered if a special file with a
> special content exists.
>
> This thorn was written by Christian Ott based on an original idea by
> Steve White.
>
> -erik
>
> -- 
> Erik Schnetter <schnetter at cct.lsu.edu>
> http://www.cct.lsu.edu/~eschnett/
>
>
>
>
> --- StripMime Report -- processed MIME parts ---
> multipart/mixed
>   text/plain (text body -- kept)
>   application/x-gzip
> ---
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers

Dr. Bruno Giacomazzo
Department of Astronomy
University of Maryland
College Park
MD 20742-2421
USA

Tel.  : +1 301 405 0676
Fax  : +1 301 314 9067
Cell. : +1 443 535 5846
email : bgiacoma at astro.umd.edu

----------------------------------------------------------------------
There are only 10 types of people in the world:
Those who understand binary, and those who don't
----------------------------------------------------------------------



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From schnetter at cct.lsu.edu  Mon Jan 11 14:40:09 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Mon, 11 Jan 2010 14:40:09 -0600
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
	<6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
Message-ID: <3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>

Bruno

The two thorns are indeed very similar, and the new TerminationTrigger is based on AEIThorns/TriggerTermination.  The difference is

- AEIThorns/TriggerTermination requires PBS, which does not exist on all machines
- TerminationTrigger also terminates a simulation when the user creates a certain file.

-erik



On Jan 11, 2010, at 14:12 , Bruno Giacomazzo wrote:

> Hi Erik,
> 	why you don't use AEIThorns/ManualTermination (svn co https://svn.aei.mpg.de:/numrel/AEIThorns/ManualTermination/trunk ManualTermination)?
> 
> 	It does the same identical thing and, being under AEIThorns, it should be also public available. I use it regularly to stop jobs some minutes before the walltime limit or when I want to force a job to write a checkpoint file and then quit (by editing the content of a file that is checked regularly). This seems to be the same thing that is done by TerminationTrigger.
> 
> Cheers,
> Bruno
> 
> 
> On Jan 11, 2010, at 3:02 PM, Erik Schnetter wrote:
> 
>> I suggest to add a new thorn to CactusUtils: TerminationTrigger.
>> 
>> This thorn watches the elapsed walltime.  If only n minutes are left 
>> before the some limit set by the user, it triggers termination of the 
>> simulation.  Termination is also triggered if a special file with a 
>> special content exists.
>> 
>> This thorn was written by Christian Ott based on an original idea by 
>> Steve White.
>> 
>> -erik
>> 
>> -- 
>> Erik Schnetter <schnetter at cct.lsu.edu>   
>> http://www.cct.lsu.edu/~eschnett/
>> 
>> 
>> 
>> 
>> --- StripMime Report -- processed MIME parts ---
>> multipart/mixed
>>   text/plain (text body -- kept)
>>   application/x-gzip
>> ---
>> _______________________________________________
>> Developers mailing list
>> Developers at cactuscode.org
>> http://www.cactuscode.org/mailman/listinfo/developers
> 
> Dr. Bruno Giacomazzo
> Department of Astronomy
> University of Maryland
> College Park
> MD 20742-2421
> USA
> 
> Tel.  : +1 301 405 0676
> Fax  : +1 301 314 9067
> Cell. : +1 443 535 5846
> email : bgiacoma at astro.umd.edu
> 
> ----------------------------------------------------------------------
> There are only 10 types of people in the world:
> Those who understand binary, and those who don't
> ----------------------------------------------------------------------
> 
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers


-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From bgiacoma at astro.umd.edu  Mon Jan 11 14:47:18 2010
From: bgiacoma at astro.umd.edu (Bruno Giacomazzo)
Date: Mon, 11 Jan 2010 15:47:18 -0500
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
	<6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
	<3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>
Message-ID: <EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>

Hi Erik,
	thank you for the explanation.

	AEIThorns/ManualTermination can be used without problems also on  
machines that don't have PBS (such as damiana at the AEI for  
example). One needs simply to add this line to the submission script:

export MANUAL_TERMINATION_JOB_ID=${JOB_NAME}.${JOB_ID}

Cheers,
Bruno

On Jan 11, 2010, at 3:40 PM, Erik Schnetter wrote:

> Bruno
>
> The two thorns are indeed very similar, and the new  
> TerminationTrigger is based on AEIThorns/TriggerTermination.  The  
> difference is
>
> - AEIThorns/TriggerTermination requires PBS, which does not exist  
> on all machines
> - TerminationTrigger also terminates a simulation when the user  
> creates a certain file.
>
> -erik
>
>
>
> On Jan 11, 2010, at 14:12 , Bruno Giacomazzo wrote:
>
>> Hi Erik,
>> 	why you don't use AEIThorns/ManualTermination (svn co https:// 
>> svn.aei.mpg.de:/numrel/AEIThorns/ManualTermination/trunk  
>> ManualTermination)?
>>
>> 	It does the same identical thing and, being under AEIThorns, it  
>> should be also public available. I use it regularly to stop jobs  
>> some minutes before the walltime limit or when I want to force a  
>> job to write a checkpoint file and then quit (by editing the  
>> content of a file that is checked regularly). This seems to be the  
>> same thing that is done by TerminationTrigger.
>>
>> Cheers,
>> Bruno
>>
>>
>> On Jan 11, 2010, at 3:02 PM, Erik Schnetter wrote:
>>
>>> I suggest to add a new thorn to CactusUtils: TerminationTrigger.
>>>
>>> This thorn watches the elapsed walltime.  If only n minutes are left
>>> before the some limit set by the user, it triggers termination of  
>>> the
>>> simulation.  Termination is also triggered if a special file with a
>>> special content exists.
>>>
>>> This thorn was written by Christian Ott based on an original idea by
>>> Steve White.
>>>
>>> -erik
>>>
>>> -- 
>>> Erik Schnetter <schnetter at cct.lsu.edu>
>>> http://www.cct.lsu.edu/~eschnett/
>>>
>>>
>>>
>>>
>>> --- StripMime Report -- processed MIME parts ---
>>> multipart/mixed
>>>   text/plain (text body -- kept)
>>>   application/x-gzip
>>> ---
>>> _______________________________________________
>>> Developers mailing list
>>> Developers at cactuscode.org
>>> http://www.cactuscode.org/mailman/listinfo/developers
>>
>> Dr. Bruno Giacomazzo
>> Department of Astronomy
>> University of Maryland
>> College Park
>> MD 20742-2421
>> USA
>>
>> Tel.  : +1 301 405 0676
>> Fax  : +1 301 314 9067
>> Cell. : +1 443 535 5846
>> email : bgiacoma at astro.umd.edu
>>
>> --------------------------------------------------------------------- 
>> -
>> There are only 10 types of people in the world:
>> Those who understand binary, and those who don't
>> --------------------------------------------------------------------- 
>> -
>>
>> _______________________________________________
>> Developers mailing list
>> Developers at cactuscode.org
>> http://www.cactuscode.org/mailman/listinfo/developers
>
>
> -- 
> Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/ 
> ~eschnett/
>
>
>
>
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers

Dr. Bruno Giacomazzo
Department of Astronomy
University of Maryland
College Park
MD 20742-2421
USA

Tel.  : +1 301 405 0676
Fax  : +1 301 314 9067
Cell. : +1 443 535 5846
email : bgiacoma at astro.umd.edu

----------------------------------------------------------------------
There are only 10 types of people in the world:
Those who understand binary, and those who don't
----------------------------------------------------------------------


From schnetter at cct.lsu.edu  Mon Jan 11 15:01:09 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Mon, 11 Jan 2010 15:01:09 -0600
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
	<6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
	<3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>
	<EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>
Message-ID: <25EFD2F8-5D1D-4CF6-988D-9104189D68E1@cct.lsu.edu>

Bruno

I see that you speak of AEIThorns/ManualTermination, not of AEIThorns/TriggerTermination.  I was confused.

The new thorn CactusUtils/TerminationTrigger is just a newer version of AEIThorns/ManualTermination.  It has a new name so that there are no conflicts when people continue to use the old thorn for some time.

Setting the environment variable by hand is not necessary any more; the code works fine if it does not exist.

-erik

On Jan 11, 2010, at 14:47 , Bruno Giacomazzo wrote:

> Hi Erik,
> 	thank you for the explanation.
> 
> 	AEIThorns/ManualTermination can be used without problems also on  
> machines that don't have PBS (such as damiana at the AEI for  
> example). One needs simply to add this line to the submission script:
> 
> export MANUAL_TERMINATION_JOB_ID=${JOB_NAME}.${JOB_ID}
> 
> Cheers,
> Bruno
> 
> On Jan 11, 2010, at 3:40 PM, Erik Schnetter wrote:
> 
>> Bruno
>> 
>> The two thorns are indeed very similar, and the new  
>> TerminationTrigger is based on AEIThorns/TriggerTermination.  The  
>> difference is
>> 
>> - AEIThorns/TriggerTermination requires PBS, which does not exist  
>> on all machines
>> - TerminationTrigger also terminates a simulation when the user  
>> creates a certain file.
>> 
>> -erik
>> 
>> 
>> 
>> On Jan 11, 2010, at 14:12 , Bruno Giacomazzo wrote:
>> 
>>> Hi Erik,
>>> 	why you don't use AEIThorns/ManualTermination (svn co https:// 
>>> svn.aei.mpg.de:/numrel/AEIThorns/ManualTermination/trunk  
>>> ManualTermination)?
>>> 
>>> 	It does the same identical thing and, being under AEIThorns, it  
>>> should be also public available. I use it regularly to stop jobs  
>>> some minutes before the walltime limit or when I want to force a  
>>> job to write a checkpoint file and then quit (by editing the  
>>> content of a file that is checked regularly). This seems to be the  
>>> same thing that is done by TerminationTrigger.
>>> 
>>> Cheers,
>>> Bruno
>>> 
>>> 
>>> On Jan 11, 2010, at 3:02 PM, Erik Schnetter wrote:
>>> 
>>>> I suggest to add a new thorn to CactusUtils: TerminationTrigger.
>>>> 
>>>> This thorn watches the elapsed walltime.  If only n minutes are left
>>>> before the some limit set by the user, it triggers termination of  
>>>> the
>>>> simulation.  Termination is also triggered if a special file with a
>>>> special content exists.
>>>> 
>>>> This thorn was written by Christian Ott based on an original idea by
>>>> Steve White.
>>>> 
>>>> -erik
>>>> 
>>>> -- 
>>>> Erik Schnetter <schnetter at cct.lsu.edu>
>>>> http://www.cct.lsu.edu/~eschnett/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> --- StripMime Report -- processed MIME parts ---
>>>> multipart/mixed
>>>>  text/plain (text body -- kept)
>>>>  application/x-gzip
>>>> ---
>>>> _______________________________________________
>>>> Developers mailing list
>>>> Developers at cactuscode.org
>>>> http://www.cactuscode.org/mailman/listinfo/developers
>>> 
>>> Dr. Bruno Giacomazzo
>>> Department of Astronomy
>>> University of Maryland
>>> College Park
>>> MD 20742-2421
>>> USA
>>> 
>>> Tel.  : +1 301 405 0676
>>> Fax  : +1 301 314 9067
>>> Cell. : +1 443 535 5846
>>> email : bgiacoma at astro.umd.edu
>>> 
>>> --------------------------------------------------------------------- 
>>> -
>>> There are only 10 types of people in the world:
>>> Those who understand binary, and those who don't
>>> --------------------------------------------------------------------- 
>>> -
>>> 
>>> _______________________________________________
>>> Developers mailing list
>>> Developers at cactuscode.org
>>> http://www.cactuscode.org/mailman/listinfo/developers
>> 
>> 
>> -- 
>> Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/ 
>> ~eschnett/
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Developers mailing list
>> Developers at cactuscode.org
>> http://www.cactuscode.org/mailman/listinfo/developers
> 
> Dr. Bruno Giacomazzo
> Department of Astronomy
> University of Maryland
> College Park
> MD 20742-2421
> USA
> 
> Tel.  : +1 301 405 0676
> Fax  : +1 301 314 9067
> Cell. : +1 443 535 5846
> email : bgiacoma at astro.umd.edu
> 
> ----------------------------------------------------------------------
> There are only 10 types of people in the world:
> Those who understand binary, and those who don't
> ----------------------------------------------------------------------
> 
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers


-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From cott at tapir.caltech.edu  Mon Jan 11 15:04:39 2010
From: cott at tapir.caltech.edu (Christian D. Ott)
Date: Mon, 11 Jan 2010 13:04:39 -0800
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
	<6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
	<3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>
	<EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>
Message-ID: <20100111210439.GS24961@wilson.tapir.caltech.edu>

Hi Bruno,

On Mon, Jan 11, 2010 at 03:47:18PM -0500, Bruno Giacomazzo wrote:
> Hi Erik,
> 	thank you for the explanation.
> 
> 	AEIThorns/ManualTermination can be used without problems also on  
> machines that don't have PBS (such as damiana at the AEI for  
> example). One needs simply to add this line to the submission script:
> 
> export MANUAL_TERMINATION_JOB_ID=${JOB_NAME}.${JOB_ID}
> 

I would think that this still requires the availability of a command
like qstat or so for the thorn to figure out the remaining wall time.
So this is suboptimal and not good for the inclusion in Cactus.

Independent of what is included in Cactus, people can of course
continue to use their own thorns or other public thorns.

 - Christian 


From bgiacoma at astro.umd.edu  Mon Jan 11 15:12:20 2010
From: bgiacoma at astro.umd.edu (Bruno Giacomazzo)
Date: Mon, 11 Jan 2010 16:12:20 -0500
Subject: [Developers] CactusUtils/TerminationTrigger
In-Reply-To: <20100111210439.GS24961@wilson.tapir.caltech.edu>
References: <833AACF1-1C1C-4C33-AC02-B23F96EBD95C@cct.lsu.edu>
	<6DCD36F2-E396-4A14-8E43-6C764D66C74F@astro.umd.edu>
	<3CDC23B6-A162-47D9-A3F1-24A47A5CB61D@cct.lsu.edu>
	<EBF4D13A-F5F4-47F4-B00D-242E72BF1B13@astro.umd.edu>
	<20100111210439.GS24961@wilson.tapir.caltech.edu>
Message-ID: <60B758A1-94EB-4709-87F1-FD5287D6CFBF@astro.umd.edu>

Dear Erik and Christian,
	thank you for the explanation.

	I was just trying to understand the differences between these two  
thorns and if it would be worth for me to switch to the new one or  
not. I don't know the technical details of ManualTermination, but up  
to now I never had problems with it on different machines. In case it  
happens, it's useful to know that there is something else I could use.

Cheers,
Bruno

On Jan 11, 2010, at 4:04 PM, Christian D. Ott wrote:

> Hi Bruno,
>
> On Mon, Jan 11, 2010 at 03:47:18PM -0500, Bruno Giacomazzo wrote:
>> Hi Erik,
>> 	thank you for the explanation.
>>
>> 	AEIThorns/ManualTermination can be used without problems also on
>> machines that don't have PBS (such as damiana at the AEI for
>> example). One needs simply to add this line to the submission script:
>>
>> export MANUAL_TERMINATION_JOB_ID=${JOB_NAME}.${JOB_ID}
>>
>
> I would think that this still requires the availability of a command
> like qstat or so for the thorn to figure out the remaining wall time.
> So this is suboptimal and not good for the inclusion in Cactus.
>
> Independent of what is included in Cactus, people can of course
> continue to use their own thorns or other public thorns.
>
>  - Christian
>
> _______________________________________________
> Developers mailing list
> Developers at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/developers

Dr. Bruno Giacomazzo
Department of Astronomy
University of Maryland
College Park
MD 20742-2421
USA

Tel.  : +1 301 405 0676
Fax  : +1 301 314 9067
Cell. : +1 443 535 5846
email : bgiacoma at astro.umd.edu

----------------------------------------------------------------------
There are only 10 types of people in the world:
Those who understand binary, and those who don't
----------------------------------------------------------------------

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From schnetter at cct.lsu.edu  Sun Jan 17 22:31:03 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Sun, 17 Jan 2010 22:31:03 -0600
Subject: [Developers] Error in parameter file parser
Message-ID: <B5AE02C3-5559-4E1C-AD61-E7E01B564D7A@cct.lsu.edu>

The parameter file parser can get confused with detecting the end of the buffer when the last line is in a comment or in a string, and may overrun the end of the buffer.  The symptoms are error messages past the last line of the parameter file, because the memory after the buffer end is interpreted as (probably mal-formed) parameter file content.  This happens especially if the parameter file is shortened by expanding e.g. $parfile.

Since the paring routine is quite complex, this patch works around this problem by increasing the size of the buffer by a few characters and setting these to NUL.  This is obviously only a work-around; the parser should be corrected.  Since the paring routine is quite complex, a bit of restructuring would be in order.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From schnetter at cct.lsu.edu  Mon Jan 18 14:18:37 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Mon, 18 Jan 2010 14:18:37 -0600
Subject: [Developers] TimerReport: Output more than one clock
Message-ID: <2B18B574-49B6-4A69-AF51-36834D662089@cct.lsu.edu>

Currently, thorn CactusUtils/TimerReport outputs one clock only for each 
timer.  This clock can be selected with the parameter all_timers_clock.  
This makes the output much more readable, since there may be many 
clocks.

The enclosed patch adds a new array parameter all_timers_clocks[] that 
allows multiple clocks to be specified.  They are output into a 
different file each, with the file name containing the clock name.  This 
affects the output_all_timers, output_all_timers_together, and 
output_all_timers_readable functionality.

Implementation-wise, there is now a for loop surrounding the output code 
that traverses all clocks.

This makes is possible to output e.g. the wall time as well as several 
PAPI clocks.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   
http://www.cct.lsu.edu/~eschnett/




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From knarf at cct.lsu.edu  Tue Jan 26 16:31:09 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Tue, 26 Jan 2010 16:31:09 -0600
Subject: [Developers] CactusEinstein: Excision in HydroBase
Message-ID: <20100126223109.GP18541@numrel07.cct.lsu.edu>

Hi,

the attched patch adds excision definitions for HydroBase:

- New parameter "hydro_excision" to turn the storage for the excision
  mask on/off (default off)
- Excision mask (being INTEGER for the moment, might change to
  BYTE later)
- Initialization of the mask to 'normal'
- Headerfile with definitions of the msak values:
  HYDROEXCISION_NORMAL / HYDROEXCISION_EXCISED
- schedule group definition in POSTSTEP to schedle thorns setting the
  mask before that and thorns using the mask after it

Frank


Index: interface.ccl
=========================
=========================
=================
RCS file: /cactusdevcvs/CactusEinstein/HydroBase/interface.ccl,v
retrieving revision 1.11
diff -u -r1.11 interface.ccl
--- interface.ccl	8 Dec 2009 19:46:35 -0000	1.11
+++ interface.ccl	26 Jan 2010 21:07:15 -0000
@@ -4,6 +4,10 @@
 
 inherits: InitBase
 
+USES INCLUDE: HydroBase.h
+
+INCLUDE HEADER: HydroBase.h in HydroBase.h
+
 public:
 
 # These variables correspond to the Valencia formulation
@@ -34,3 +38,6 @@
 CCTK_REAL Y_e     type = GF Timelevels = 3 tags='ProlongationParamet
er="HydroBase::prolongation_type" tensortypealias="Scalar" interpolator
="matter"' "electron fraction"
 
 CCTK_REAL Bvec[3] type = GF Timelevels = 3 tags='ProlongationParamet
er="HydroBase::prolongation_type" tensortypealias="U" interpolator="m
atter"' "Magnetic field components B^i"
+
+# This may become CCTK_BYTE when Carpet enables it by default
+CCTK_INT hydro_excision_mask type = GF Timelevels = 1 tags='Prolonga
tion="None" checkpoint="no"' "Mask for hydro excision"
Index: param.ccl
=========================
=========================
=================
RCS file: /cactusdevcvs/CactusEinstein/HydroBase/param.ccl,v
retrieving revision 1.7
diff -u -r1.7 param.ccl
--- param.ccl	7 Dec 2009 17:12:39 -0000	1.7
+++ param.ccl	26 Jan 2010 21:07:15 -0000
@@ -53,3 +53,8 @@
 {
   "none" :: "Evolution for Bvec is disabled"
 } "none"
+
+BOOLEAN hydro_excision "Turn on of off (default) storage for hydro excisio
n"
+{
+} "no"
+
Index: schedule.ccl
=========================
=========================
=================
RCS file: /cactusdevcvs/CactusEinstein/HydroBase/schedule.ccl,v
retrieving revision 1.8
diff -u -r1.8 schedule.ccl
--- schedule.ccl	7 Dec 2009 17:12:39 -0000	1.8
+++ schedule.ccl	26 Jan 2010 21:07:15 -0000
@@ -46,6 +46,11 @@
   }
 }
 
+if (hydro_excision)
+{
+  STORAGE: hydro_excision_mask
+}
+
 schedule group HydroBase_Initial at CCTK_INITIAL    \
     after (ADMBase_InitialData ADMBase_InitialGauge \
            IOUtil_RecoverIDFromDatafiles)           \
@@ -137,3 +142,16 @@
     LANG: C
   } "Set magnetic field to 0"
 }
+
+if (hydro_excision)
+{
+  schedule GROUP HydroBase_ExcisionHasBeenSet at CCTK_PostStep
+  {
+  } "Group to schedule thorns changing the mask before and thorns using th
e mask after"
+
+  schedule HydroBase_InitExcisionMask in HydroBase_Initial
+  {
+    LANG: C
+  } "Initialize hydro excision mask to 'no excision everywhere'"
+}
+
Index: src/HydroBase.h
=========================
=========================
=================
RCS file: src/HydroBase.h
diff -N src/HydroBase.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/HydroBase.h	26 Jan 2010 21:07:15 -0000
@@ -0,0 +1,2 @@
+#define HYDROEXCISION_NORMAL  0
+#define HYDROEXCISION_EXCISED 1
Index: src/Initialisation.c
=========================
=========================
=================
RCS file: /cactusdevcvs/CactusEinstein/HydroBase/src/Initialisation.c,v
retrieving revision 1.3
diff -u -r1.3 Initialisation.c
--- src/Initialisation.c	7 Dec 2009 17:12:39 -0000	1.3
+++ src/Initialisation.c	26 Jan 2010 21:07:15 -0000
@@ -1,7 +1,7 @@
 #include <cctk.h>
 #include <cctk_Arguments.h>
 #include <cctk_Parameters.h>
-
+#include "HydroBase.h"
 
 
 void HydroBase_Zero (CCTK_ARGUMENTS)
@@ -166,3 +166,16 @@
                "Unsupported parameter value for InitBase::initial_data_set
up_method");
   }
 }
+
+void HydroBase_InitExcisionMask (CCTK_ARGUMENTS)
+{
+  DECLARE_CCTK_ARGUMENTS;
+  DECLARE_CCTK_PARAMETERS;
+  
+  int const np = cctk_lsh[0] * cctk_lsh[1] * cctk_lsh[2];
+  
+  #pragma omp parallel for
+  for (int i=0; i<np; ++i) {
+    hydro_excision_mask[i] = HYDROEXCISION_NORMAL;
+  }
+}


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From knarf at cct.lsu.edu  Tue Jan 26 16:46:24 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Tue, 26 Jan 2010 16:46:24 -0600
Subject: [Developers] [Patches] CactusEinstein: Excision in HydroBase
In-Reply-To: <20100126223109.GP18541@numrel07.cct.lsu.edu>
References: <20100126223109.GP18541@numrel07.cct.lsu.edu>
Message-ID: <20100126224624.GQ18541@numrel07.cct.lsu.edu>

Hi,

On Tue, Jan 26, 2010 at 04:31:09PM -0600, Frank Loeffler wrote:
> the attched patch adds excision definitions for HydroBase:
> 
> - New parameter "hydro_excision" to turn the storage for the excision
>   mask on/off (default off)

One question more related to taste than anything else is: should it (in
various places) be "hydro_excision" or "hydroexcision", so with or
without the "_". The patch is inconsistent in this, which should
probably be changed. The question is in which direction.

Frank

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From schnetter at cct.lsu.edu  Tue Jan 26 17:22:51 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Tue, 26 Jan 2010 17:22:51 -0600
Subject: [Developers] [Patches] CactusEinstein: Excision in HydroBase
In-Reply-To: <20100126224624.GQ18541@numrel07.cct.lsu.edu>
References: <20100126223109.GP18541@numrel07.cct.lsu.edu>
	<20100126224624.GQ18541@numrel07.cct.lsu.edu>
Message-ID: <4045BC89-CBB4-4470-928B-BF6923A552BA@cct.lsu.edu>

On Jan 26, 2010, at 16:46 , Frank Loeffler wrote:

> Hi,
> 
> On Tue, Jan 26, 2010 at 04:31:09PM -0600, Frank Loeffler wrote:
>> the attched patch adds excision definitions for HydroBase:
>> 
>> - New parameter "hydro_excision" to turn the storage for the excision
>>  mask on/off (default off)
> 
> One question more related to taste than anything else is: should it (in
> various places) be "hydro_excision" or "hydroexcision", so with or
> without the "_". The patch is inconsistent in this, which should
> probably be changed. The question is in which direction.


The thorn is called HydroBase, which turns into hydro_base if only lower case letters are used.  I would use the same convention for excision.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From knarf at cct.lsu.edu  Tue Jan 26 17:35:03 2010
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Tue, 26 Jan 2010 17:35:03 -0600
Subject: [Developers] [Patches] CactusEinstein: Excision in HydroBase
In-Reply-To: <4045BC89-CBB4-4470-928B-BF6923A552BA@cct.lsu.edu>
References: <20100126223109.GP18541@numrel07.cct.lsu.edu>
	<20100126224624.GQ18541@numrel07.cct.lsu.edu>
	<4045BC89-CBB4-4470-928B-BF6923A552BA@cct.lsu.edu>
Message-ID: <20100126233503.GR18541@numrel07.cct.lsu.edu>

On Tue, Jan 26, 2010 at 05:22:51PM -0600, Erik Schnetter wrote:
> The thorn is called HydroBase, which turns into hydro_base if only lower case letters are used.  I would use the same convention for excision.

That sounds good. The same would hold for only upper case letters.

Frank

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From schnetter at cct.lsu.edu  Sun Jan 31 19:28:01 2010
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Sun, 31 Jan 2010 19:28:01 -0600
Subject: [Developers] [Patches] RPATHDIRS for thorn-internal libraries
In-Reply-To: <20091027200122.GE22099@numrel07.cct.lsu.edu>
References: <20091027200122.GE22099@numrel07.cct.lsu.edu>
Message-ID: <D6FA4A0B-9BA8-45F9-B367-35873D26EDA4@cct.lsu.edu>

This patch makes Cactus add run-time linker directory paths for every 
linker directory path that it uses to build the executable.  This means 
that, at run time, the same shared library should be used that was also 
found when linking the executable.

It introduces as new configuration variable RUNDIR_PREFIX which defaults 
to "-Wl,-rpath,", and which can be changed e.g. to "-R" if appropriate.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   
http://www.cct.lsu.edu/~eschnett/




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