Re: [gmx-users] number of DD cells

[Mark Abraham]

On 05/03/11, "Justin A. Lemkul"   wrote:
> 
> 
> Moeed wrote:
> >Hello,
> >
> >I am attempting to increase the density using NPT. As I increase the 
> >pressure to compress the system after some steps simulation crashes. I 
> >thought maybe its becasue I am compressing too fast but even when I take a 
> >stepwise approach to compress gradually the same error comes up. The density 
> >at the point of crash is about 30 SI while I need 650 which is the actual 
> >density. Topology file is generated successfully and also I did EM before MD.
> >
> >Initial box size is 30 nm. As suggested in the link below I reduced the size 
> >to 20 nm (there are 2500 atoms in the system ) but the same error appears.
> >http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html
> >
> >I also tried less -np from 7 to 4 but no success.
> >
> >Can you please tell me what this exclamation mark mean which I get at times 
> >in parallel trials.(vol 0.99 !)
> >
> 
> Domain decomposition relies on dividing your system up into reliably-sized 
> domains in order to communicate force, coordinate, energy, etc. information.  
> If something happens to skew or annihilate these domains, the algorithm 
> crashes. The exclamation marks indicate (in a general sense) that the DD 
> algorithm has detected something dangerously wrong.
> 
> If you're trying to make drastic changes to the size or dimensions of your 
> system, DD is a bad choice and you'll likely have to use particle 
> decomposition (mdrun -pd).
> 

Or during compression, do regular and frequent grompp -t .trr -e .edr restarts 
so that the DD information in the checkpoint file is not propagated, and so you 
can do a new DD based on the current volume.

Mark


> 
> 
> 
> 
> >fourierspacing  =  0.3 
> 
> You're setting yourself up for inaccurate PME calculations with this.  Use 
> 0.1 - 0.12 unless you've got some compelling reason to decrease your accuracy.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
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>
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Re: [gmx-users] number of DD cells

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Moeed wrote:

Hello Justin,

Thanks.

1- I changed the setting below because of the note I used to get:

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing



I'm guessing this pertains to your "expanded" system, before you've 
obtained an optimum density?  If so, you're only going to be losing 
performance for some simulations, but not all.  It also depends on just 
how bad the load imbalance is.  If you can set it such that you can 
easily specify -npme to match the PP:PME ratio, then you shouldn't be 
hurt too badly.


Also, earlier on I read one of your messages about the trade off 
between accuracy and speed for this setting and that no systematic 
study has been done how exactly accuracy is changing. I actually need 
to work with systems with 40 000 atoms or even more and electrostatics 
slows down my runs to a great extent. Can you please give an idea on 
to what extent the accuracy affects the result say for 
fourierspacing  =  0.2 . I mean it affects second decimal or...? I 
need to go for a setting which 


You may want to look into g_tune_pme.  It should provide this sort of 
information.  There was also some discussion about this just a few weeks 
ago, but I don't have the time or desire to go rooting through the list 
archive at the moment.




Sorry, that should be g_pme_error.

-Justin

speeds up calculations as much as possible while being reasonable. How 
would you deal with this? What value would you pick?




Ideally, one that is well-tested and that you can defend to a critical 
audience.  If 0.12 is standard, and I have no desire to experiment with 
accuracy, I tend to stick with that :)


-Justin


Thank you,
moeed


fourierspacing  =  0.3   


You're setting yourself up for inaccurate PME calculations with
this.  Use 0.1 - 0.12 unless you've got some compelling reason to
decrease your accuracy.

-Justin

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php 


Web:http://mmrg.chemeng.mcgill.ca/





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] number of DD cells

[Justin A. Lemkul]

Moeed wrote:

Hello Justin,

Thanks.

1- I changed the setting below because of the note I used to get:

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing



I'm guessing this pertains to your "expanded" system, before you've obtained an 
optimum density?  If so, you're only going to be losing performance for some 
simulations, but not all.  It also depends on just how bad the load imbalance 
is.  If you can set it such that you can easily specify -npme to match the 
PP:PME ratio, then you shouldn't be hurt too badly.


Also, earlier on I read one of your messages about the trade off between 
accuracy and speed for this setting and that no systematic study has 
been done how exactly accuracy is changing. I actually need to work with 
systems with 40 000 atoms or even more and electrostatics slows down my 
runs to a great extent. Can you please give an idea on to what extent 
the accuracy affects the result say for fourierspacing  =  0.2 . I 
mean it affects second decimal or...? I need to go for a setting which 


You may want to look into g_tune_pme.  It should provide this sort of 
information.  There was also some discussion about this just a few weeks ago, 
but I don't have the time or desire to go rooting through the list archive at 
the moment.


speeds up calculations as much as possible while being reasonable. How 
would you deal with this? What value would you pick?




Ideally, one that is well-tested and that you can defend to a critical audience. 
 If 0.12 is standard, and I have no desire to experiment with accuracy, I tend 
to stick with that :)


-Justin


Thank you,
moeed


fourierspacing  =  0.3



You're setting yourself up for inaccurate PME calculations with
this.  Use 0.1 - 0.12 unless you've got some compelling reason to
decrease your accuracy.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] number of DD cells

[Moeed]

Hello Justin,

Thanks.

1- I changed the setting below because of the note I used to get:

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

Also, earlier on I read one of your messages about the trade off between
accuracy and speed for this setting and that no systematic study has been
done how exactly accuracy is changing. I actually need to work with systems
with 40 000 atoms or even more and electrostatics slows down my runs to a
great extent. Can you please give an idea on to what extent the accuracy
affects the result say for fourierspacing  =  0.2 . I mean it affects
second decimal or...? I need to go for a setting which speeds up
calculations as much as possible while being reasonable. How would you deal
with this? What value would you pick?

Thank you,
moeed


>  fourierspacing  =  0.3
>>
>
> You're setting yourself up for inaccurate PME calculations with this.  Use
> 0.1 - 0.12 unless you've got some compelling reason to decrease your
> accuracy.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>




-- 
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:
http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/
-- 
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Re: [gmx-users] number of DD cells

[Justin A. Lemkul]

Moeed wrote:

Hello,

I am attempting to increase the density using NPT. As I increase the 
pressure to compress the system after some steps simulation crashes. I 
thought maybe its becasue I am compressing too fast but even when I take 
a stepwise approach to compress gradually the same error comes up. The 
density at the point of crash is about 30 SI while I need 650 which is 
the actual density. Topology file is generated successfully and also I 
did EM before MD.


Initial box size is 30 nm. As suggested in the link below I reduced the 
size to 20 nm (there are 2500 atoms in the system ) but the same error 
appears.

http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html

I also tried less -np from 7 to 4 but no success.

Can you please tell me what this exclamation mark mean which I get at 
times in parallel trials.(vol 0.99 !)




Domain decomposition relies on dividing your system up into reliably-sized 
domains in order to communicate force, coordinate, energy, etc. information.  If 
something happens to skew or annihilate these domains, the algorithm crashes. 
The exclamation marks indicate (in a general sense) that the DD algorithm has 
detected something dangerously wrong.


If you're trying to make drastic changes to the size or dimensions of your 
system, DD is a bad choice and you'll likely have to use particle decomposition 
(mdrun -pd).




fourierspacing  =  0.3 


You're setting yourself up for inaccurate PME calculations with this.  Use 0.1 - 
0.12 unless you've got some compelling reason to decrease your accuracy.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] number of DD cells

[Moeed]

Hello,

I am attempting to increase the density using NPT. As I increase the
pressure to compress the system after some steps simulation crashes. I
thought maybe its becasue I am compressing too fast but even when I take a
stepwise approach to compress gradually the same error comes up. The density
at the point of crash is about 30 SI while I need 650 which is the actual
density. Topology file is generated successfully and also I did EM before
MD.

Initial box size is 30 nm. As suggested in the link below I reduced the size
to 20 nm (there are 2500 atoms in the system ) but the same error appears.
http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html

I also tried less -np from 7 to 4 but no success.

Can you please tell me what this exclamation mark mean which I get at times
in parallel trials.(vol 0.99 !)

Thank you for your time.


vol 0.99! imb F 47% step 168000, will finish Fri Mar  4 00:51:29 2011
vol 0.99! imb F 42% step 168100, will finish Fri Mar  4 00:51:26 2011
vol 0.99! imb F 44% step 168200, will finish Fri Mar  4 00:51:30 2011
vol 1.00! imb F 46% step 168300, will finish Fri Mar  4 00:51:27 2011
vol 1.00! imb F 48% step 168400, will finish Fri Mar  4 00:51:25 2011

---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 2592

Fatal error:
The X-size of the box (5.499734) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (7) times the smallest allowed cell
size (0.785678)


Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 2592

Fatal error:
The X-size of the box (4.999741) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (4) times the smallest allowed cell
size (1.25)


pbc  =  xyz


;Run control
integrator  =  md
dt  =  0.002
nsteps  =  100 ;5000
nstcomm =  100

;Output control
nstenergy   =  100
nstxout =  100
nstvout =  0
nstfout =  0
nstlog  =  1000
nstxtcout  =  1000

;Neighbor searching
nstlist =  10
ns_type =  grid

;Electrostatics/VdW
coulombtype =  PME
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9 ;0

;Cut-offs
rlist   =  1.25
rcoulomb=  1.25 ;1.1
rvdw=  1.0

;PME parameters
fourierspacing  =  0.3
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol =  1e-5
optimize_fft  =  yes

;Temperature coupling
Tcoupl  =  v-rescale
tc-grps =  System  ;HEX
tau_t   =  0.1 ;0.1
ref_t   =  400 ;300

;Pressure coupling
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic
tau_p   =  1  1   ;0.5
compressibility =  4.5e-5 4.5e-5
ref_p   =  88

;Velocity generation
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

;Bonds
constraints = all-bonds
constraint-algorithm = lincs
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Re: [gmx-users] number of DD cells

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi Mark,

I ran on 48 processors.the error is:

The X-size of the box (5.312040) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (0.885281)



I would say this further confirms Mark's suspicions.  Whatever you're doing to 
the system is causing it to rapidly collapse, a behavior that is now independent 
of the number of DD cells.


-Justin



Kind regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
[mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list
for GROMACS users Subject: Re: [gmx-users] number of DD cells

On 27/12/2010 7:51 AM, Poojari, Chetan wrote:

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five:
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size
of the box (4.800448) times the triclinic skew factor (1.00) is smaller
than the number of DD cells (4) times the smallest allowed cell size
(1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds. My system box
size is  6 x 6 x 12 nm


That's a large box deformation... 6nm to 4.8nm. I'd say your system is 
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on

fewer processors to see whether when the DD box size is larger whether you
get other explosion symptoms.

Mark -- gmx-users mailing listgmx-users@gromacs.org 
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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich 
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher 
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft

(stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
Schmidt 

 




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] number of DD cells

[Poojari, Chetan]

Hi Mark,

I ran on 48 processors.the error is:

The X-size of the box (5.312040) times the triclinic skew factor (1.00) is 
smaller than the number of DD cells (6) times the smallest allowed cell size 
(0.885281)


Kind regards,
chetan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: 27 December 2010 00:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] number of DD cells

On 27/12/2010 7:51 AM, Poojari, Chetan wrote:
> Hi,
>
> I am following umbrella sampling tutorial for my membrane protein system.
>
> While running continuous pulling simulation (mdrun). under step five: 
> Generating Configurations of the tutorial. I get the below error.
>
> The system ran initially but corrupted very soon with warning " The X-size of 
> the box (4.800448) times the triclinic skew factor (1.00) is smaller than 
> the number of DD cells (4) times the smallest allowed cell size (1.20) "
>
> I am using 64 cores with -npme = 16. I haven't set any -dds.
> My system box size is  6 x 6 x 12 nm

That's a large box deformation... 6nm to 4.8nm. I'd say your system is
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try
running on fewer processors to see whether when the DD box size is
larger whether you get other explosion symptoms.

Mark
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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Re: [gmx-users] number of DD cells

[Mark Abraham]

On 27/12/2010 7:51 AM, Poojari, Chetan wrote:

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five: 
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size of the 
box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of 
DD cells (4) times the smallest allowed cell size (1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds.
My system box size is  6 x 6 x 12 nm


That's a large box deformation... 6nm to 4.8nm. I'd say your system is 
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try 
running on fewer processors to see whether when the DD box size is 
larger whether you get other explosion symptoms.


Mark
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[gmx-users] number of DD cells

[Poojari, Chetan]

Hi,

To my earlier post on number of DD cells.i included -dds 0.6 and everything 
seems to run fine.

Is this the possible solution to the error or is there other way to handle this 
warning ?


Kind regards,
chetan.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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[gmx-users] number of DD cells

[Poojari, Chetan]

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five: 
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size of 
the box (4.800448) times the triclinic skew factor (1.00) is smaller than 
the number of DD cells (4) times the smallest allowed cell size (1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds.
My system box size is  6 x 6 x 12 nm



Please can I know what might be the problem.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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