Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent

From: Antje Wolf <antje.wolf.scai.fraunhofer.de>
Date: Wed, 2 Mar 2011 08:44:39 +0100 (CET)

Hi Ross,

I see exactly the same error with a NPT simulation in a chloroform/methanol box on a Tesla C1060. I am using the most recent version of AMBER 11 with bug fixes 1 to 12 applied. In serial and MPI PMEMD the simulation is running without problems.

Cheers,
Antje

----- Urspr├╝ngliche Mail -----
| Hi Viktor,
|
| Can you please confirm that you are using a fully up to date version
| of
| AMBER patched up to bugfix.12. If you haven't updated then please
| patch it,
| recompile and try again. If you still see this problem with a fully up
| to
| date version please send me the input files so I can see if I can
| reproduce
| this error.
|
| Thank you.
|
| All the best
| Ross
|
| > -----Original Message-----
| > From: vitor.felix.ua.pt [mailto:vitor.felix.ua.pt]
| > Sent: Monday, February 28, 2011 1:05 AM
| > To: amber.ambermd.org
| > Subject: [AMBER] NPT simulation crash using a GPU CARD for a
| > simulation
| > carried out in a organic explicit solvent
| >
| > Dear Amber community
| >
| > I am interested to run a MD simulation in a NPT ensemble using a
| > NVIDIA
| > GPU C2050. The solvent is a mixture composed of methanol and
| > chloroform
| > and the periodic system contains only 7858 atoms. The simulation
| > runs
| > well in both NVT and NVE ensembles.When the NPT is used, the
| > simulation
| > stops in the begging with message given below. Furthermore, the same
| > problem occurs with a pure solvent such as chloroform. In contrast ,
| > when the mixture of solvent is composed of water and an organic
| > solvent (the system has approximately the same size in number of
| > atoms) the NPT simulation runs without any problems as happened with
| > much larger size simulations carried in TIP3P water model. The
| > problem
| > seems to me related with the type of explicit solvent used. The
| > system
| > is quite small and I don┬┤t believe that the problem is related with
| > amount of GPU memory required by a NPT simulation.
| > Searching on the internet I found the same message type for other
| > GPU
| > cards, but not for Tesla C2050.
| >
| > Any help would be appreciated about this issue.
| >
| > Thank you very much in advance
| > Vitor Felix
| >
| > #######################################################
| > Error: unspecified launch failure launching kernel kNLSkinTest
| > cudaFree GpuBuffer::Deallocate failed unspecified launch failure
| >
| > Begin of the NPT simulation
| > ---------------------------------------------------
| > APPROXIMATING switch and d/dx switch using CUBIC SPLINE
| > INTERPOLATION
| > using 5000.0 points per unit in tabled values
| > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| > | CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
| > ---------------------------------------------------
| > |---------------------------------------------------
| > | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| > | with 50.0 points per unit in tabled values
| > | Relative Error Limit not exceeded for r .gt. 2.27
| > | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| > | with 50.0 points per unit in tabled values
| > | Relative Error Limit not exceeded for r .gt. 2.78
| > ##########################################################
| > ##########################
| >
| > --
| > *************************************
| > Vitor Felix
| > Department of Chemistry
| > University of Aveiro
| > 3810-193 Aveiro, Portugal
| > Tel: 351 234 370 200 ext: 22102
| > http://molecular-modeling.dq.ua.pt
| >
| >
| > _______________________________________________
| > AMBER mailing list
| > AMBER.ambermd.org
| > http://lists.ambermd.org/mailman/listinfo/amber
|
|
| _______________________________________________
| AMBER mailing list
| AMBER.ambermd.org
| http://lists.ambermd.org/mailman/listinfo/amber

-- 
Antje Wolf
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Department Bioinformatics
Schloss Birlinghoven
D-53754 Sankt Augustin
Tel.: +49 2241 14 2552
E-mail: antje.wolf.scai.fraunhofer.de
Internet: http://www.scai.fraunhofer.de
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 02 2011 - 00:00:02 PST
Custom Search