Re: [gmx-users] Cluster recommendations

Intel nodes with 1 or 2 GPUs will give you the best performance and the best performance/price. Best, Carsten Thanks again. Best, D 2015-01-16 14:46 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, On 16 Jan 2015, at 12:28, David McGiven davidmcgiv...@gmail.com wrote: Hi

Re: [gmx-users] PME update

/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de

Re: [gmx-users] Cluster recommendations

/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten

Re: [gmx-users] Cluster recommendations

Hi David, On 16 Jan 2015, at 12:28, David McGiven davidmcgiv...@gmail.com wrote: Hi Carsten, Thanks for your answer. 2015-01-16 11:11 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, we are just finishing an evaluation to find out which is the optimal hardware for Gromacs

Re: [gmx-users] Performance difference between MPI ranks and OpenMP

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Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails

] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 8. Januar 2015 15:51 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails On 08 Jan 2015, at 15:32, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, I was benchmarking my first system and I

Re: [gmx-users] Performance difference between MPI ranks and OpenMP

-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 8. Januar 2015 15:48 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Performance difference between MPI ranks and OpenMP On 08 Jan 2015, at 15:38, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi list

Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails

--- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 4 -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner

Re: [gmx-users] Using COM pulling and Enforced Rotations together

be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t rot_type0= flex Use flex-t instead, this should do the trick. What works with pulling: iso-pf, pm-pf, rm-pf, rm2-pf, flex-t, flex2-t Happy pulling! Carsten -- Dr. Carsten Kutzner Max Planck

Re: [gmx-users] Illegal instruction flag raised in GMX 5.0.4

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Re: [gmx-users] Installing GTX 980 on linux - which distro should i use?

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Re: [gmx-users] Working on a GPU cluster with GROMACS 5

requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551

Re: [gmx-users] GXT690 vs GTX Titan black

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Re: [gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09

)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49

Re: [gmx-users] Question about GPU acceleration in GROMACS 5

://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302

Re: [gmx-users] running g_tune_pme on stampede

* For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen

Re: [gmx-users] Performance of GPU Workstation (GPU selection)

/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http

Re: [gmx-users] Installing gromacs 5.0.2 double precision with shared fftw libraries

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Wednesday, November 19, 2014 11:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installing

Re: [gmx-users] Version problem

. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- Gromacs Users mailing

Re: [gmx-users] GPU cards supported by Gromacs?

. Much appreciated if anyone could provide such information about how reliable the 980s are. Best, Jane On Tue, Nov 4, 2014 at 1:36 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, On 04 Nov 2014, at 22:33, Jian Yin janeyin...@gmail.com wrote: Hi there! I just wonder what

Re: [gmx-users] GPU cards supported by Gromacs?

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Re: [gmx-users] MD workstation for Gromacs

://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302

Re: [gmx-users] GPU performance in Gromacs 5

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Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

Of Carsten Kutzner Sent: Montag, 29. September 2014 19:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi On 29 Sep 2014, at 18:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That seems suitable. Oh, it just occurred to me

Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

--- -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Donnerstag, 25. September 2014 19:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users

Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz

Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

anyway. So even if you say g_tune_pme -np 48 -s input.tpr we first check with mpirun -np 2 mdrun -s input.tpr and only after that continue with -np 48. Carsten We should just make the check optional, instead of being a deal breaker. Mark On Sep 29, 2014 4:35 PM, Carsten Kutzner ckut

Re: [gmx-users] g_tune_pme and verlet

visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313

Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

for this case I guess we also need to make the test optional. Carsten Mark On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It can't be fixed, because there is no surefire way

Re: [gmx-users] Performance of GTX 980 and 970

-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner

Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry

Re: [gmx-users] Hyper-threading Gromacs 5.0.1

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax

Re: [gmx-users] GPU job failed

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Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What went wrong ?

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Re: [gmx-users] GPU and MPI

/stupid? Cheers, Oliver On 08/29/2014 05:15 PM, Carsten Kutzner wrote: Hi Dawei, On 29 Aug 2014, at 16:52, Da-Wei Li lida...@gmail.com wrote: Dear Carsten Thanks for the clarification. Here it is my benchmark for a small protein system (18k atoms). (1) 1 node (12 cores/node, no GPU

Re: [gmx-users] GPU and MPI

nodes will result 33 ns/day, that is, it is about 3 time slower than MD run on one node (2GPU+12core). I have no idea what is wrong. dawei On Mon, Sep 1, 2014 at 5:34 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, take a look at mdrun’s hidden but sometimes useful options: mdrun

Re: [gmx-users] GPU and MPI

, and the last 5 DD ranks to GPU id 1. Carsten dawei On Mon, Sep 1, 2014 at 8:39 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Dawei, on two nodes, regarding the cases with and without GPUs, do you use the same domain decomposition in both cases? Carsten On 01 Sep 2014, at 14:30

Re: [gmx-users] GPU and MPI

Hi Dawei, the mapping of GPUs to PP ranks is printed for the Master node only, but if this node reports two GPUs, then all other PP ranks will also use two GPUs (or an error is reported). The scaling will depend also on your system size, if this is too small, then you might be better off by

Re: [gmx-users] GPU and MPI

, 2014 at 10:36 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Dawei, the mapping of GPUs to PP ranks is printed for the Master node only, but if this node reports two GPUs, then all other PP ranks will also use two GPUs (or an error is reported). The scaling will depend also on your

Re: [gmx-users] pme ranks

On 22 Aug 2014, at 12:48, xiexiao...@sjtu.edu.cn wrote: Does anyone know that what the pme ranks mean? See for example [1] in the section Multiple-Program, Multiple-Data PME Parallelization. Best, Carsten 1. Hess, B., Kutzner, C., van der Spoel, D. Lindahl, E. GROMACS 4: Algorithms

Re: [gmx-users] Job Submission script for Multiple nodes GPUs

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Re: [gmx-users] Job Submission script for Multiple nodes GPUs calculation

post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] Interteting flooding results

-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner

Re: [gmx-users] Can we set the number of pure PME nodes when using GPUCPU?

posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical

Re: [gmx-users] my log file to the mdrun error message that on Tue 15, July...

, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl

Re: [gmx-users] Implementations of/similar to accelerated MD (aMD) in GROMACS

* For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen

Re: [gmx-users] question about Computational Electrophysiology

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Re: [gmx-users] use -maxwarn option

-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner

Re: [gmx-users] Use trjconv in parallel,

On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello, in short : it is possible ? I use the gromacs v4.6.5. No. Carsten Thanks Stéphane -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs 5.0

requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49

Re: [gmx-users] Non-neutral system

Hi, technically, you can use PME with charged systems in Gromacs. However, if the charges in your system are distributed inhomogeneously (as, e.g. in a water/membrane system), you will get artefacts, as described in http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf Best, Carsten On 23 Apr

Re: [gmx-users] g_tune_pme scalevdw option not working?

the bug report - http://redmine.gromacs.org/issues/1460 - and assigned it to you. I also set the priority to low, don't know if it matters. Cheers, João 2014-03-13 18:04 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Dear João, On 13 Mar 2014, at 14:38, João Rodrigues anar...@gmail.com

Re: [gmx-users] g_tune_pme scalevdw option not working?

? Thanks for reporting this! Also, why is my rlist changing since it is equal to rcoulomb? It should be kept the same (line 1004) right? This is a feature of the Verlet scheme, see http://www.gromacs.org/Documentation/Cut-off_schemes Best, Carsten -- Dr. Carsten Kutzner Max Planck

Re: [gmx-users] g_tune_pme scalevdw option not working?

- and assigned it to you. I also set the priority to low, don't know if it matters. Cheers, João 2014-03-13 18:04 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Dear João, On 13 Mar 2014, at 14:38, João Rodrigues anar...@gmail.com wrote: Hi all, I've been playing with g_tune_pme (neat

Re: [gmx-users] Launching MPI/OpenMP hybrid run

On 04 Mar 2014, at 13:08, Alexander Björling alex.bjorl...@gmail.com wrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I would like to have one MPI process on each CPU, with OpenMP threads on the 8 cores of each. I've

Re: [gmx-users] Launching MPI/OpenMP hybrid run

On 04 Mar 2014, at 13:43, alex.bjorling alex.bjorl...@gmail.com wrote: Carsten Kutzner wrote On 04 Mar 2014, at 13:08, Alexander Björling lt; alex.bjorling@ gt; wrote: Dear users, I'm trying to run simulations on a cluster of nodes, each sporting two AMD Opteron 8-core CPU:s. I

Re: [gmx-users] Issues running Gromacs with MPI/OpenMP in cpu cluster

Hi Mousumi, from the fact that you get lots of backup files directly at the beginning I suspect that your mdrun is not MPI-enabled. This behavior is exactly what one would get when launching a number of serial mdrun’s on the same input file. Maybe you need to look for a mdrun_mpi executable.

Re: [gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone

Hi, start with using as many MPI processes as you have GPUs. GROMACS will use several OpenMP threads per MPI process to use all your CPU cores. You can also do that manually with mpirun -np 2 mdrun-mpi -ntomp 6 Carsten On 12/10/2013 10:30 AM, rajat desikan wrote: Dear all, I recently