Re: [gmx-users] how to run g_tune_pme in cluster?
yes, here is the contents for it: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, 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. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, 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. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, 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. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VERSION 4.6-dev-20120423-25c75 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, 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. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: :-) G R O M A C S (-: GRowing Old MAkes el Chrono Sweat :-) VER
Re: [gmx-users] how to run g_tune_pme in cluster?
On Apr 26, 2012, at 11:37 AM, Albert wrote: > hello: > it can find mdrun correctly. and it is only give me the log file as I > mentioned in previous thread. What files are produced by g_tune_pme? Is there a benchtest.log? Can you cat its contents? Carsten > > thank you very much > > On 04/26/2012 09:53 AM, Carsten Kutzner wrote: >> Hi, >> >> what output does g_tune_pme provide? What is in "log" and in >> "perf.out"? >> Can it find the correct mdrun / mpirun executables? >> >> Carsten >> >> >> On Apr 26, 2012, at 9:28 AM, Albert wrote: >> >>> Hello: >>> Does anybody have any idea how to run g_tune_pme in a cluster? I tried >>> many times with following command: >>> >>> g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log >>> -launch -nt 24> log& >>> >>> but it always failed. >>> >>> >>> Option Type Value Description >>> -- >>> -[no]h bool no Print help info and quit >>> -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting >>> to be sent to a process whose contact information is unknown in file >>> rml_oob_send.c at line 105 >>> [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] >>> [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to >>> be sent to a process whose contact information is unknown in file >>> base/plm_base_proxy.c at line 86 >>> >>> -- >>> 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 > > -- > 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 -- 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
Re: [gmx-users] how to run g_tune_pme in cluster?
hello: it can find mdrun correctly. and it is only give me the log file as I mentioned in previous thread. thank you very much On 04/26/2012 09:53 AM, Carsten Kutzner wrote: Hi, what output does g_tune_pme provide? What is in "log" and in "perf.out"? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24> log& but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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 -- 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
Re: [gmx-users] how to run g_tune_pme in cluster?
Hi, what output does g_tune_pme provide? What is in "log" and in "perf.out"? Can it find the correct mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: > Hello: > Does anybody have any idea how to run g_tune_pme in a cluster? I tried many > times with following command: > > g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log > -launch -nt 24 > log & > > but it always failed. > > > Option Type Value Description > -- > -[no]h bool no Print help info and quit > -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to > be sent to a process whose contact information is unknown in file > rml_oob_send.c at line 105 > [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] > [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to > be sent to a process whose contact information is unknown in file > base/plm_base_proxy.c at line 86 > > -- > 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 -- 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
[gmx-users] how to run g_tune_pme in cluster?
Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 > log & but it always failed. Option Type Value Description -- -[no]h bool no Print help info and quit -[[CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 105 [CUDANodeA:03384] [[60523,1],22] could not get route to [[INVALID],INVALID] [CUDANodeA:03384] [[60523,1],22] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 86 -- 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
