[gmx-users] powercut command
Justin Lemkul
jalemkul at vt.edu
Thu Apr 13 17:42:01 CEST 2017
On 4/13/17 11:25 AM, Anshul Lahariya wrote:
> i was failed to diagnose. plzz help me
>
Start here:
http://www.catb.org/esr/faqs/smart-questions.html
As I already said, no one on this list can tell anything about your system
because you have provided no useful diagnostic information or description of
what you're doing. If you want free help, you have to make it easy for people
to help you, with clear, concise communication about what you are doing.
-Justin
> On Thu, Apr 13, 2017 at 5:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/13/17 7:59 AM, Anshul Lahariya wrote:
>>
>>> Now i perform a new md, there is a problem with this error
>>>
>>>
>>> [anshu at dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0
>>> :-) GROMACS - gmx mdrun, 2016.2 (-:
>>>
>>> GROMACS is written by:
>>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
>>> Bjelkmar
>>> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
>>> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
>>> Karkoulis
>>> Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
>>> Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
>>> Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
>>> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
>>> Teemu Virolainen Christian Wennberg Maarten Wolf
>>> and the project leaders:
>>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>>
>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>> Copyright (c) 2001-2015, The GROMACS development team at
>>> Uppsala University, Stockholm University and
>>> the Royal Institute of Technology, Sweden.
>>> check out http://www.gromacs.org for more information.
>>>
>>> GROMACS is free software; you can redistribute it and/or modify it
>>> under the terms of the GNU Lesser General Public License
>>> as published by the Free Software Foundation; either version 2.1
>>> of the License, or (at your option) any later version.
>>>
>>> GROMACS: gmx mdrun, version 2016.2
>>> Executable: /usr/bin/gmx
>>> Data prefix: /usr
>>> Working dir: /home/anshu/Pharma/AhpE_MSH
>>> Command line:
>>> gmx mdrun -v -deffnm md_1_0
>>>
>>>
>>> NOTE: Error occurred during GPU detection:
>>> OpenCL error -1001
>>> Can not use GPU acceleration, will fall back to CPU kernels.
>>>
>>>
>>> Running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs
>>> Hardware detected:
>>> CPU info:
>>> Vendor: Intel
>>> Brand: Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
>>> SIMD instructions most likely to fit this hardware: AVX2_256
>>> SIMD instructions selected at GROMACS compile time: SSE2
>>>
>>> Hardware topology: Full, with devices
>>>
>>> Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
>>> machine, which is better.
>>>
>>> Reading file md_1_0.tpr, VERSION 2016.2 (single precision)
>>> Changing nstlist from 10 to 25, rlist from 1.4 to 1.431
>>>
>>> Using 1 MPI thread
>>> Using 4 OpenMP threads
>>>
>>> starting mdrun 'Protein in water'
>>> 5000000 steps, 10000.0 ps.
>>> step 40800, will finish Sun Apr 16 06:11:14 2017
>>> Step 40875, time 81.75 (ps) LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 0.013405, max 0.537354 (between atoms 1541 and 1542)
>>> bonds that rotated more than 30 degrees:
>>> atom 1 atom 2 angle previous, current, constraint length
>>> 1541 1542 90.0 0.1330 0.2045 0.1330
>>>
>>> step 40875: One or more water molecules can not be settled.
>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>> Wrote pdb files with previous and current coordinates
>>> Segmentation fault (core dumped)
>>> [anshu at dhcppc58 AhpE_MSH]$
>>>
>>>
>>>
>> Your system is unstable. Follow the link I posted before. It's
>> impossible for anyone to diagnose anything based on this generic failure
>> message.
>>
>> -Justin
>>
>>
>>>
>>>
>>>
>>> On Thu, Apr 13, 2017 at 4:45 PM, Anshul Lahariya <
>>> anshullahariya17 at gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>> okkk,,, thank u justin sir
>>>>
>>>> On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>>
>>>>> On 4/13/17 6:19 AM, Anshul Lahariya wrote:
>>>>>
>>>>> now i got this error
>>>>>>
>>>>>>
>>>>>> Program: gmx mdrun, version 2016.2
>>>>>> Source file: src/gromacs/mdlib/constr.cpp (line 167)
>>>>>>
>>>>>> Fatal error:
>>>>>> Too many LINCS warnings (1000)
>>>>>> If you know what you are doing you can adjust the lincs warning
>>>>>> threshold in
>>>>>> your mdp file
>>>>>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>>>>>> but normally it is better to fix the problem
>>>>>>
>>>>>> For more information and tips for troubleshooting, please check the
>>>>>> GROMACS
>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>> -------------------------------------------------------
>>>>>> [root at dhcppc58 AhpE_MSH]#
>>>>>>
>>>>>>
>>>>>> You simulation is crashing and cannot be continued. Consult
>>>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>>>>> Diagnosing_an_Unstable_System
>>>>>
>>>>> Also, do NOT do your normal work as root. That is extremely dangerous.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Apr 13, 2017 at 3:43 PM, Anshul Lahariya <
>>>>>> anshullahariya17 at gmail.com
>>>>>>
>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>> thankss tasneem.
>>>>>>
>>>>>>>
>>>>>>> let me try.
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
>>>>>>> anshullahariya17 at gmail.com> wrote:
>>>>>>>
>>>>>>> powercut take place and md stops, so i want to continue my md
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [root at dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr
>>>>>>>> -g
>>>>>>>> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>>>>>> :-) GROMACS - gmx mdrun, 2016.2 (-:
>>>>>>>>
>>>>>>>> GROMACS is written by:
>>>>>>>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
>>>>>>>> Bjelkmar
>>>>>>>> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit
>>>>>>>> Groenhof
>>>>>>>> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
>>>>>>>> Karkoulis
>>>>>>>> Peter Kasson Jiri Kraus Carsten Kutzner Per
>>>>>>>> Larsson
>>>>>>>> Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik
>>>>>>>> Marklund
>>>>>>>> Teemu Murtola Szilard Pall Sander Pronk Roland
>>>>>>>> Schulz
>>>>>>>> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
>>>>>>>> Tieleman
>>>>>>>> Teemu Virolainen Christian Wennberg Maarten Wolf
>>>>>>>> and the project leaders:
>>>>>>>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der
>>>>>>>> Spoel
>>>>>>>>
>>>>>>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>>>>>>> Copyright (c) 2001-2015, The GROMACS development team at
>>>>>>>> Uppsala University, Stockholm University and
>>>>>>>> the Royal Institute of Technology, Sweden.
>>>>>>>> check out http://www.gromacs.org for more information.
>>>>>>>>
>>>>>>>> GROMACS is free software; you can redistribute it and/or modify it
>>>>>>>> under the terms of the GNU Lesser General Public License
>>>>>>>> as published by the Free Software Foundation; either version 2.1
>>>>>>>> of the License, or (at your option) any later version.
>>>>>>>>
>>>>>>>> GROMACS: gmx mdrun, version 2016.2
>>>>>>>> Executable: /usr/bin/gmx
>>>>>>>> Data prefix: /usr
>>>>>>>> Working dir: /home/anshu/Pharma/AhpE_MSH
>>>>>>>> Command line:
>>>>>>>> gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o
>>>>>>>> md_1_0.xtc
>>>>>>>> -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>>>>>>
>>>>>>>>
>>>>>>>> -------------------------------------------------------
>>>>>>>> Program: gmx mdrun, version 2016.2
>>>>>>>> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
>>>>>>>> Function: void gmx::CommandLineParser::parse(int*, char**)
>>>>>>>>
>>>>>>>> Error in user input:
>>>>>>>> Invalid command-line options
>>>>>>>> In command-line option -o
>>>>>>>> File name 'md_1_0.xtc' cannot be used for this option.
>>>>>>>> Only the following extensions are possible:
>>>>>>>> .trr, .cpt, .tng
>>>>>>>>
>>>>>>>> For more information and tips for troubleshooting, please check the
>>>>>>>> GROMACS
>>>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>>> -------------------------------------------------------
>>>>>>>> [root at dhcppc58 AhpE_MSH]# ^C
>>>>>>>> [root at dhcppc58 AhpE_MSH]#
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> plzzz help me and suggest me the command for continuation of my md
>>>>>>>> run
>>>>>>>>
>>>>>>>> On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <
>>>>>>>> tasneemkausar12 at gmail.com> wrote:
>>>>>>>>
>>>>>>>> please give the exact command and error message.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
>>>>>>>>> anshullahariya17 at gmail.com
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> dear das sir,
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -cpi was already added to the command but my problem is not solved
>>>>>>>>>>
>>>>>>>>>> On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
>>>>>>>>>> anshullahariya17 at gmail.com
>>>>>>>>>>
>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> error says, xtc file is not used for this option . plzz use trr,
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> cpt, tng
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> help me out
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebamir85 at gmail.com>
>>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> please put this command line
>>>>>>>>>>>
>>>>>>>>>>>> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi
>>>>>>>>>>>>
>>>>>>>>>>>> xxx.cpt -o
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> md_1_0.xtc
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> good luck
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
>>>>>>>>>>>> anshullahariya17 at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> My md was running. Suddenly power supply was cuts due to some
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> reason
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> and my
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> my MD stops..
>>>>>>>>>>>>> To continue my MD, I use command:-
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
>>>>>>>>>>>>>
>>>>>>>>>>>>> 10ns.cpt
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> -cpo 10ns.cpt -append
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> but shows error.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Error in user input:
>>>>>>>>>>>>> Invalid command-line options
>>>>>>>>>>>>> Unknown command-line option -md_1_0.xtc
>>>>>>>>>>>>>
>>>>>>>>>>>>> For more information and tips for troubleshooting, please check
>>>>>>>>>>>>>
>>>>>>>>>>>>> the
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> GROMACS
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>>>> [root at dhcppc58 AhpE_MSH]#
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Plzz.. help me out....
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>>>
>>>>>>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>>>>
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>>>>>>>>>>>>>
>>>>>>>>>>>>> -users or
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>>
>>>>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>>>>>>>>> -users
>>>>>>>>>>>>
>>>>>>>>>>>> or
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>>>> 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-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/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-request at gromacs.org.
>>>>>
>>>>>
>>>>
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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