[gmx-users] powercut command
Anshul Lahariya
anshullahariya17 at gmail.com
Thu Apr 13 17:26:04 CEST 2017
i was failed to diagnose. plzz help me
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
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>>>>>>>>>>>
>>>>>>>>>>
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>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> --
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>>>>>>>>>> --
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>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>> --
>>>>>>>>>
>>>>>>>> Gromacs Users mailing list
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>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> 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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>>>> Gromacs Users mailing list
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>>>>
>>>>
>>>
>>>
> --
> ==================================================
>
> 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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