[gmx-users] Segmentation Fault (Address not mapped)
darrellk at ece.ubc.ca
darrellk at ece.ubc.ca
Thu Jul 16 07:54:08 CEST 2009
Hi Mark,
I do not do any equilibration, I only do energy minimization as in the
"GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please
let me know if I need to do equilibration and what is the difference
between energy minimization and equilibration as this is not clear to me.
Here is an mdp file for a run that actually completed successfully:
title =Graphene
;warnings =10
cpp =cpp
;define =-DPOSRES
constraints =none
integrator =md
dt =0.002 ; ps
nsteps =10000
nstcomm =100
nstxout =100
;nstvout =1000
nstfout =0
nstlog =100
nstenergy =100
nstlist =100
ns_type =grid
rlist =2.0
coulombtype =PME
rcoulomb =2.0
vdwtype =cut-off
rvdw =5.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =4
ewald_rtol =1e-5
optimize_fft =yes
; This section freezes graphene lattice
energygrps = Grph NH3
energygrp_excl = Grph Grph
freezegrps = Grph ; Freeze graphene lattice
freezedim = Y Y Y; in all directions
Tcoupl =berendsen
tau_t =0.5 0.5
tc-grps =NH3 Grph
ref_t =300 300
;coupl = parrinello-rahman
;tau_p = 1.5
;compressibility = 1.3
;ref_p = 0.061
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
And here is a copy of an mdp file for a run that did not complete
successfully:
title =Graphene
;warnings =10
cpp =cpp
;define =-DPOSRES
constraints =none
integrator =md
dt =0.002 ; ps
nsteps =30000
nstcomm =500
nstxout =500
;nstvout =1000
nstfout =0
nstlog =500
nstenergy =500
nstlist =500
ns_type =grid
rlist =2.0
coulombtype =PME
rcoulomb =2.0
vdwtype =cut-off
rvdw =5.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =4
ewald_rtol =1e-5
optimize_fft =yes
; This section freezes graphene lattice
energygrps = Grph NH3
energygrp_excl = Grph Grph
freezegrps = Grph ; Freeze graphene lattice
freezedim = Y Y Y; in all directions
Tcoupl =berendsen
tau_t =0.5 0.5
tc-grps =NH3 Grph
ref_t =300 300
;coupl = parrinello-rahman
;tau_p = 1.5
;compressibility = 1.3
;ref_p = 0.061
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Please let me know what you think might be the problem.
Thanks
Darrell
>Date: Thu, 16 Jul 2009 09:47:49 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4A5E6AA5.4040809 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>darrellk at ece.ubc.ca wrote:
>> Hi Mark,
>> Yes, I know that the box dimensions are defined in the last line of the
>> .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm
>> in the .gro file.
>
>OK.
>
>> I looked through my .gro file to ensure none of the atoms had coordinates
>> outside the 38x38x38 box. While I was reviewing the file I did notice
>> that some coordinates had negative values, slightly negative, but
>> negative none the less. Could this be causing the segmentation fault
>> between time step 10,000 and time step 30,000? Why wouldn't the
>> negative coordinates cause a segmentation fault much earlier?
>
>The absolute value of the coordinates is irrelevant.
>
>Your choice of 2.0 for rcoulomb is likely suboptimal for PME. Some
>smaller value is probably more efficient, but this will not be the cause
>of your problem.
>
>What is your system preparation regime? (i.e. EM + equilibration)
>
>Can you post a corrected and current .mdp file?
>
>Mark
>
>>> Date: Wed, 15 Jul 2009 16:59:21 +1000
>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID: <4A5D7E49.9020700 at anu.edu.au>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> darrellk at ece.ubc.ca wrote:
>>>> Hi Justin,
>>>> I was experiencing the problem before someone suggested using editconf so
>>>> I do not think the problem is being caused by editconf. But anyway here
>>>> is my editconf command. Let me know if you a source of error in this
>>>> command line.
>>>>
>>>> editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
>>>>
>>>> I did not want to add in additional space between the solvent and the box
>>>> as I saw no reason for doing so. And hence that is why I originally did
>>>> not use editconf.
>>>>
>>>> My box dimensions are 38nm x 38nm x 38nm.
>>> The box dimensions are defined in the bottom line of the .gro file, and
>>> not by the positions of the atoms in that file. If you haven't ever set
>>> them to be suitable for your coordinates with editconf, then they might
>>> not be.
>>>
>>> Mark
>>>
>>> I used cutoffs of 2 nm & 5 nm
>>>> for my system so ensure the cutoff occured at a distance where the
>>>> potentials were stabalized (not changing). I guess I could use shorter
>>>> cutoffs such as 1.5 nm & 2 nm and this may decrease my computation time.
>>>> I also thought that I needed to use larger cut-offs since I am dealing
>>>> in the gas phase and there is greater ditance between the atoms in my
>>>> simulation than in liquid-based simulations.
>>>>
>>>> In the .log files, I do not see any LINCS warnings or neighborlist
>>>> errors.
>>>>
>>>> I ran gmxcheck on a .trr file and was presented with the following
>>>> output:
>>>> *********************************************
>>>> Checking file mdtraj.trr
>>>> trn version: GMX_trn_file (single precision)
>>>> Reading frame 0 time 0.000
>>>> # Atoms 10482
>>>> Last frame 5 time 1.000
>>>>
>>>>
>>>> Item #frames Timestep (ps)
>>>> Step 6 0.2
>>>> Time 6 0.2
>>>> Lambda 6 0.2
>>>> Coords 6 0.2
>>>> Velocities 6 0.2
>>>> Forces 0
>>>> Box 6 0.2
>>>> *********************************************
>>>>
>>>> I ran two additional simulations with different values for nsteps and
>>>> nstxxxx paramaters and have the following to report:
>>>>
>>>> When I run a simulation with the following parameters it completes
>>>> successfully and I see, in the log file, the system output every 100
>>>> time steps.
>>>> nsteps =10000
>>>> nstcomm =100
>>>> nstxout =100
>>>> nstfout =0
>>>> nstlog =100
>>>> nstenergy =100
>>>> nstlist =100
>>>>
>>>> When I run a simulation with the following parameters it fails with a
>>>> sementation fault and, in the log file, I do not see system output every
>>>> 500 time steps.
>>>> nsteps =30000
>>>> nstcomm =500
>>>> nstxout =500
>>>> nstfout =0
>>>> nstlog =500
>>>> nstenergy =500
>>>> nstlist =500
>>>>
>>>> Please let me know what you think might be the problem.
>>>>
>>>> Thank you very much.
>>>>
>>>> Darrell
>>>>
>>>>
>>>>> Date: Mon, 13 Jul 2009 15:37:15 -0400
>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>> Message-ID: <4A5B8CEB.4020609 at vt.edu>
>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>
>>>>>
>>>>>
>>>>> darrellk at ece.ubc.ca wrote:
>>>>>> Hi Mark,
>>>>>> I used editconf on my .gro file with zero space between my solvent and
>>>>>> the box and the resulting box had the exact same dimension as the
>>>>>> initial box. I also performed a number of simulation runs with different
>>>>> If you're using editconf to define zero space, what's the point? I only ask
>>>>> because it is a potential source of error if you think you're adding zero space,
>>>>> but something else might be going on. Maybe you can post your editconf command
>>>>> line.
>>>>>
>>>>> What are your box dimensions? Are cut-off lengths of 2.0 and 5.0 nm appropriate
>>>>> for your system? How did you determine that these cut-off's should be used?
>>>>>
>>>>>> mdp parameters hoping this would provide me some indication of the cause
>>>>>> of the fault but to no avail. I looked through the log files, error
>>>>>> files, and output files and could not find any output to help me
>>>>>> identify the source of my error.
>>>>>>
>>>>> It is very odd that Gromacs isn't report anything at all. No LINCS warnings?
>>>>> No neighborlist errors? These would be in the .log file.
>>>>>
>>>>>> Could you please let me know how I can look at my structure at each point
>>>>>> as you indicate below as I do not see any files output that provide me
>>>>>> to do so? I tried to look at the .trr file but when I try to load it
>>>>>> into VMD, it causes an error. I am assuming this error is caused because
>>>>>> the .trr file did not complete correctly due to the segmentation fault.
>>>>>> Please advise.
>>>>>>
>>>>> How early is the segmentation fault occurring? I have found it useful sometimes
>>>>> to set nstxout (or nstxtcout) = 1 to try to catch the first few frames if the
>>>>> explosion is occurring early. In any case, gmxcheck will help determine how
>>>>> many frames are present, as well as the integrity of the file (broken frames, etc).
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Darrell
>>>>>>
>>>>>>> Date: Tue, 07 Jul 2009 09:19:42 +1000
>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>>>> Message-ID: <4A52868E.6010807 at anu.edu.au>
>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>>
>>>>>>> darrellk at ece.ubc.ca wrote:
>>>>>>>> Hi Mark,
>>>>>>>> I added the energy group exclusions as indicated in your previous
>>>>>>>> response but am still experiencing the same problem. I looked at the
>>>>>>>> .log files and see that in one log file it tells me that my box is
>>>>>>>> exploding. However, I do not have many molecules in my simulation and
>>>>>>>> therefore do not think that it is possible that my box is exploding from
>>>>>>>> pressure.
>>>>>>> Sure, but if there's something malformed with your model physics or
>>>>>>> starting configuration, then large forces can make anything explode.
>>>>>>>
>>>>>>> Look at your structures at each point and see where things start to go
>>>>>>> wrong. Make sure you've used editconf on your starting structure to
>>>>>>> provide the right box dimensions.
>>>>>>>
>>>>>>> Mark
>>>>>>>
>>>>>>>> Maybe if I re-state my simulation it will help you in providing me
>>>>>>>> direction on what might be causing the problem. My simulation consists
>>>>>>>> of a graphene lattice with a layer of ammonia molecules above it. The
>>>>>>>> box is very large and there is lots of empty space in the box. So I am a
>>>>>>>> little confused as to how the box could be exploding.
>>>>>>>>
>>>>>>>> Thanks again in advance for your help.
>>>>>>>>
>>>>>>>> Darrell Koskinen
>>>>>>>>
>>>>>>>>> Date: Fri, 03 Jul 2009 11:41:45 +1000
>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>>>>>> Message-ID: <4A4D61D9.6080700 at anu.edu.au>
>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>>>>>>>
>>>>>>>>> darrellk at ece.ubc.ca wrote:
>>>>>>>>>> Dear GROMACS Gurus,
>>>>>>>>>> I am experiencing a segmentation fault when mdrun executes. My simulation
>>>>>>>>>> has a graphene lattice with an array (layer) of ammonia molecules above
>>>>>>>>>> it. The box is three times the width of the graphene lattice, three
>>>>>>>>>> times the length of the graphene lattice, and three times the height
>>>>>>>>>> between the graphene lattice and the ammonia molecules. I am including
>>>>>>>>>> the mdp file and the error message.
>>>>>>>>> Probably your system is exploding when integration fails with excessive
>>>>>>>>> forces. You should look at the bottom of stdout, stderr, *and* the .log
>>>>>>>>> file to diagnose. The error message you give below is merely the
>>>>>>>>> diagnostic trace from the MPI library, and it not useful for finding out
>>>>>>>>> what GROMACS thinks the problem might be. Further advice below.
>>>>>>>>>
>>>>>>>>>> ***************************************************************************
>>>>>>>>>> .mdp file
>>>>>>>>>> title =FWS
>>>>>>>>>> ;warnings =10
>>>>>>>>>> cpp =cpp
>>>>>>>>>> ;define =-DPOSRES
>>>>>>>>>> ;constraints =all-bonds
>>>>>>>>>> integrator =md
>>>>>>>>>> dt =0.002 ; ps
>>>>>>>>>> nsteps =100000
>>>>>>>>>> nstcomm =1000
>>>>>>>>>> nstxout =1000
>>>>>>>>>> ;nstvout =1000
>>>>>>>>>> nstfout =0
>>>>>>>>>> nstlog =1000
>>>>>>>>>> nstenergy =1000
>>>>>>>>>> nstlist =1000
>>>>>>>>>> ns_type =grid
>>>>>>>>>> rlist =2.0
>>>>>>>>>> coulombtype =PME
>>>>>>>>>> rcoulomb =2.0
>>>>>>>>>> vdwtype =cut-off
>>>>>>>>>> rvdw =5.0
>>>>>>>>>> fourierspacing =0.12
>>>>>>>>>> fourier_nx =0
>>>>>>>>>> fourier_ny =0
>>>>>>>>>> fourier_nz =0
>>>>>>>>>> pme_order =4
>>>>>>>>>> ewald_rtol =1e-5
>>>>>>>>>> optimize_fft =yes
>>>>>>>>>>
>>>>>>>>>> ; This section added in to freeze hydrogen atoms at edge of graphene
>>>>>>>>>> lattice to prevent movement of lattice
>>>>>>>>>> ;energygrp_excl = Edge Edge Edge Grph Grph Grph
>>>>>>>>>> freezegrps = Edge Grph ; Hydrogen atoms in graphene lattice are
>>>>>>>>>> associated with the residue Edge
>>>>>>>>> See comments in 7.3.24 of manual. You need the energy group exclusions.
>>>>>>>>>
>>>>>>>>> Mark
>>>>>>>>>
>>>>>>>>>> freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions
>>>>>>>>>>
>>>>>>>>>> ;Tcoupl =berendsen
>>>>>>>>>> ;tau_t =0.1 0.1
>>>>>>>>>> ;tc-grps =protein non-protein
>>>>>>>>>> ;ref_t = 300 300
>>>>>>>>>>
>>>>>>>>>> ;Pcoupl = parrinello-rahman
>>>>>>>>>> ;tau_p = 0.5
>>>>>>>>>> ;compressibility = 4.5e-5
>>>>>>>>>> ;ref_p = 1.0
>>>>>>>>>>
>>>>>>>>>> ;gen_vel = yes
>>>>>>>>>> ;gen_temp = 300.0
>>>>>>>>>> ;gen_seed = 173529
>>>>>>>>>> ***************************************************************************
>>>>>>>>>>
>>>>>>>>>> ***************************************************************************
>>>>>>>>>> ERROR IN OUTPUT FILE
>>>>>>>>>> [node16:25758] *** Process received signal ***
>>>>>>>>>> [node16:25758] Signal: Segmentation fault (11)
>>>>>>>>>> [node16:25758] Signal code: Address not mapped (1)
>>>>>>>>>> [node16:25758] Failing at address: 0xfffffffe1233e230
>>>>>>>>>> [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80]
>>>>>>>>>> [node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
>>>>>>>>>> [0x2ba295dd0606]
>>>>>>>>>> [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
>>>>>>>>>> [0x2ba295dd4058]
>>>>>>>>>> [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de)
>>>>>>>>>> [0x2ba295dba5be]
>>>>>>>>>> [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
>>>>>>>>>> [0x2ba295ddeaff]
>>>>>>>>>> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193]
>>>>>>>>>> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0]
>>>>>>>>>> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
>>>>>>>>>> [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
>>>>>>>>>> [0x3833e1d8b4]
>>>>>>>>>> [node16:25758] [ 9] mdrun_mpi [0x40429a]
>>>>>>>>>> [node16:25758] *** End of error message ***
>>>>>>>>>> mpirun noticed that job rank 7 with PID 25758 on node node16 exited on
>>>>>>>>>> signal 11 (Segmentation fault).
>>>>>>>>>> 7 processes killed (possibly by Open MPI)
>>>>>>>>>> ***************************************************************************
>>>>>>>>>>
>>>>>>>>>> Could you please let me know what you think may be causing the fault?
>>>>>>>>>>
>>>>>>>>>> Much thanks in advance.
>>>>>>>>>>
>>>>>>>>>> Darrell Koskinen
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before posting!
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>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before posting!
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>>>>
>>>
>>> ------------------------------
>>>
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>>> *****************************************
>>>
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