[gmx-users] Segmentation Fault (Address not mapped)
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 16 13:15:12 CEST 2009
darrellk at ece.ubc.ca wrote:
> 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.
>
Did the EM converge satisfactorily? What was Fmax?
Unlike EM, equilibration is an MD process; for a protein system, one generally
position-restrains the protein and allows the surrounding solvent to optimize
around the structure.
-Justin
> 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!
>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>>> 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
>>>>>>
>>>>>> ========================================
>>>>> _______________________________________________
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>>>>>
>>>> ------------------------------
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--
========================================
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
========================================
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