[gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 3
Avijeet Kulshrestha
avijeetkulshrestha at gmail.com
Mon Sep 2 15:33:36 CEST 2019
In continuation of your response (Please see trailing email) to my query,
please find below the error message of .log file. This is when I am using 8
processors without -rdd option.
and I have user-defined bonded, angle potential which I am providing by
supplying tabulated data. I have position restraint also on backbone atoms
of the protein.
*Initializing Domain Decomposition on 8 ranksDynamic load balancing:
autoWill sort the charge groups at every domain (re)decompositionInitial
maximum inter charge-group distances: two-body bonded interactions:
12.145 nm, LJ-14, atoms 11 568 multi-body bonded interactions: 1.124 nm,
G96Angle, atoms 3767 3770Minimum cell size due to bonded interactions:
13.359 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans:
1.360 nmEstimated maximum distance required for P-LINCS: 1.360 nmScaling
the initial minimum size with 1/0.8 (option -dds) = 1.25Optimizing the DD
grid for 8 cells with a minimum initial size of 16.699 nmThe maximum
allowed number of cells is: X 0 Y 0 Z
1-------------------------------------------------------Program gmx mdrun,
VERSION 5.1.5Source code file:
/Apps/gromacs-5.1.5/src/gromacs/domdec/domdec.cpp, line: 6987Fatal
error:There is no domain decomposition for 8 ranks that is compatible with
the given box and a minimum cell size of 16.6989 nmChange the number of
ranks or mdrun option -rdd or -ddsLook in the log file for details on the
domain decompositionFor more information and tips for troubleshooting,
please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>-------------------------------------------------------*
> Hi all,
> I am running martini coarse-grained simulation with 15 fs of time step in
> gromacs 2018.6. I have 25859 number of atoms and my box size is:
> 12.00000 14.00000 18.00000
> Where I have Protein, membrane (DPPC) and ions.
> I have minimized energy with 16 processor and -rdd option as 2.5. It
worked
> fine but later in NVT simulation, this started giving errors.
> *I am getting the following error without -rdd option when I used 1 node
> and 8 processor per node:*
> Fatal error:
> There is no domain decomposition for 8 ranks that is compatible with the
> given
> box and a minimum cell size of 7.69783 nm
This minimum cell size is significantly larger than a normal simulation
would require. Do you have restraints or other non-standard interactions
defined? The .log file snippet that describes the DD setup would be
useful for tracking the issue down.
-Justin
On Mon, 2 Sep 2019 at 12:25, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: simulation termination problem (Prabir Khatua)
> 2. Re: wham analysis (Justin Lemkul)
> 3. Re: Domain decomposition error while running coarse grained
> simulations on cluster (Justin Lemkul)
> 4. Re: mdrun error (Justin Lemkul)
> 5. regarding changing the scale from ps to ns (sudha bhagwati)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 1 Sep 2019 12:10:04 -0500
> From: Prabir Khatua <prabir07chem at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation termination problem
> Message-ID:
> <
> CAObZXoOgMnZMKy8Ddreyhfh7CjM9yCPpo3fg6DMOE5fN-mgx0g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks Justin. The problem has been fixed.
>
> On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/29/19 12:31 PM, Prabir Khatua wrote:
> > > Hello Gromacs users,
> > >
> > > I am trying to simulate a system of atom size 3,58,973 in gromacs
> 5.1.5.
> > > However, my simulation is being terminated in between with the
> following
> > > error.
> > >
> > > File input/output error:
> > > Cannot rename checkpoint file; maybe you are out of disk space?
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > I did not find any solution with respect to the error I was having in
> the
> > > mentioned website. What I found was related to memory issue. I do not
> > know
> > > whether this is the same issue.
> >
> > The issue is not related to memory, it is (potentially) related to disk
> > space. Do you have enough space on the filesystem to write output files?
> > This can also happen sometimes when the filesystem blips. There's not
> > much you can do about that except complain to your sysadmin about
> > integrity of the filesystem.
> >
> > -Justin
> >
> > > Please note that I was successfully able to run another simulation of a
> > > system having relatively less number of atoms with same script. The run
> > > command that I used for the simulation was
> > >
> > > mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt
> > >
> > > I ran both the simulations on two nodes having 24 cpu cores in each one
> > of
> > > the nodes.
> > > I am also not able to figure out one issue. The log file of the system
> > > where the simulation was successfully completed showed
> > >
> > > Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible
> > GPUs
> > > Cores per node: 24
> > > Logical cores per node: 24
> > > Compatible GPUs per node: 0
> > >
> > > However, in the unsuccessful case, the log file showed
> > >
> > > Running on 1 node with total 24 cores, 24 logical cores
> > >
> > > Thus, it looks like the simulation was running on single node although
> I
> > > asked it to run on two nodes. I have no idea how to fix this issue.
> > Please
> > > help me fix this issue or what I am doing wrong.
> > >
> > > Thanks in advance,
> > >
> > > Prabir
> > >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > 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.
> >
>
>
> --
>
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 1 Sep 2019 13:21:23 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] wham analysis
> Message-ID: <65191dc8-43fd-bc2f-6b9a-20903052df32 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/1/19 5:35 AM, Negar Parvizi wrote:
> > Dear all,
> > I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial )
> for my file which is protein-ligand complex.
> > The pulling force was in Y direction. when Umbrella sampling finished,
> "Wham" couldn't analysis the data because wham is in z direction.what
> should I do now for wham analysis? how can I change it to Y direction?
> > I sent message in gromacs comunity , what Justin said:
> > "WHAM does not presuppose the axis or vector; it does what you tell it.
> If you're referring to the x-axis label in the PMF profile being "z," that
> is just a generic (and perhaps imprecise) label that should be changed to
> the Greek character xi, per conventional notation."
> > I didn't understand it.
>
> I made a guess based on minimal information. You asserted that you
> pulled along y but WHAM indicated the bias was along z. I know that the
> default x-axis label in profile.xvg says "z" and it causes confusion. So
> I provided the comment that I did.
>
> However, it is clear from the gmx wham output below that you did *not*
> apply a bias along y, as you stated:
>
> > File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N
> Y], (1 dimensions)
>
> This means your reaction coordinate was the z-axis.
>
> > So I decided copy the error:
> >
> > Here is the error:
> >
> >> Found 25 tpr and 25 pull force files in tpr-files.dat and
> pullf-files.dat, respectively
> >> Reading 12 tpr and pullf files
> >> Automatic determination of boundaries...
> >> Reading file umbrella0.tpr, VERSION 5.1.4 (single precision)
> >> File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N
> Y], (1 dimensions)
> > Pull group coordinates not expected in pullx files.
> > crd 0) k = 1000 position = 0.840198
> > Use option -v to see this output for all input tpr files
> >
> >> Reading pull force file with pull geometry distance and 1 pull
> dimensions
> >> Expecting these columns in pull file:
> > 0 reference columns for each individual pull coordinate
> > 1 data columns for each pull coordinate
> >> With 1 pull groups, expect 2 columns (including the time column)
> >> Reading file umbrella71.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella98.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella111.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella119.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella139.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella146.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella157.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella180.tpr, VERSION 5.1.4 (single precision)
> >> Reading file umbrella202.tpr, VERSION 5.1.4 (single precision)
>
> What happens next? Nothing here says "error," however it looks like your
> input files are of an unexpected format. Perhaps you've switched
> pullx.xvg and pullf.xvg. As someone else suggested, you can use
> pullf.xvg files to get the PMF profile and avoid the issue entirely.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 1 Sep 2019 13:22:15 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Domain decomposition error while running
> coarse grained simulations on cluster
> Message-ID: <71840e02-8747-38b0-d2a0-39da5adbb404 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/1/19 5:44 AM, Avijeet Kulshrestha wrote:
> > Hi all,
> > I am running martini coarse-grained simulation with 15 fs of time step in
> > gromacs 2018.6. I have 25859 number of atoms and my box size is:
> > 12.00000 14.00000 18.00000
> > Where I have Protein, membrane (DPPC) and ions.
> > I have minimized energy with 16 processor and -rdd option as 2.5. It
> worked
> > fine but later in NVT simulation, this started giving errors.
> > *I am getting the following error without -rdd option when I used 1 node
> > and 8 processor per node:*
> > Fatal error:
> > There is no domain decomposition for 8 ranks that is compatible with the
> > given
> > box and a minimum cell size of 7.69783 nm
>
> This minimum cell size is significantly larger than a normal simulation
> would require. Do you have restraints or other non-standard interactions
> defined? The .log file snippet that describes the DD setup would be
> useful for tracking the issue down.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 1 Sep 2019 13:23:48 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] mdrun error
> Message-ID: <a3299ee2-b645-a330-65f8-3bd18d65a3ed at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 9/1/19 7:02 AM, m g wrote:
> > Dear Justin,
> There are many other people on this list, and I don't always have answers
> :)
>
> > I'm simulating a system with "wall" for z direction, but I gave this
> error in minimization step "software inconsistency error: lost particles
> while sorting",.Would you please help me? I used the following?parameter:
>
> What GROMACS version are you using? CPU or GPU? Does the simulation work
> without the walls? You need to provide a lot more diagnostic
> information. This is a cryptic error that suggests something very
> fundamental is wrong. That also makes it very hard to diagnose.
>
> If you're not using the latest version of GROMACS, start there. I recall
> some bug fixes that may be relevant. If the error is reproducible in
> 2019.3, please post a more complete description of what you're doing.
>
> -Justin
>
> > integrator? ??? =steep
> >
> > emtol?????? ?? ?????= 100.0emstep????????????? = 0.01nsteps???????????
> ??? = 5000nstlist?????????? ??? = 1cutoff-scheme?????? =
> Verletns_type?????????? ??? = gridrlist?????? ?? ?????= 1.2? ??coulombtype
> ?? ?????= PMErcoulomb??? ?? ?????= 1.2vdwtype???????????? =
> cutoffvdw-modifier??????? = force-switchrvdw-switch???????? =
> 1.0rvdw??????? ? ??????= 1.2????????? ??DispCorr??????????? = nopbc ?
> ??????????????=xy? ? ? ? ? ? ? ? ? ??nwall?????????????? =
> 2wall_type?????????? = 10-4wall_r_linpot?????? = 1wall_atomtype?????? = ca?
> cawall_density??????? = 60? 60wall_ewald_zfac???? = 3ewald-geometry????? =
> 3dc
> >
> > Thanks,Ganj
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 2 Sep 2019 12:23:25 +0530
> From: sudha bhagwati <sudhabhagwati at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] regarding changing the scale from ps to ns
> Message-ID:
> <CAAjYSb-58-5qEeM+Rq-Yv3yTApA8cb1ktL_DP74n8MoK3j=
> 34g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx users,
>
> I am using the GROAMCS 5.1.4 version.
>
> ----------------------------------------------------------------------------------------------------------------------------------------
> Running the commands below:
>
>
> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
> *OR*
> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
>
>
> Error while executing commands:
>
> *Error in user input:*
>
> *Invalid command-line options Unknown command-line option -tu*
>
> ----------------------------------------------------------------------------------------------------------------------------------------
>
> -tu flag is not working for commands showed above. I want to generate my
> plots for nanosecond scale using xmgrace. Could you please help me out with
> this issue. I'd be really grateful to you.
>
> Thank you.
>
>
> --
> Thanks & regards
> ~
> Sudha Bhagwati
>
>
> ------------------------------
>
> --
> 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
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>
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