[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60
Stephen Cox
stephen.cox.10 at ucl.ac.uk
Fri Mar 9 14:32:58 CET 2012
On 9 March 2012 13:03, gmx-users-request at gromacs.org <
gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. Re: GROMACS stalls for NPT simulation when using -npme and
> -dd flags (Mark Abraham)
> 2. Error Message in Make clean command for installation. (a a)
> 3. Re: Error Message in Make clean command for installation.
> (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 09 Mar 2012 23:42:33 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] GROMACS stalls for NPT simulation when using
> -npme and -dd flags
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F59FAB9.6010805 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 9/03/2012 9:43 PM, Stephen Cox wrote:
> > Dear users,
> >
> > I'm trying to run an isotropic NPT simulation on a cubic cell
> > containing TIP4P/ice water and methane. I'm using the
> > Parrinello-Rahman barostat. I've been playing around with the
> > different decomposition flags of mdrun to get better performance and
> > scaling and have found that the standard -npme (half number of cores)
> > works pretty well. I've also tried using the -dd flags, and I appear
> > to get decent performance and scaling. However, after a few
> > nanoseconds (corresponding to about 3 hours run time), the program
> > just stalls; no output and no error messages. I realise NPT may cause
> > domain decompositon some issues if the cell vectors vary wildly, but
> > this isn't happening in my system.
> >
> > Has anybody else experienced issues with domain decomposition and NPT
> > simulations? If so, are there any workarounds? For the moment, I've
> > had to resort to using -pd, which is giving relatively poor
> > performance and scaling, but at least it isn't dying!
> >
> > I'm using GROMACS 4.5.5 with an intel compiler (I followed the
> > instructions online, with static linking) and using the command:
> >
> > #!/bin/bash -f
> > # ---------------------------
> > #$ -V
> > #$ -N test
> > #$ -S /bin/bash
> > #$ -cwd
> > #$ -l vf=2G
> > #$ -pe ib-ompi 32
> > #$ -q infiniband.q
> >
> > mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2
> >
> > Below is my grompp.mdp.
> >
> > Thanks,
> > Steve
> >
> > P.S. I think that there may be an issue with memory leak that occurs
> > for domain decomposition with NPT. I seem to remember seeing this
> > happening on my desktop and my local cluster. I don't see this with
> > NVT simulations. This would be consistent with the lack of error
> > message: I've just run a short test run and the memory usage was
> > climbing streadily.
> >
> > ; run control
> > integrator = md
> > dt = 0.002
> > nsteps = -1
> > comm_mode = linear
> > nstcomm = 10
> >
> > ; energy minimization
> > emtol = 0.01
> > emstep = 0.01
> >
> > ; output control
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog = 0
> > nstcalcenergy = 2500
> > nstenergy = 2500
> > nstxtcout = 2500
> >
> > ; neighbour searching
> > nstlist = 1
> > ns_type = grid
> > pbc = xyz
> > periodic_molecules = no
> > rlist = 0.90
> >
> > ; electrostatics
> > coulombtype = pme
> > rcoulomb = 0.90
> >
> > ; vdw
> > vdwtype = cut-off
> > rvdw = 0.90
> > dispcorr = ener
> >
> > ; ewald
> > fourierspacing = 0.1
> > pme_order = 4
> > ewald_geometry = 3d
> > optimize_fft = yes
> >
> > ; temperature coupling
> > tcoupl = nose-hoover
> > nh-chain-length = 10
> > tau_t = 2.0
> > ref_t = 255.0
> > tc_grps = system
> >
> > ; pressure coupling
> > pcoupl = parrinello-rahman
> > pcoupltype = isotropic
> > ref_p = 400.0
> > tau_p = 2.0
> > compressibility = 6.5e-5
> >
> > ; constraints
> > constraint_algorithm = shake
> > shake_tol = 0.0001
> > lincs_order = 8
> > lincs_iter = 2
> >
> > ; velocity generation
> > gen_vel = yes
> > gen_temp = 255.0
> > gen_seed = -1
>
> You're generating velocities and immediately using a barostat that is
> unsuitable for equilibration.
Sorry, this is unclear: the system has already been equilibrated using NVT
then berendsen before using the parrinello-rahman barostat. I use the
generate velocities options to give me uncorrelated trajectories (I'm
investigating a stochastic process and want statistics). I appreciate the
concerns about poor equilibration, but I'm pretty sure this isn't the case
- in my experience, poor equilibration usually results in a fairly prompt
crash, with a lot of error messages and step.pdb files. Furthermore, the
cell volume seems stable over the time that I manage to simulate,
suggesting equilibration is OK.
> You're using an integration step that
> requires constraints=all-bonds but I don't see that.
Could you clarify this point for me please? Thanks.
> You may have better
> stability if you equilibrate with Berendsen barostat and then switch.
> I've seen no other reports of memory usage growing without bounds, but
> if you can observe it happening after choosing a better integration
> regime then it suggests a code problem that wants fixing.
>
I can run some tests on my desktop with a smaller system and report if I
see memory loss.
>
> Mark
>
>
>
Thanks for your quick response
> ------------------------------
>
> Message: 2
> Date: Fri, 9 Mar 2012 20:58:27 +0800
> From: a a <patd_2 at hotmail.com>
> Subject: [gmx-users] Error Message in Make clean command for
> installation.
> To: <gmx-users at gromacs.org>
> Message-ID: <COL118-W55ECB6D09526F932DD0EF4A3540 at phx.gbl>
> Content-Type: text/plain; charset="big5"
>
>
>
> Hi Mark,
> I did find the directory "gromacs-4.5.5"
> However, when I go into this folder, I have problem to do the "make"
> command. I found there is no "Make" file inside the folder. I can only
> see the following files inside this folder. Should I do "make clean" then?
> acinclude.m4 config Doxyfile.in log
> shareaclocal.m4 config.log include Makefile.am srcadmin
> configure INSTALL.automake Makefile.in testsAUTHORS
> configure.ac INSTALL.cmake mancmake COPYING
> INSTALL-GPU READMECMakeLists.txt COPYING-GPU libtool
> scripts
> Should I do Makefile.am or Makefile.in intead?
> Best regards,
> Catherine
>
> Date: Fri, 9 Mar 2012 23:22:51 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error Message when installing GROMACS.
>
>
>
>
>
>
>
>
> On 9/03/2012 10:58 PM, a a wrote:
>
>
>
>
> Dear Sir/Madam,
>
>
>
> I am trying to install the GROMACS to my new
> workstation. As my old one is not belong to me, I cannot
> install VMD to it. Please kindly help to instruct if I
> did anything wrong here. Many thanks.
>
>
>
>
> Follow the steps in
> http://www.cems.uvm.edu/~smanchu/gromacs_installation.html, I have done
> the installation
> fftw-3.0.1 at my "/Catherine/Gromacs/fftw-3.0.1"
> directory.
>
>
>
> Follow the steps in
> http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/
> ,
> i.e. [wget
> ftp://ftp.gromacs
> .org/pub/gromacs/gromacs-4.5.4.tar.gz], I have
> downloaded the gromacs to my Catherine/Gromacs/
> folder.
>
>
>
> Follow the steps in
> http://www.gromacs.org/Downloads/Installation_Instructions, I have start
> installing the
> GROMACS.
>
>
>
> > tar -xzvf
> gromacs-4.5.4.tar.gz
>
> > cd gromacs-4-5-4
>
>
>
>
>
>
>
> The instruction for this command is wrong, because this is not the
> directory created by the previous command. Please inform the author
> of the tutorial.
>
>
>
> Mark
>
>
>
>
>
>
>
>
> > make clean
> > ./configure
> --prefix=/usr/local/gromacs --program-suffix=""
> >
> make
> > make install
>
>
>
> However, when I do make
> clean, following error message appear.
>
> make: *** No rule to make target `clean'. Stop.
> When I continously doing the make after ./configure step, I
> found the following error message:
> make: *** No targets specified and no makefile found. Stop.
> Could you please kindly instruct if I have done any things
> stupidly wrong? Following is the log file for the configure.log, please
> kindly help.
> Catherine
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> 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/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
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> ------------------------------
>
> Message: 3
> Date: Sat, 10 Mar 2012 00:02:40 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Error Message in Make clean command for
> installation.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F59FF70.2020002 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 9/03/2012 11:58 PM, a a wrote:
> > Hi Mark,
> >
> > I did find the directory "gromacs-4.5.5"
> >
> > However, when I go into this folder, I have problem to do the "make"
> > command. I found there is no "Make" file inside the folder. I can
> > only see the following files inside this folder. Should I do "make
> > clean" then?
> >
> > acinclude.m4 config Doxyfile.in log share
> > aclocal.m4 config.log include Makefile.am src
> > admin configure INSTALL.automake Makefile.in tests
> > AUTHORS configure.ac INSTALL.cmake man
> > cmake COPYING INSTALL-GPU & nbsp; README
> > CMakeLists.txt COPYING-GPU libtool scripts
> >
> > Should I do Makefile.am or Makefile.in intead?
>
> "make clean" is also unnecessary, and won't work until you have done a
> configure stage. I suggest you take installation instructions from the
> GROMACS webpage, and pick up their tutorial once you have done a proper
> installation.
>
> Mark
>
> >
> > Best regards,
> >
> > Catherine
> >
> >
> > ------------------------------------------------------------------------
> > Date: Fri, 9 Mar 2012 23:22:51 +1100
> > From: Mark.Abraham at anu.edu.au
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Error Message when installing GROMACS.
> >
> > On 9/03/2012 10:58 PM, a a wrote:
> >
> > Dear Sir/Madam,
> >
> > I am trying to install the GROMACS to my new workstation. As my
> > old one is not belong to me, I cannot install VMD to it. Please
> > kindly help to instruct if I did anything wrong here. Many thanks.
> >
> > Follow the steps in
> > http://www.cems.uvm.edu/~smanchu/gromacs_installation.html
> > <http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html>, I
> > have done the installation fftw-3.0.1 at my
> > "/Catherine/Gromacs/fftw-3.0.1" directory.
> >
> > Follow the steps in
> >
> http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/
> ,
> > i.e. [wget ftp://ftp.gromacs
> > .org/pub/gromacs/gromacs-4.5.4.tar.gz], I have downloaded the
> > gromacs to my Catherine/Gromacs/ folder.
> >
> > Follow the steps in
> > http://www.gromacs.org/Downloads/Installation_Instructions, I have
> > start installing the GROMACS.
> >
> > > tar -xzvf gromacs-4.5.4.tar.gz
> > > cd gromacs-4-5-4
> >
> >
> > The instruction for this command is wrong, because this is not the
> > directory created by the previous command. Please inform the author of
> > the tutorial.
> >
> > Mark
> >
> > > make clean
> > > ./configure --prefix=/usr/local/gromacs --program-suffix=""
> > > make
> > > make install
> > *
> > *
> > However, when I do make clean, following error message appear.
> >
> > make: *** No rule to make target `clean'. Stop.
> >
> > When I continously doing the make after ./configure step, I found
> the following error message:
> >
> > make: *** No targets specified and no makefile found. Stop.
> >
> > Could you please kindly instruct if I have done any things stupidly
> wrong? Following is the log file for the configure.log, please kindly help.
> >
> > Catherine
> >
> >
> >
> >
> >
> > *
> > *
> >
> > *
> > *
> >
> >
> >
> >
> >
> > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
> >
>
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> End of gmx-users Digest, Vol 95, Issue 60
> *****************************************
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