On 9 March 2012 13:03, gmx-users-requ...@gromacs.org < gmx-users-requ...@gromacs.org> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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.abra...@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@gromacs.org> > Message-ID: <4f59fab9.6010...@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 <pat...@hotmail.com> > Subject: [gmx-users] Error Message in Make clean command for > installation. > To: <gmx-users@gromacs.org> > Message-ID: <col118-w55ecb6d09526f932dd0ef4a3...@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.abra...@anu.edu.au > To: gmx-users@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120309/bb14cb3e/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Sat, 10 Mar 2012 00:02:40 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Error Message in Make clean command for > installation. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4f59ff70.2020...@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.abra...@anu.edu.au > > To: gmx-users@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@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-requ...@gromacs.org. Can't post? > > Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120310/10239bdb/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@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! > > End of gmx-users Digest, Vol 95, Issue 60 > ***************************************** > > >
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