<br><br><div class="gmail_quote">On 9 March 2012 13:03, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Re: GROMACS stalls for NPT simulation when using -npme and<br>
-dd flags (Mark Abraham)<br>
2. Error Message in Make clean command for installation. (a a)<br>
3. Re: Error Message in Make clean command for installation.<br>
(Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 09 Mar 2012 23:42:33 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] GROMACS stalls for NPT simulation when using<br>
-npme and -dd flags<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F59FAB9.6010805@anu.edu.au">4F59FAB9.6010805@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 9/03/2012 9:43 PM, Stephen Cox wrote:<br>
> Dear users,<br>
><br>
> I'm trying to run an isotropic NPT simulation on a cubic cell<br>
> containing TIP4P/ice water and methane. I'm using the<br>
> Parrinello-Rahman barostat. I've been playing around with the<br>
> different decomposition flags of mdrun to get better performance and<br>
> scaling and have found that the standard -npme (half number of cores)<br>
> works pretty well. I've also tried using the -dd flags, and I appear<br>
> to get decent performance and scaling. However, after a few<br>
> nanoseconds (corresponding to about 3 hours run time), the program<br>
> just stalls; no output and no error messages. I realise NPT may cause<br>
> domain decompositon some issues if the cell vectors vary wildly, but<br>
> this isn't happening in my system.<br>
><br>
> Has anybody else experienced issues with domain decomposition and NPT<br>
> simulations? If so, are there any workarounds? For the moment, I've<br>
> had to resort to using -pd, which is giving relatively poor<br>
> performance and scaling, but at least it isn't dying!<br>
><br>
> I'm using GROMACS 4.5.5 with an intel compiler (I followed the<br>
> instructions online, with static linking) and using the command:<br>
><br>
> #!/bin/bash -f<br>
> # ---------------------------<br>
> #$ -V<br>
> #$ -N test<br>
> #$ -S /bin/bash<br>
> #$ -cwd<br>
> #$ -l vf=2G<br>
> #$ -pe ib-ompi 32<br>
> #$ -q infiniband.q<br>
><br>
> mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2<br>
><br>
> Below is my grompp.mdp.<br>
><br>
> Thanks,<br>
> Steve<br>
><br>
> P.S. I think that there may be an issue with memory leak that occurs<br>
> for domain decomposition with NPT. I seem to remember seeing this<br>
> happening on my desktop and my local cluster. I don't see this with<br>
> NVT simulations. This would be consistent with the lack of error<br>
> message: I've just run a short test run and the memory usage was<br>
> climbing streadily.<br>
><br>
> ; run control<br>
> integrator = md<br>
> dt = 0.002<br>
> nsteps = -1<br>
> comm_mode = linear<br>
> nstcomm = 10<br>
><br>
> ; energy minimization<br>
> emtol = 0.01<br>
> emstep = 0.01<br>
><br>
> ; output control<br>
> nstxout = 0<br>
> nstvout = 0<br>
> nstfout = 0<br>
> nstlog = 0<br>
> nstcalcenergy = 2500<br>
> nstenergy = 2500<br>
> nstxtcout = 2500<br>
><br>
> ; neighbour searching<br>
> nstlist = 1<br>
> ns_type = grid<br>
> pbc = xyz<br>
> periodic_molecules = no<br>
> rlist = 0.90<br>
><br>
> ; electrostatics<br>
> coulombtype = pme<br>
> rcoulomb = 0.90<br>
><br>
> ; vdw<br>
> vdwtype = cut-off<br>
> rvdw = 0.90<br>
> dispcorr = ener<br>
><br>
> ; ewald<br>
> fourierspacing = 0.1<br>
> pme_order = 4<br>
> ewald_geometry = 3d<br>
> optimize_fft = yes<br>
><br>
> ; temperature coupling<br>
> tcoupl = nose-hoover<br>
> nh-chain-length = 10<br>
> tau_t = 2.0<br>
> ref_t = 255.0<br>
> tc_grps = system<br>
><br>
> ; pressure coupling<br>
> pcoupl = parrinello-rahman<br>
> pcoupltype = isotropic<br>
> ref_p = 400.0<br>
> tau_p = 2.0<br>
> compressibility = 6.5e-5<br>
><br>
> ; constraints<br>
> constraint_algorithm = shake<br>
> shake_tol = 0.0001<br>
> lincs_order = 8<br>
> lincs_iter = 2<br>
><br>
> ; velocity generation<br>
> gen_vel = yes<br>
> gen_temp = 255.0<br>
> gen_seed = -1<br>
<br>
You're generating velocities and immediately using a barostat that is<br>
unsuitable for equilibration. </blockquote><div><br>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. <br>
</div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">You're using an integration step that<br>
requires constraints=all-bonds but I don't see that. </blockquote><div><br>Could you clarify this point for me please? Thanks.<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
You may have better<br>
stability if you equilibrate with Berendsen barostat and then switch.<br>
I've seen no other reports of memory usage growing without bounds, but<br>
if you can observe it happening after choosing a better integration<br>
regime then it suggests a code problem that wants fixing.<br></blockquote><div><br>I can run some tests on my desktop with a smaller system and report if I see memory loss.<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Mark<br>
<br>
<br></blockquote><div><br>Thanks for your quick response<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 9 Mar 2012 20:58:27 +0800<br>
From: a a <<a href="mailto:patd_2@hotmail.com">patd_2@hotmail.com</a>><br>
Subject: [gmx-users] Error Message in Make clean command for<br>
installation.<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL118-W55ECB6D09526F932DD0EF4A3540@phx.gbl><br>
Content-Type: text/plain; charset="big5"<br>
<br>
<br>
<br>
Hi Mark,<br>
I did find the directory "gromacs-4.5.5"<br>
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?<br>
acinclude.m4 config Doxyfile.in log shareaclocal.m4 config.log include Makefile.am srcadmin configure INSTALL.automake Makefile.in testsAUTHORS <a href="http://configure.ac" target="_blank">configure.ac</a> INSTALL.cmake mancmake COPYING INSTALL-GPU READMECMakeLists.txt COPYING-GPU libtool scripts<br>
Should I do Makefile.am or Makefile.in intead?<br>
Best regards,<br>
Catherine<br>
<br>
Date: Fri, 9 Mar 2012 23:22:51 +1100<br>
From: <a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] Error Message when installing GROMACS.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 9/03/2012 10:58 PM, a a wrote:<br>
<br>
<br>
<br>
<br>
Dear Sir/Madam,<br>
<br>
<br>
<br>
I am trying to install the GROMACS to my new<br>
workstation. As my old one is not belong to me, I cannot<br>
install VMD to it. Please kindly help to instruct if I<br>
did anything wrong here. Many thanks.<br>
<br>
<br>
<br>
<br>
Follow the steps in <a href="http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html" target="_blank">http://www.cems.uvm.edu/~smanchu/gromacs_installation.html</a>, I have done the installation<br>
fftw-3.0.1 at my "/Catherine/Gromacs/fftw-3.0.1"<br>
directory.<br>
<br>
<br>
<br>
Follow the steps in <a href="http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/" target="_blank">http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/</a>,<br>
i.e. [wget<br>
<a href="ftp://ftp.gromacs" target="_blank">ftp://ftp.gromacs</a><br>
.org/pub/gromacs/gromacs-4.5.4.tar.gz], I have<br>
downloaded the gromacs to my Catherine/Gromacs/<br>
folder.<br>
<br>
<br>
<br>
Follow the steps in <a href="http://www.gromacs.org/Downloads/Installation_Instructions" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a>, I have start installing the<br>
GROMACS.<br>
<br>
<br>
<br>
> tar -xzvf<br>
gromacs-4.5.4.tar.gz<br>
<br>
> cd gromacs-4-5-4<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
The instruction for this command is wrong, because this is not the<br>
directory created by the previous command. Please inform the author<br>
of the tutorial.<br>
<br>
<br>
<br>
Mark<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
> make clean<br>
> ./configure<br>
--prefix=/usr/local/gromacs --program-suffix=""<br>
><br>
make<br>
> make install<br>
<br>
<br>
<br>
However, when I do make<br>
clean, following error message appear.<br>
<br>
make: *** No rule to make target `clean'. Stop.<br>
When I continously doing the make after ./configure step, I found the following error message:<br>
make: *** No targets specified and no makefile found. Stop.<br>
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.<br>
Catherine<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
--<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Sat, 10 Mar 2012 00:02:40 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Error Message in Make clean command for<br>
installation.<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F59FF70.2020002@anu.edu.au">4F59FF70.2020002@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 9/03/2012 11:58 PM, a a wrote:<br>
> Hi Mark,<br>
><br>
> I did find the directory "gromacs-4.5.5"<br>
><br>
> However, when I go into this folder, I have problem to do the "make"<br>
> command. I found there is no "Make" file inside the folder. I can<br>
> only see the following files inside this folder. Should I do "make<br>
> clean" then?<br>
><br>
> acinclude.m4 config Doxyfile.in log share<br>
> aclocal.m4 config.log include Makefile.am src<br>
> admin configure INSTALL.automake Makefile.in tests<br>
> AUTHORS <a href="http://configure.ac" target="_blank">configure.ac</a> INSTALL.cmake man<br>
> cmake COPYING INSTALL-GPU & nbsp; README<br>
> CMakeLists.txt COPYING-GPU libtool scripts<br>
><br>
> Should I do Makefile.am or Makefile.in intead?<br>
<br>
"make clean" is also unnecessary, and won't work until you have done a<br>
configure stage. I suggest you take installation instructions from the<br>
GROMACS webpage, and pick up their tutorial once you have done a proper<br>
installation.<br>
<br>
Mark<br>
<br>
><br>
> Best regards,<br>
><br>
> Catherine<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
> Date: Fri, 9 Mar 2012 23:22:51 +1100<br>
> From: <a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Error Message when installing GROMACS.<br>
><br>
> On 9/03/2012 10:58 PM, a a wrote:<br>
><br>
> Dear Sir/Madam,<br>
><br>
> I am trying to install the GROMACS to my new workstation. As my<br>
> old one is not belong to me, I cannot install VMD to it. Please<br>
> kindly help to instruct if I did anything wrong here. Many thanks.<br>
><br>
> Follow the steps in<br>
> <a href="http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html" target="_blank">http://www.cems.uvm.edu/~smanchu/gromacs_installation.html</a><br>
> <<a href="http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html" target="_blank">http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html</a>>, I<br>
> have done the installation fftw-3.0.1 at my<br>
> "/Catherine/Gromacs/fftw-3.0.1" directory.<br>
><br>
> Follow the steps in<br>
> <a href="http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/" target="_blank">http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/</a>,<br>
> i.e. [wget <a href="ftp://ftp.gromacs" target="_blank">ftp://ftp.gromacs</a><br>
> .org/pub/gromacs/gromacs-4.5.4.tar.gz], I have downloaded the<br>
> gromacs to my Catherine/Gromacs/ folder.<br>
><br>
> Follow the steps in<br>
> <a href="http://www.gromacs.org/Downloads/Installation_Instructions" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a>, I have<br>
> start installing the GROMACS.<br>
><br>
> > tar -xzvf gromacs-4.5.4.tar.gz<br>
> > cd gromacs-4-5-4<br>
><br>
><br>
> The instruction for this command is wrong, because this is not the<br>
> directory created by the previous command. Please inform the author of<br>
> the tutorial.<br>
><br>
> Mark<br>
><br>
> > make clean<br>
> > ./configure --prefix=/usr/local/gromacs --program-suffix=""<br>
> > make<br>
> > make install<br>
> *<br>
> *<br>
> However, when I do make clean, following error message appear.<br>
><br>
> make: *** No rule to make target `clean'. Stop.<br>
><br>
> When I continously doing the make after ./configure step, I found the following error message:<br>
><br>
> make: *** No targets specified and no makefile found. Stop.<br>
><br>
> 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.<br>
><br>
> Catherine<br>
><br>
><br>
><br>
><br>
><br>
> *<br>
> *<br>
><br>
> *<br>
> *<br>
><br>
><br>
><br>
><br>
><br>
> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a> Please search the<br>
> archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before<br>
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><br>
><br>
<br>
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</font></span></blockquote></div><br>