[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60
Stephen Cox
stephen.cox.10 at ucl.ac.uk
Mon Mar 12 12:41:25 CET 2012
Hi,
so further to my last email, I have run a quick test on my desktop machine
(4 cores, 12Gb RAM). It seems that when running the parrinello-rahman
barostat with domain decomposition (-dd 2 2 1) that I'm still getting
memory leak (this time with GNU compilers). I followed proper equilibration
with the berendsen barostat (although I didn't think this was the problem)
and also added the "constraints = all-bonds" line, but this has made no
difference to my results (I'm using "[ constraints ]" in my topology file).
To give an idea of the rate of memory loss, initial memory consumption was
0.1% total memory per process, which rose steadily to 0.5% total memory
after 5 minutes. After 17mins, memory consumption is 1.7% total memory and
rising. Running with "-pd", memory usage is constant at 0.1% total memory.
The system is 328 TIP4P/ice + 64 all-atomic methane. This problem has
occurred for me on different architectures and with different compilers
(and different system sizes). It would be good if anybody familiar with the
source could take a look, or if anybody knows any compiler flags that would
prevent memory leak.
Thanks,
Steve
On 9 March 2012 13:32, Stephen Cox <stephen.cox.10 at ucl.ac.uk> wrote:
>
>
> 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
>> 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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>> ------------------------------
>>
>> 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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>> ------------------------------
>>
>> --
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>>
>> End of gmx-users Digest, Vol 95, Issue 60
>> *****************************************
>>
>>
>>
>
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