Hi, That sounds like a memory leak. Could you please file a bug report in redmine preferably with: - configure options (+config.log or CMakeCache.txt would be ideal) - compiler version, external library versions (fft, blas, lapack) - input (tpr at least) - full mdrun command line
Cheers, -- Szilárd On Tue, Mar 13, 2012 at 10:18 AM, Stephen Cox <[email protected]> wrote: > My Gmail doesn't show the subject line when hitting reply, so apologies for > the double post, but I thought I'd put it out there with an amended subject > line in case it's of use to anyone else.... > > > > 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 <[email protected]> wrote: > >> >> >> On 9 March 2012 13:03, [email protected] < >> [email protected]> wrote: >> >>> Send gmx-users mailing list submissions to >>> [email protected] >>> >>> 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 >>> [email protected] >>> >>> You can reach the person managing the list at >>> [email protected] >>> >>> 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 <[email protected]> >>> Subject: Re: [gmx-users] GROMACS stalls for NPT simulation when using >>> -npme and -dd flags >>> To: Discussion list for GROMACS users <[email protected]> >>> Message-ID: <[email protected]> >>> 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 >> >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
