Hi Mark, We have few nodes with 64 GB memory and many other with 16 GB of memory. I am attempting a simulation of around 100 M atoms.
I did find some document which says one need (50bytes)*NATOMS on master node, also one needs (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this true? Thank you, amit On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:) > ----- Original Message ----- > From: Amit Choubey <kgp.a...@gmail.com> > Date: Friday, February 26, 2010 20:05 > Subject: [gmx-users] gromacs memory usage > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > Hi, > > I am having trouble with running gromacs with a large system. I am trying > to use several processors for the md. The error is a memory allocation error > and it might be due to low RAM or large no of particles. I want to know the > detailed memory usage of mdrun ie say for N atoms how much memory does the > master node need and then also whats the memory requirement for the other > nodes. By master node i mean the node that does the domain decomposition > calculation etc during the start of mdrun. A webpage which describes the > memory requirement at various stages during mdrun will be very helpful. > > The master node does not have a significantly larger memory footprint than > any other, during setup or the run... For example, a 50K-atom system runs > fine on 64 BlueGene/L processors with a hard limit of 500MB per processor > for OS+code+data+MPI. > > Does your system run on 1 processor, with and without MPI? How much > (physical) memory do you have for how large a system? > > Mark > -- > 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/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/mailing_lists/users.php >
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