[gmx-users] GROMACS 4.6.5 is released

[João Henriques]

Thank you Szillárd, that will indeed affect me and other users at the
cluster.

Best regards,
João


On Thu, Dec 5, 2013 at 8:08 AM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> The first update on the redmine page does describe the source of the
> issue - although perhaps not in the most user-friendly manner.
>
> Translating it to a simple example, if you have dual-socket 8c nodes
> and 2 GPUs per node:
>
> mpirun -np 4 mdrun -ntomp 4 -gpu_id 0011 #single node 4 ranks per
> node, 2-way rank-GPU sharing
> mpirun -np 4 mdrun -ntomp 8 -gpu_id 01 #two nodes 2 ranks per node, no
> GPU sharing
> will work, but
>
> mpirun -np 8 mdrun -ntomp 4 -gpu_id 0011 #two nodes 4 ranks per node,
> 2-way rank-GPU sharing
>
> will crash.
>
> Cheers
> --
> Szilárd
>
>
> On Wed, Dec 4, 2013 at 5:38 PM, João Henriques
> <joao.henriques.32353 at gmail.com> wrote:
> > I did read it and wasn't very enlightened by it, that's why I kindly
> > requested for further information on the subject. "under certain
> > circumstances (but quite often), a segmentation fault occurs" definitely
> > sounds serious, but it's not very explicit.
> >
> > In any case, I'll request a new install and tell them to remove the
> > previous version form the cluster. We don't want segmentation faults to
> > happen under certain circumstances :)
> >
> > Thank you,
> >
> > /J
> >
> >
> > On Wed, Dec 4, 2013 at 2:27 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
> >
> >> On Wed, Dec 4, 2013 at 10:15 AM, João Henriques
> >> <joao.henriques.32353 at gmail.com> wrote:
> >> > Soon enough we will have daily releases :P
> >>
> >> I hope you're not suggesting that we should release less frequently! :)
> >>
> >> > Mark, can you please elaborate just a tiny bit longer on how relevant
> >> were
> >> > the "GPU-load balancing and GPU-sharing bugs introduced in a bug fix
> in
> >> > 4.6.4"? I'm asking this because I just requested the support team at
> my
> >> > local cluster to install 4.6.4 and I don't have the nerve to request
> >> > another install so soon.
> >>
> >> As always, read the release notes and if interested in details, links
> >> to the redmine page of bugs are listed there as well:
> >> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >> >
> >> > Cheers,
> >> >
> >> > /J
> >> >
> >> > On Tue, Dec 3, 2013 at 12:41 AM, Mark Abraham <
> mark.j.abraham at gmail.com
> >> >wrote:
> >> >
> >> >> Hi GROMACS users,
> >> >>
> >> >> GROMACS 4.6.5 is officially released. It contains a significant bug
> fix
> >> >> when using GPUs in a multi-node simulation, introduced in another
> recent
> >> >> bug fix. We encourage all users to upgrade their installations from
> >> earlier
> >> >> 4.6.x releases.
> >> >>
> >> >> You can find the code, manual, release notes, installation
> instructions
> >> and
> >> >> test suite at the links below. Note that the tests and manual have
> not
> >> >> changed since 4.6.4.
> >> >>
> >> >> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz
> >> >> ftp://ftp.gromacs.org/pub/manual/manual-4.6.5.pdf
> >> >>
> >> >>
> >>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.5
> >> >> http://www.gromacs.org/Documentation/Installation_Instructions
> >> >> http://gromacs.googlecode.com/files/regressiontests-4.6.5.tar.gz
> >> >>
> >> >> Happy simulating!
> >> >>
> >> >> Mark Abraham
> >> >>
> >> >> GROMACS development manager
> >> >> --
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