[gmx-users] GROMACS 4.6.5 is released

[Szilárd Páll]

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
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-request at gromacs.org.
>> >>
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.