Re: [gmx-users] GROMACS 4.6.5 is released
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.szil...@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.32...@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.szil...@gmail.com wrote: On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@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.abra...@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-usersor send a mail to gmx-users-requ...@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-requ...@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-requ...@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-requ...@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
Re: [gmx-users] GROMACS 4.6.5 is released
On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@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.abra...@gmail.comwrote: 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-requ...@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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] GROMACS 4.6.5 is released
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.szil...@gmail.com wrote: On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@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.abra...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] GROMACS 4.6.5 is released
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.32...@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.szil...@gmail.com wrote: On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@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.abra...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
