Re: [gmx-users] install and mdrun problems
Hello Sir, I hope you are good and doing well. With such settings, I would do the following steps 1. Make up to date the system BIOS. 2. Double Check the appropriate installation of GROMACS dependencies *viz.*, MPI thread, Open MP threads, *etc. * 3. Re-install gmx 4. Re-install Ubuntu and gmx 5. Sudo apt-get update 6. gmx info Just for example, please find a link for MD-Certified systems/engines up to 1000 ns/ day <https://www.exxactcorp.com/Molecular-Dynamics-Solutions> for personal/multi-user environments. I hope it helps. Sincerely, Kunal [kunal_lif...@mail.vidyasagar.ac.in] On Mon, 2 Mar 2020 at 22:07, Bogdanov, Vladimir wrote: > Hi Kunal, > > Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix > Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD > 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. > > It looks like the reason of my PC shut down is lying in the Bios settings, > but I don't know the version of BIOS, I can look it later, if you need. > -- > *From:* gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Kunal > Dutta > *Sent:* Monday, March 2, 2020 8:56 AM > *To:* gmx-us...@gromacs.org > *Cc:* gromacs.org_gmx-users@maillist.sys.kth.se < > gromacs.org_gmx-users@maillist.sys.kth.se> > *Subject:* Re: [gmx-users] install and mdrun problems > > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > > posting! > > > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > > > * For (un)subscribe requests visit > > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > *--Every life is precious* > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or send a mail to gmx-users-requ...@gromacs.org. > -- *--Every life is precious* -- 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] install and mdrun problems
Have you tried running stress test benchmarks for CPU and GPU? Or just looking up any similar issues reported by other users of your MB and CPU models? Sudden shutdowns at high load are generally caused by power or cooling failure. Or both, like CPU or GPU VRMs overheating, since they're commonly both insufficient for the power they are supposed to pull through and insufficiently cooled at the same time. 03.03.2020 03:37, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: It looks like the reason of my PC shut down is lying in the Bios settings, but I don't know the version of BIOS, I can look it later, if you need. -- 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] install and mdrun problems
Hi Kunal, Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler. It looks like the reason of my PC shut down is lying in the Bios settings, but I don't know the version of BIOS, I can look it later, if you need. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kunal Dutta Sent: Monday, March 2, 2020 8:56 AM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] install and mdrun problems Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ > before > posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ > > * For (un)subscribe requests visit > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ > or > send a mail to gmx-users-requ...@gromacs.org. > -- *--Every life is precious* -- Gromacs Users mailing list * Please search the archive at https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6U0p3M3g$ before posting! * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm5wA753og$ * For (un)subscribe requests visit https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!j5dcEaTwxthJSs8M7xWD0tdUryOKno2-7Ms8wZeaWyfY4mrnFMg0KSQvBm6dRBldnw$ 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] install and mdrun problems
Hi Dallas, The temperature of CPU is fine, it is less than 59C. Mdrun started work properly after I changed Bios settings to the default settings. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Monday, March 2, 2020 1:14 AM To: GROMACS users Subject: Re: [gmx-users] install and mdrun problems Sounds bit like it may be overheating. Are all ventilation fans fully operational? On Mon, 2 Mar. 2020, 2:38 pm Bogdanov, Vladimir, wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > Gromacs Users mailing list > > * Please search the archive at > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOjowitk0g$ > before > posting! > > * Can't post? Read > https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOiJ4yRjLA$ > > * For (un)subscribe requests visit > https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOgPV7JmZQ$ > or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOjowitk0g$ before posting! * Can't post? Read https://urldefense.com/v3/__http://www.gromacs.org/Support/Mailing_Lists__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOiJ4yRjLA$ * For (un)subscribe requests visit https://urldefense.com/v3/__https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users__;!!KGKeukY!gb8ztML0kYUHnTz6ZqzcdMVDlhGPkn7p8Pzs891Y7KuGeKxrubP6nwk-YOgPV7JmZQ$ 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] install and mdrun problems
Hello, If you try an updated version, please try an actually recent one, either 2019.6 or the 2020 release. If you could provide us with some error or log messages we might be able to find out what happened there. Cheers Paul On 02/03/2020 16:03, Kamran Gul, M.Phil. Scholar, Institute of Chemical Sciences, UoP wrote: Try gromacs 2019.2. And then update your cuda and nvidia. On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta, wrote: Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: Hi all, I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but when I did make check, my PC turned off. I also tried to install Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried to do mdrun, my PC also shut down. I also tried the following combination: nvidia-smi 440.59, CUDA 9.2. Any ideas would be helpful. Thanks, Vlad -- 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. -- *--Every life is precious* -- 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. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] install and mdrun problems
Try gromacs 2019.2. And then update your cuda and nvidia. On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta, wrote: > Hello Sir, > May I know the detailed configuration of your system. > Sincerely, > Kunal > > > > > On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir > wrote: > > > Hi all, > > > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), > but > > when I did make check, my PC turned off. I also tried to install > > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I > tried > > to do mdrun, my PC also shut down. I also tried the following > combination: > > nvidia-smi 440.59, CUDA 9.2. > > > > Any ideas would be helpful. > > > > Thanks, > > Vlad > > -- > > 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. > > > > > -- > *--Every life is precious* > -- > 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] install and mdrun problems
Hello Sir, May I know the detailed configuration of your system. Sincerely, Kunal On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > 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. > -- *--Every life is precious* -- 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] install and mdrun problems
Sounds bit like it may be overheating. Are all ventilation fans fully operational? On Mon, 2 Mar. 2020, 2:38 pm Bogdanov, Vladimir, wrote: > Hi all, > > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but > when I did make check, my PC turned off. I also tried to install > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried > to do mdrun, my PC also shut down. I also tried the following combination: > nvidia-smi 440.59, CUDA 9.2. > > Any ideas would be helpful. > > Thanks, > Vlad > -- > 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.
[gmx-users] install and mdrun problems
Hi all, I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2), but when I did make check, my PC turned off. I also tried to install Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I tried to do mdrun, my PC also shut down. I also tried the following combination: nvidia-smi 440.59, CUDA 9.2. Any ideas would be helpful. Thanks, Vlad -- 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.
