On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo <stefano.guglie...@unito.it> wrote: > > As an update, I have just tried a run with cpu only after compiling with > AVX2_128 and the workstation turned off after few minutes.
That is suspicious. Perhaps a CPU cooling issue? Otherwise you may have a BIOS/firmware issue or, less likely but possibly, a a faulty CPU. -- Szilárd > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > Mail > priva di virus. www.avast.com > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > <#m_360888458910571867_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > Il giorno gio 12 set 2019 alle ore 15:19 Stefano Guglielmo < > stefano.guglie...@unito.it> ha scritto: > > > Hi Szilard, > > thanks for your reply. > > The compiler is gcc 4.8.5. > > I put below the link where you can find the files coming from cmake and > > the output for "AUTO" SIMD instruction. As for cpu only, as you had > > suggested previously I tried a run (after compiling with AVX2_256) and it > > worked without any problems for about 5 hours. I will try with AVX2_128 as > > well. > > > > Stefano > > > > https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0 > > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > Mail > > priva di virus. www.avast.com > > <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > <#m_360888458910571867_m_-3568712886600561053_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > Il giorno gio 12 set 2019 alle ore 14:28 Szilárd Páll < > > pall.szil...@gmail.com> ha scritto: > > > >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo > >> <stefano.guglie...@unito.it> wrote: > >> > > >> > I apologize for the mistake, there was a typo in the object that could > >> be > >> > misleading, so I re-post with the correct object, > >> > sorry. > >> > > >> > ---------- Forwarded message --------- > >> > Da: Stefano Guglielmo <stefano.guglie...@unito.it> > >> > Date: mer 11 set 2019 alle ore 17:17 > >> > Subject: SMD options > >> > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > >> > > >> > > >> > Hi all, > >> > following my previous post regarding anomalous crashing of the system on > >> > running gromacs on two gpus, I have some new elements to add. > >> > I tested the workstation with two tools for gpu and cpu I found on the > >> web > >> > (gpu_burn and stress); I ran the two of them at the same time for two > >> hours > >> > pushing both gpus (2 x 250 W) and cpu (250 W), and no error reports or > >> > overheating have resulted, so I would say that the hardware seems to be > >> > stable. > >> > Despite this, I found something that perhaps could be not normal during > >> > gromacs compilation: setting -DGMX_SIMD=AUTO, results in "SIMD > >> > instructions: NONE"; in this condition I can run gromacs without any > >> > unexpected crash, even though a little less efficiently; setting > >> -DGMX_SIMD > >> > to AVX_256, AVX2_128 and AVX2_256 produces clean compilation and > >> > installation (with all the tests passed), but on running the sudden > >> turning > >> > off happens in the conditions I had described in the previous posts > >> > (gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 > >> > -gputasks 00 -pin on -pinoffset 0 -pinstride 1 > >> > plus > >> > gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0 > >> > -gputasks 11 -pin on -pinoffset 28 -pinstride 1) > >> > Do you think that there could be a relationship between SIMD options > >> > setting and the crash of the system? > >> > >> Unlikely, but not impossible. I would however expect that a CPU-only > >> GROMACS run would also lead to a crash. Can you try to do an AVX2_128 > >> CPU-only run (e.g. mdrun -ntmpi 64 -ntomp 1 -nb cpu) and let it run > >> for a few hours? > >> > >> > Does anyone have any idea about the > >> > reason why gromacs does not seem to automatically recognize any options > >> for > >> > my AMD threadripper? Can there be any solutions for this? > >> > >> That is certainly unexpected, perhaps there is an issue with your > >> compler toolchains. What compiler are you using? Can you please share > >> your cmake detection output and CMakeCache.txt? > >> > >> Cheers, > >> -- > >> Szilárd > >> > >> > Thanks again > >> > Stefano > >> > PS: the workstation is running with centOS 7 and aThreadripper 2990WX > >> cpu. > >> > > >> > -- > >> > Stefano GUGLIELMO PhD > >> > Assistant Professor of Medicinal Chemistry > >> > Department of Drug Science and Technology > >> > Via P. Giuria 9 > >> > 10125 Turin, ITALY > >> > ph. +39 (0)11 6707178 > >> > > >> > > >> > < > >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail > >> > > >> > Mail > >> > priva di virus. www.avast.com > >> > < > >> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail > >> > > >> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > >> > > >> > > >> > -- > >> > Stefano GUGLIELMO PhD > >> > Assistant Professor of Medicinal Chemistry > >> > Department of Drug Science and Technology > >> > Via P. Giuria 9 > >> > 10125 Turin, ITALY > >> > ph. +39 (0)11 6707178 > >> > -- > >> > 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. > > > > > > > > -- > > Stefano GUGLIELMO PhD > > Assistant Professor of Medicinal Chemistry > > Department of Drug Science and Technology > > Via P. Giuria 9 > > 10125 Turin, ITALY > > ph. +39 (0)11 6707178 > > > > > > -- > Stefano GUGLIELMO PhD > Assistant Professor of Medicinal Chemistry > Department of Drug Science and Technology > Via P. Giuria 9 > 10125 Turin, ITALY > ph. +39 (0)11 6707178 > -- > 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.