On Thu, Sep 12, 2019 at 3:25 PM Stefano Guglielmo <stefano.guglie...@unito.it> wrote: > > Hi Szilard, > thanks for your reply. > The compiler is gcc 4.8.5.
That is ancient. From your cmake.out: -- Detection for best SIMD instructions failed, using SIMD - None -- SIMD instructions disabled Update your compiler toolchain to a modern compiler (e.g. gcc 8), you'll also get much better performance. Cheers, -- Szilárd > 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> > <#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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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