Hi, In that case, I would look at
$builddir/CMakeFiles/CMakeError.log (and maybe $builddir/CMakeFiles/CMakeOutput.log) to see what was reported about that attempted compilation of GmxDetectCpu program. Depending what is learned, you might want to try your usual cmake call, and then cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED and the contents of $builddir/CMakeFiles/CMakeTmp directory might also help (docs at https://cmake.org/cmake/help/latest/command/try_compile.html) Mark On Thu, 12 Sep 2019 at 17:52, Stefano Guglielmo <stefano.guglie...@unito.it> wrote: > Hi Mark, > actually running cmake in the output I can read "Did not detect build CPU > vendor - detection program did not compile". > Any suggestions about the origin of the issue and possible solutions? > > Thanks > Stefano > > < > 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 17:26 Mark Abraham < > mark.j.abra...@gmail.com> ha scritto: > > > Hi, > > > > There will have been reports by cmake about whether the detection program > > compiled and/or ran successfully, which would be useful diagnostic > > information. Please run cmake in a fresh build directory and look for > that. > > It is possible to run that program individually, if the issue is that it > > compiles and fails to run somehow (e.g. that linking is broken) > > > > Mark > > > > On Thu, 12 Sep 2019 at 17:06, Stefano Guglielmo < > > stefano.guglie...@unito.it> > > wrote: > > > > > I cannot say about BIOS/firmware yet, I made a quite "standard" > > > installation of centOS 7, but I'll try to check; as for cpu, for what > it > > > means, I made the stress test which brought up temperature for two > hours > > > together with gpu_burn, so I would exclude cooling failure. > > > > > > A further update: I yum-installed devtoolset-8-toolchain, so now cmake > > > finds gcc 8.3.1, but again SIMD instructions detection failed. > > > Sorry for bothering but I must say that I am getting a bit confused. > > > > > > Stefano > > > > > > < > > > > > > 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 16:35 Szilárd Páll < > > > pall.szil...@gmail.com> ha scritto: > > > > > > > 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. > > > > > > > > > > > > -- > > > 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 > > > < > 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> > -- > 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.