[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

Hi Mark,
thank you for your reply. I inspected CMakeError.log and CMakeOutputlog:
though several errors were reported in the first one, no mention to
GmxDetectCpu at all.
When trying "cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED",
the output is:
"debug trycompile on
-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations:
-- Configuring done
-- Generating done
-- Build files have been written to: /home/stefano/gromacs-2019.2/build"
and $builddir/CMakeFiles/CMakeTmp directory contains some files and
subdirectories but, to be honest, I have no idea where to find possibly
relevant information.
CMakeError.log and CMakeOutputlog files can be found at:
https://www.dropbox.com/sh/rh3gdpoxrbqzdfx/AACXoXZ8Zw1-ItD9lnrDr1TNa?dl=0

Stefano

Il giorno gio 12 set 2019 alle ore 18:16 Mark Abraham <
mark.j.abraham at gmail.com> ha scritto:

> 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.guglielmo at 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.abraham at 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.guglielmo at 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.szilard at gmail.com> ha scritto:
> > > >
> > > > > On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
> > > > > <stefano.guglielmo at 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.guglielmo at 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.szilard at gmail.com> ha scritto:
> > > > > > >
> > > > > > >> On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
> > > > > > >> <stefano.guglielmo at 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.guglielmo at unito.it>
> > > > > > >> > Date: mer 11 set 2019 alle ore 17:17
> > > > > > >> > Subject: SMD options
> > > > > > >> > To: <gromacs.org_gmx-users at 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
> > > > > > >> > --
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> > > > > > > --
> > > > > > > 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
> > > > > > --
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> > > > --
> > > > 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
> > > > --
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> >
> > --
> > 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
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> > >
> > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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-- 
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