Re: [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.abra...@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.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_source=link_campaign=sig-email_content=webmail
> > >
> > Mail
> > priva di virus. www.avast.com
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > Mail
> > > > priva di virus. www.avast.com
> > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > > > >  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_source=link_campaign=sig-email_content=webmail
> > > > > >
> > > > > > Mail
> > > > > > priva di virus. www.avast.com
> > > > > > <
> > > > >
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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 

Re: [gmx-users] Fwd: SIMD options

[Mark Abraham]

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 
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_source=link_campaign=sig-email_content=webmail
> >
> Mail
> priva di virus. www.avast.com
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail
> > > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > > >  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_source=link_campaign=sig-email_content=webmail
> > > > >
> > > > > Mail
> > > > > priva di virus. www.avast.com
> > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail
> > > >
> > > > Mail
> > > > > > priva di virus. www.avast.com
> > > > > > <
> > > >
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

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


Mail
priva di virus. www.avast.com

<#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_source=link_campaign=sig-email_content=webmail
> > >
> > Mail
> > priva di virus. www.avast.com
> > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > >  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_source=link_campaign=sig-email_content=webmail
> > > >
> > > > Mail
> > > > priva di virus. www.avast.com
> > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > > > priva di virus. www.avast.com
> > > > > <
> > >
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > > > >>  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 
> > > > >> > Date: mer 11 set 2019 alle ore 17:17
> > > > >> > Subject: SMD options
> > > > >> > To: 
> > > > >> >
> > > > >> >
> > > > >> > 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
> > > > 

Re: [gmx-users] Fwd: SIMD options

[Mark Abraham]

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 
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_source=link_campaign=sig-email_content=webmail
> >
> Mail
> priva di virus. www.avast.com
> <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> >  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_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > > > priva di virus. www.avast.com
> > > > <
> >
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > > >>  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 
> > > >> > Date: mer 11 set 2019 alle ore 17:17
> > > >> > Subject: SMD options
> > > >> > To: 
> > > >> >
> > > >> >
> > > >> > 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
> > > >> > 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

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


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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
>  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_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > priva di virus. www.avast.com
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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_source=link_campaign=sig-email_content=webmail>
> Mail
> > > priva di virus. www.avast.com
> > > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
> > >>  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 
> > >> > Date: mer 11 set 2019 alle ore 17:17
> > >> > Subject: SMD options
> > >> > To: 
> > >> >
> > >> >
> > >> > 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 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo
 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

> 
> Mail
> priva di virus. www.avast.com
> 
> <#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
> >
> >
> > 
> >  Mail
> > priva di virus. www.avast.com
> > 
> > <#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
> >>  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 
> >> > Date: mer 11 set 2019 alle ore 17:17
> >> > Subject: SMD options
> >> > To: 
> >> >
> >> >
> >> > 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_source=link_campaign=sig-email_content=webmail
> >> >
> >> > Mail
> >> > priva di virus. www.avast.com
> >> > <
> >> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
> >> >
> >> > <#m_-7114857415897320041_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >> >
> >> >
> >> > --
> 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

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.


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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
>
>
> 
>  Mail
> priva di virus. www.avast.com
> 
> <#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
>>  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 
>> > Date: mer 11 set 2019 alle ore 17:17
>> > Subject: SMD options
>> > To: 
>> >
>> >
>> > 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_source=link_campaign=sig-email_content=webmail
>> >
>> > Mail
>> > priva di virus. www.avast.com
>> > <
>> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 3:25 PM Stefano Guglielmo
 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
>
> 
> Mail
> priva di virus. www.avast.com
> 
> <#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
> >  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 
> > > Date: mer 11 set 2019 alle ore 17:17
> > > Subject: SMD options
> > > To: 
> > >
> > >
> > > 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_source=link_campaign=sig-email_content=webmail
> > >
> > > Mail
> > > priva di virus. www.avast.com
> > > <
> > https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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.
> > 

Re: [gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

 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


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<#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
>  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 
> > Date: mer 11 set 2019 alle ore 17:17
> > Subject: SMD options
> > To: 
> >
> >
> > 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_source=link_campaign=sig-email_content=webmail
> >
> > Mail
> > priva di virus. www.avast.com
> > <
> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_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
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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
-- 
Gromacs Users 

Re: [gmx-users] Fwd: SIMD options

[Szilárd Páll]

On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo
 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 
> Date: mer 11 set 2019 alle ore 17:17
> Subject: SMD options
> To: 
>
>
> 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
>
>
> 
> Mail
> priva di virus. www.avast.com
> 
> <#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.
-- 
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[gmx-users] Fwd: SIMD options

[Stefano Guglielmo]

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 
Date: mer 11 set 2019 alle ore 17:17
Subject: SMD options
To: 


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? 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?
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



Mail
priva di virus. www.avast.com

<#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
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mail to gmx-users-requ...@gromacs.org.