[gmx-users] SIMD options - detection program issue

) was not that smart in managing the cpu (I also found some posts on the web regarding issues of threadripper 2990wx and centos). Still I can not find an explanation of the compilation error of detect program. Anyway, thanks to all of you for sharing suggestions and opinions, Stefano -- Stefano

Re: [gmx-users] Fwd: SIMD options

nt 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 &g

Re: [gmx-users] Fwd: SIMD options

ram 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

Re: [gmx-users] Fwd: SIMD options

vast.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..

Re: [gmx-users] Fwd: SIMD options

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 repl

Re: [gmx-users] Fwd: SIMD options

tps://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 14:28 Szilárd Páll < pall.szil...@gmail.com> ha scritto: > On Thu, Sep 12, 2019 at 8:58 AM Stefano Gu

[gmx-users] Fwd: SIMD options

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

[gmx-users] SMD options

here 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 -- Stefano GUGLIELMO PhD

Re: [gmx-users] simulation on 2 gpus

cally help to diagnose the problem? Any opinion is appreciated, thanks Il giorno mercoledì 21 agosto 2019, Szilárd Páll ha scritto: > Hi Stefano, > > > On Tue, Aug 20, 2019 at 3:29 PM Stefano Guglielmo > wrote: > > > > Dear Szilard, > > > > thanks for the v

Re: [gmx-users] simulation on 2 gpus

-ntmpi 1 -npme 0 -gputasks 00 -pin on -pinoffset 0 -pinstride 1. Thanks again Stefano Il giorno ven 16 ago 2019 alle ore 17:48 Szilárd Páll < pall.szil...@gmail.com> ha scritto: > On Mon, Aug 5, 2019 at 5:00 PM Stefano Guglielmo > wrote: > > > > Dear Paul, > > tha

Re: [gmx-users] simulation on 2 gpus

pi 8 -npme 1 > -gputasks -pin on > > > > Depending on the molecular system/model -ntomp -4 -ntmpi 16 may be > faster - of course adjusting -gputasks > > > > Rarely do I find that not using ntomp and ntpmi is faster, but it is > neve

Re: [gmx-users] simulation on 2 gpus

8-55 NUMA node2 CPU(s): 8-15,40-47 NUMA node3 CPU(s): 24-31,56-63 ..." Thanks Stefano -- 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/si

Re: [gmx-users] simulation on 2 gpus

if I run a > simulation > > with -ntmpi 4 -ntmpi 5 -pme gpu -npme 1 -pme gpu, each one of those ranks > > will have 5 CPUs, but the PME rank will only use one of them. You can > > specify the number of PME cores per rank with -ntomp_pme. This is useful > in > > restricted

[gmx-users] simulation on 2 gpus

to run as fast as possible. I was wondering if some of you has experience of running on more than one gpu with several cores and can give some hints as starting point. Thanks Stefano -- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology Via P

Re: [gmx-users] rtx 2080 gpu

i Stefano, > > What was your compilation command? (it may be helpful to add SIMD > support appropriate to your processor > > http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support > ) > > Did you run make test after compiling? > > Benson > >

[gmx-users] rtx 2080 gpu

runtime: N/A NOTE: Detection of GPUs failed. The API reported: unknown error GROMACS cannot run tasks on a GPU. Does anyone have any suggestions? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Department of Drug Science and Technology

Re: [gmx-users] extra-bond

properly all the residues. Thanks again Stefano Il giorno sab 9 mar 2019 alle ore 22:58 Justin Lemkul ha scritto: > > > On 3/9/19 12:23 PM, Stefano Guglielmo wrote: > > Dear gromacs users, > > I have a system with a topology generated from Amber and then converted > >

Re: [gmx-users] info about gpus

Hi, > > > > > > It greatly depends what your use-case is, i.e. simulation system and > > > type of study (but if you want to scale I assume you want few longer > > > trajectories). > > > > > > Cheers, > > > -- > > > Szilárd > > >

[gmx-users] extra-bond

? Thanks in advance Stefano -- 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] info about gpus

-- 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.ava

[gmx-users] ndx file with frames

by, let's say, trjconv. Does anyone have any suggestions? Thanks in advance Stefano -- 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

Re: [gmx-users] fatal error with mpi

; > On Fri, Jun 22, 2018, 15:57 Stefano Guglielmo > wrote: > > > Thanks Mark. I must say that I tried reducing timestep (as low as 0.5 > fs-1) > > and temperature as well (5K both in NvT and NpT) but the simulation > crashed > > in any case with warning about cutoff

Re: [gmx-users] fatal error with mpi

ollisions > can be more violent than normal, and the timestep is now too large. But you > need to look at the trajectory to understand if this might be the case. > > Mark > > On Fri, Jun 22, 2018 at 3:19 PM Stefano Guglielmo < > stefano.guglie...@unito.it> wrote: >

Re: [gmx-users] fatal error with mpi

code bug. What version were you using? > > Mark > > On Thu, Jun 21, 2018 at 2:36 PM Stefano Guglielmo < > stefano.guglie...@unito.it> wrote: > > > Dear users, > > > > I have installed gromacs with MPI instead of its native tMPI and I am > > enco

[gmx-users] fatal error with mpi

em because the same system run with the native tMPI works properly (it has already been termalized and gradually equilibrated); neverthless I tried to reduce dt and temperature but without any benefit. Does anybody have any suggestions? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Assistant

Re: [gmx-users] opnempi

Thanks, I did it 2018-06-21 1:08 GMT+02:00 Benson Muite : > Hi, > > Might try using ccmake to get user interface and check variables are setup > correctly. > > Regards, > Benson > > On 06/21/2018 02:03 AM, Stefano Guglielmo wrote: > >> Dear gromacs users,

[gmx-users] opnempi

=/usr/lib64/openmpi/bin/mpicxx compilation and installation end up correctly, but when trying to run mdrun, gromacs still uses its own tMPI; how can I avoid tMPI and "force" to MPI? Thanks in advance Stefano -- Stefano GUGLIELMO PhD Assistant Professor of Medicinal Chemistry Departme

Re: [gmx-users] spatial restraints

> I think this is a minimal alteration to your topology. > > Regards, > Simon > > 在 2018年6月19日週二 08:17，Stefano Guglielmo 寫道： > > > Hello gromacs users, > > > > I would like to know if it is possible to add spatial restraints to a > > selected subgroup of

[gmx-users] spatial restraints

the atoms that should be restrained to the existing topology. Thanks in advance Stefano -- 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