[gmx-users] Dual Xeon workstation - starting one job/cpu
Jernej Zidar
jernej.zidar at gmail.com
Wed Mar 23 11:47:09 CET 2016
Hi Mark,
Thank you for the advice and the journal article! I'm studying the paper
now.
Best,
Jernej
On Wed, Mar 23, 2016 at 5:26 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
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> 1. Re: Error in installing Gromacs in Cygwin (Mark Abraham)
> 2. Re: Error in installing Gromacs in Cygwin (Mark Abraham)
> 3. Re: elastic restraints in MARTINI simulation (Mark Abraham)
> 4. Error in installing gromacs (ISHRAT JAHAN)
> 5. Re: elastic restraints in MARTINI simulation (James Starlight)
> 6. Re: Dual Xeon workstation - starting one job/cpu (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Mar 2016 08:36:16 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error in installing Gromacs in Cygwin
> Message-ID:
> <
> CAMNuMARJr2z7OBymH_EOabjdnMx4ozADs-dcPWmt1k8D39z8Pw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Don't know - we don't really support a Cygwin build any more. But you might
> need to source GMXRC properly, per install guide, or do a statically linked
> build of GROMACS.
>
> Mark
>
> On Wed, Mar 23, 2016 at 9:30 AM tasneem kausar <tasneemkausar12 at gmail.com>
> wrote:
>
> > Dear all
> > I have installed gromacs-5.1.2 in cygwin 64 bit computer. cmake have
> > finished successfully during installation. While executing the command
> > "cygcheck /usr/local/gromacs/bin/pdb2gmx.exe" it gives following error-
> > cygcheck: track_down: could not find cyggmx-6.dll
> >
> > cygcheck: track_down: could not find cyggmxpreprocess-6.dll
> >
> > Kindly provide the solution of this error.
> >
> >
> >
> > Thanks and Regards
> > --
> > 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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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 23 Mar 2016 08:36:16 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Error in installing Gromacs in Cygwin
> Message-ID:
> <
> CAMNuMARJr2z7OBymH_EOabjdnMx4ozADs-dcPWmt1k8D39z8Pw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Don't know - we don't really support a Cygwin build any more. But you might
> need to source GMXRC properly, per install guide, or do a statically linked
> build of GROMACS.
>
> Mark
>
> On Wed, Mar 23, 2016 at 9:30 AM tasneem kausar <tasneemkausar12 at gmail.com>
> wrote:
>
> > Dear all
> > I have installed gromacs-5.1.2 in cygwin 64 bit computer. cmake have
> > finished successfully during installation. While executing the command
> > "cygcheck /usr/local/gromacs/bin/pdb2gmx.exe" it gives following error-
> > cygcheck: track_down: could not find cyggmx-6.dll
> >
> > cygcheck: track_down: could not find cyggmxpreprocess-6.dll
> >
> > Kindly provide the solution of this error.
> >
> >
> >
> > Thanks and Regards
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 23 Mar 2016 08:37:13 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] elastic restraints in MARTINI simulation
> Message-ID:
> <
> CAMNuMARsvFpHyN6kq6LqYwO1FNSRDbbD9d0HOP8+qeH1Wbyw1g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Tsjerk, does it make sense to try to have grompp observe the particle
> density and guide the default of -rdd accordingly?
>
> Mark
>
> On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi James,
> >
> > Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
> > (especially if you use a larger time step, like 30 fs).
> >
> > Cheers,
> >
> > Tsjerk
> > On Mar 23, 2016 09:08, "James Starlight" <jmsstarlight at gmail.com> wrote:
> >
> > > Hello,
> > >
> > >
> > > I am trying to perform 2 MARTINI simulations of several membrane
> > > receptors within membrane i) with eldyn restrains applied on the
> > > protein tetriary structure and ii) unrestrained md. I have no problems
> > > in the i) case but in the ii) my simulation is very unstable under
> > > pruduction run- it begins OK after long period of equilibration but
> > > suddenly is crashed after 20-50ns of C run although I reduced the
> > > integration time-step twisely in comparison to restrained run (0.005
> > > vs 0.01)
> > >
> > > Fatal error:
> > > 1 of the 20932 bonded interactions could not be calculated because
> > > some atoms involved moved further apart than the multi-body cut-off
> > > distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see
> > > option -rdd, for pairs and tabulated bonds also see option -ddcheck
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > might another tricks be used here besides elastic restraints consisted
> > > of mostly of md simulation setups e.g switching to the another
> > > termostat (right now martini uses berendsen with gmx 4.5) e.g ussing
> > > of sd integraator instead7
> > >
> > > Thanks for help!
> > >
> > > James
> > > --
> > > 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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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 23 Mar 2016 14:11:21 +0530
> From: ISHRAT JAHAN <jishrat17 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error in installing gromacs
> Message-ID:
> <CA+NjHRkgyYmC2dxTrs=
> joP8Abn4MhUXAZy7tPBWMi+MW4Dx-yA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all
> I have installed gromacs on cygwin 64 bit computer and it has installed
> successfully but when i run the command -pdb2gmx.exe following error occued
>
> C:/cygwin64/usr/local/gromacs/bin/pdb2gmx.exe: error while loading shared
> libraries: cyggmxpreprocess-6.dll: cannot open shared object file: No such
> file or directory
> kindly resolve the above problem.
>
> Thanks and Regards.
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 23 Mar 2016 10:03:06 +0100
> From: James Starlight <jmsstarlight at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] elastic restraints in MARTINI simulation
> Message-ID:
> <
> CAALQopyzVWHtgU4ixdv7Tsq_g48xGjTQ1g8qe7_gtErB5L3srQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> OK, I will try now!
> May the error be related to big shift of the receptor within thw
> membrane plane due to the tranlational diffusion7
> I made vizualization of the trajectory in VMD and observed relatively
> big motion of the protein within membrane plane due to the tendency of
> the oligomerization of several subunits.
>
> 2016-03-23 9:37 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > Hi,
> >
> > Tsjerk, does it make sense to try to have grompp observe the particle
> > density and guide the default of -rdd accordingly?
> >
> > Mark
> >
> > On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
> >
> >> Hi James,
> >>
> >> Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
> >> (especially if you use a larger time step, like 30 fs).
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >> On Mar 23, 2016 09:08, "James Starlight" <jmsstarlight at gmail.com>
> wrote:
> >>
> >> > Hello,
> >> >
> >> >
> >> > I am trying to perform 2 MARTINI simulations of several membrane
> >> > receptors within membrane i) with eldyn restrains applied on the
> >> > protein tetriary structure and ii) unrestrained md. I have no problems
> >> > in the i) case but in the ii) my simulation is very unstable under
> >> > pruduction run- it begins OK after long period of equilibration but
> >> > suddenly is crashed after 20-50ns of C run although I reduced the
> >> > integration time-step twisely in comparison to restrained run (0.005
> >> > vs 0.01)
> >> >
> >> > Fatal error:
> >> > 1 of the 20932 bonded interactions could not be calculated because
> >> > some atoms involved moved further apart than the multi-body cut-off
> >> > distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see
> >> > option -rdd, for pairs and tabulated bonds also see option -ddcheck
> >> > For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> > website at http://www.gromacs.org/Documentation/Errors
> >> >
> >> > might another tricks be used here besides elastic restraints consisted
> >> > of mostly of md simulation setups e.g switching to the another
> >> > termostat (right now martini uses berendsen with gmx 4.5) e.g ussing
> >> > of sd integraator instead7
> >> >
> >> > Thanks for help!
> >> >
> >> > James
> >> > --
> >> > 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-request at 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-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
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> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 23 Mar 2016 09:24:55 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Dual Xeon workstation - starting one job/cpu
> Message-ID:
> <
> CAMNuMAQo4YNKijKqo+R6MGsSC0jxLHSjTtE0ijY9mdxFQYJeTw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You should take a look at
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/abstract for
> background information.
>
> On Wed, Mar 23, 2016 at 6:28 AM Jernej Zidar <jernej.zidar at gmail.com>
> wrote:
>
> > Hi,
> > Recently I received a dual Xeon ( 2x E5-2630v3) workstation with two
> > Tesla K40c cards.
> >
> > I'm now trying to figure out how to start one job/cpu.
> >
>
> The easy answer if you're running multiple identical simulations is to use
> gmx mdrun -multism (see
>
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-multi-simulations
> )
>
> For CPU1, this is not a problem:
> > gmx mdrun -v -deffnm test -gpu_id 0000 -ntomp 4 -pin on -maxh 0.15
> -nsteps
> > -1
> > #above starts a job on CPU1 with 4 MPI tasks and 4 OpenMP tthreads
> >
>
> How are you observing that? By default mdrun will spread those 16 threads
> over your 16 real cores.
>
> Fro CPU2, this is a bit more problematic because neither "-pinoffset" or
> > "-pinstride" make no difference. The second job appears to always start
> on
> > the CPU2.
> >
>
> I don't understand that, unless your machine is somehow observing that
> there are idle cores and placing the threads there.
>
>
> > I had some success running a job like this:
> > gmx mdrun -v -deffnm test2 -gpu_id 1111 -ntomp 4 -maxh 0.15 -nsteps -1
> > #above starts a job on CPU2 but without CPU pinning performance is poor
> >
> > How to overcome this? From the tests I've done so fare it is actually
> to
> > run two jobs that occupy one CPU each rather that a job that would occupy
> > both CPUs at the same time.
> > Is this even possible without resorting to OpenMPI?
> >
>
> Sure.
>
> gmx mdrun -gpu_id 0000 -pin on -pinoffset 0 -pinstride 1 -ntomp 4
> gmx mdrun -gpu_id 1111 -pin on -pinoffset 16 -pinstride 1 -ntomp 4
>
> but this guarantees the GPUs lie idle during the update and constraint
> phases. I expect that
>
> gmx mdrun -gpu_id 0011 -pin on -pinoffset 0 -pinstride 1 -ntomp 4
> gmx mdrun -gpu_id 0011 -pin on -pinoffset 16 -pinstride 1 -ntomp 4
>
> will give you better throughput, because the GPU tasks in the two mdruns
> will naturally run out of phase with each other, leading to higher
> utilization of each individual GPU.
>
> Mark
>
> Thanks,
> > Jernej Zidar
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
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