[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10
Rossen Apostolov
rossen at kth.se
Fri Feb 7 08:09:17 CET 2014
Hi William,
If you want to file a bug report you can do that at redmine.gromacs.org.
It seems that you are already registered, maybe twice:
wrww <http://redmine.gromacs.org/users/853/edit> Will Welch
wwelch000 at gmail.com <mailto:wwelch000 at gmail.com>
02/03/2014 11:33 PM
wwelch at wisc.edu <http://redmine.gromacs.org/users/164/edit> Will
empty wwelch at wisc.edu <mailto:wwelch at wisc.edu>
Do you have problems logging it?
Rossen
On 07/02/14 01:40, William Welch wrote:
> I'm not sure if I'm replying correctly, but I just wanted to mention that I
> would love to file a report to the redmine list, but I have not been
> approved to do so. Is there another place I can report this problem?
> Will
>
>
> On Mon, Feb 3, 2014 at 2:35 PM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
>> Send gromacs.org_gmx-users mailing list submissions to
>> gromacs.org_gmx-users at maillist.sys.kth.se
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or, via email, send a message with subject or body 'help' to
>> gromacs.org_gmx-users-request at maillist.sys.kth.se
>>
>> You can reach the person managing the list at
>> gromacs.org_gmx-users-owner at maillist.sys.kth.se
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: multiple GPU on multiple nodes (Szil?rd P?ll)
>> 2. Re: question (Thomas Piggot)
>> 3. Annealing doesn't work with Andersen thermostat? (William Welch)
>> 4. Re: Annealing doesn't work with Andersen thermostat?
>> (Michael Shirts)
>> 5. intel GPU acceleration? (Albert)
>> 6. Re: intel GPU acceleration? (Tamas Horvath)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 3 Feb 2014 20:36:30 +0100
>> From: Szil?rd P?ll <pall.szilard at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] multiple GPU on multiple nodes
>> Message-ID:
>> <
>> CANnYEw6u_34+0dXZTc5e-KM3+Uc6SKvLUw6pm53iH4AxZ97LDw at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> On Sat, Feb 1, 2014 at 12:06 AM, cyberjhon <cyberjhon at hotmail.com> wrote:
>>> Hi Szilard
>>>
>>> Thanks for your answer but I think that I did not make myself clear
>> enough
>>> I am trying to use 2 GPUs, each one in a different node.
>>> but it seems that gromacs only detects the one.
>> How do you know that it only detects one?
>>
>> The message which says "1 GPU detected on host nid00900:" does not
>> mean that only one GPU was detected. The log file is written on a
>> single rank (master rank = #0) and that's where you get the detection
>> output. The GPU setup is assumed to be homogenous across nodes, i.e.
>> if on node nid00900 you have one GPU and you run two PP ranks on it
>> (-gpu_id 00) this will mean that on another rank, e.g. nid00901, the
>> same setup will apply.
>>
>> Cheers,
>> --
>> Szil?rd
>>
>>> When I submit the job, I ask for two nodes, and the two nodes are being
>>> given.
>>> but the gromacs gpu version only is detecting one and one GPU.
>>>
>>> Do you know any way to make that it detects both nodes and therefore both
>>> GPUs ?
>>>
>>> Thanks
>>>
>>> John Michael
>>>
>>>
>>>
>>> --
>>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/multiple-GPU-on-multiple-nodes-tp5014085p5014203.html
>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>> --
>>> 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: 2
>> Date: Mon, 3 Feb 2014 19:38:03 +0000
>> From: Thomas Piggot <t.piggot at soton.ac.uk>
>> To: <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] question
>> Message-ID: <52EFF01B.2060801 at soton.ac.uk>
>> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>>
>> I guess the force field to use is a bit down to choice, however I would
>> say that there are several force fields which should not be used in this
>> case. There are several force fields/parameterisations that do not
>> behave well for these two types of lipids (e.g. many Berger based
>> parameters). As suggested, a thorough search through the literature is
>> really what you need to do (e.g. for PG
>> http://pubs.acs.org/doi/abs/10.1021/jp900645z ; for both (and apologies
>> for the self promotion) the supp info from
>> http://pubs.acs.org/doi/abs/10.1021/jp207013v and many more papers that
>> are out there). For making a choice between force fields you should
>> weigh up things like accuracy, speed of simulation, lipid diffusion
>> rates, inclusion of other components of your system (e.g. proteins,
>> etc.) and so on.
>>
>> Cheers
>>
>> Tom
>>
>> On 02/03/2014 07:06 PM, Justin Lemkul wrote:
>>>
>>> On 2/3/14, 2:03 PM, nafas wrote:
>>>> Hi
>>>> thanks for your help.
>>>> I think charmm force field imust use.but i dont know who can i found
>>>> its files ?
>>>>
>>> The full CHARMM36 force field in Gromacs format can be obtained from
>>> http://mackerell.umaryland.edu/CHARMM_ff_params.html.
>>>
>>> -Justin
>>>
>>>> On Monday, February 3, 2014 9:19 PM, Justin Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>
>>>>
>>>> On 2/3/14, 12:30 PM, nafas wrote:
>>>> > Hi
>>>> > I am tring with mixture pope/popg for simulatie membrane bacteria
>>>> that i use
>>>> of gromos53a6 force field.
>>>> > what force field should i use?charmm force field?
>>>> >
>>>>
>>>> What does your scrutiny of the literature tell you? Which force
>>>> field succeeds
>>>> in the most meaningful ways?
>>>>
>>>>
>>>> > in program have been used pope.itp ,popg.itp, .....files .
>>>> > I want to run grompp command but give afatall error:not found NH3L
>>>> atomtype.
>>>> > grompp -f minim.mdp -c ......gro -p ....top -o em.tpr
>>>> >
>>>> > I dont know what is problem?
>>>>
>>>>
>>>> You have not constructed the force field correctly. Without
>>>> significantly more
>>>> detail, there's nothing useful to suggest beyond a thorough read
>>>> through Chapter
>>>> 5 of the manual.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu
>>>> <mailto:jalemkul at outerbanks.umaryland.edu> |
>>>> (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>>
>>>> ==================================================
>>>>
>>>>
>> --
>> Dr Thomas Piggot
>> University of Southampton, UK.
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 3 Feb 2014 13:02:27 -0700
>> From: William Welch <wwelch000 at gmail.com>
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] Annealing doesn't work with Andersen thermostat?
>> Message-ID:
>> <
>> CAEy4365XycLRK+phHuin7jv1V96ps2++cg4xvh+cjae4v2O4+A at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>> I am doing some simulations on simple Lennard-Jones spheres and course
>> grained hydrocarbon models. I have been using the annealing utility
>> successfully until I switched from the V-rescale thermostat to the Andersen
>> thermostat. When I use the Andersen thermostat, the system gets to the
>> first temperature and then stays there. This does not happen if I switch to
>> a different thermostat. My guess is that Andersen not available with
>> annealing, at least in the version I'm using (4.6) , however I have not
>> been able to find any reference to that online or in the mailing list. Here
>> is one of the mdp files that produced a simulation that did not work. .
>>
>> title = 8pore
>> integrator = md-vv
>> dt = 0.003 ; ps !
>> nsteps = 2500000 ; total 7500 ps.
>> nstcomm = 1
>> nstxout = 2000
>> nstvout = 2000
>> nstfout = 0
>> nstlog = 100
>> nstenergy = 1
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.5
>> rcoulomb = 1.5
>> rvdw = 1.5
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = Andersen
>> tc-grps = LJ BL
>> tau_t = 0.1 0.1
>> ref_t = 230 230
>> ; Energy monitoring
>> energygrps = LJ BL
>> energygrp-excl = BL BL
>> freezegrps = BL
>> freezedim = Y Y Y
>> ; Isotropic pressure coupling is now on
>> ;Pcoupl = berendsen
>> ;Pcoupltype = isotropic
>> ;tau_p = 0.5
>> ;compressibility = 4.5e-5
>> ;ref_p = 1.0
>> annealing = single single
>> annealing-npoints = 20 20
>> annealing-time = 0 200 400 800 1200 1600 2000 2400 2800 3200 3600
>> 4000 4400 4800 5200 5600 6000 6400 6800 7200 0 200 400 800 1200 1600 2000
>> 2400 2800 3200 3600 4000 4400 4800 5200 5600 6000 6400 6800 7200
>> annealing-temp = 100 200 230 240 250 260 270 280 290 300 310 320 330
>> 340 350 360 370 380 390 400 100 200 230 240 250 260 270 280 290 300 310 320
>> 330 340 350 360 370 380 390 400
>> ;Generate velocites is off at 300 K.
>> gen_vel = yes
>> gen_temp = 230.0
>> ;gen_seed = 173529
>>
>> Velocities are generated at 230 (which is kind of strange, but changing
>> that doesn't do anything) and the system cools to 100K and then stays
>> there. The output in the md.log file shows that the correct ref_t is being
>> read, but the actual temperature of the system does not increase. The same
>> input using the md integrator and the V-rescaling thermostat does what it's
>> supposed to.
>> Will
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 3 Feb 2014 15:52:06 -0500
>> From: Michael Shirts <mrshirts at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Annealing doesn't work with Andersen
>> thermostat?
>> Message-ID:
>> <CA+zJb=gfrqK9WDBgFvw2Hy6mhba5=
>> 484nxW+d4v1Vf6ifE6PyA at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi, William-
>>
>> Interesting. There's too many conditionals with the current patchwork
>> of temperature control methods, so there is an ongoing (though too
>> slow) effort to reorganize the algorithms to eliminate such errors as
>> this.
>>
>> For a medium-term solution, I'd suggest filing a redmine issue
>> (redmine.gromacs.org) on this error so that it gets fixed for the next
>> round of update.
>>
>> In the short-term, if you are interested in introducing stochasticness
>> into the annealing, I'd suggest using the sd integrator for now.
>>
>> On Mon, Feb 3, 2014 at 3:02 PM, William Welch <wwelch000 at gmail.com> wrote:
>>> Hi,
>>> I am doing some simulations on simple Lennard-Jones spheres and course
>>> grained hydrocarbon models. I have been using the annealing utility
>>> successfully until I switched from the V-rescale thermostat to the
>> Andersen
>>> thermostat. When I use the Andersen thermostat, the system gets to the
>>> first temperature and then stays there. This does not happen if I switch
>> to
>>> a different thermostat. My guess is that Andersen not available with
>>> annealing, at least in the version I'm using (4.6) , however I have not
>>> been able to find any reference to that online or in the mailing list.
>> Here
>>> is one of the mdp files that produced a simulation that did not work. .
>>>
>>> title = 8pore
>>> integrator = md-vv
>>> dt = 0.003 ; ps !
>>> nsteps = 2500000 ; total 7500 ps.
>>> nstcomm = 1
>>> nstxout = 2000
>>> nstvout = 2000
>>> nstfout = 0
>>> nstlog = 100
>>> nstenergy = 1
>>> nstlist = 10
>>> ns_type = grid
>>> rlist = 1.5
>>> rcoulomb = 1.5
>>> rvdw = 1.5
>>> ; Berendsen temperature coupling is on in two groups
>>> Tcoupl = Andersen
>>> tc-grps = LJ BL
>>> tau_t = 0.1 0.1
>>> ref_t = 230 230
>>> ; Energy monitoring
>>> energygrps = LJ BL
>>> energygrp-excl = BL BL
>>> freezegrps = BL
>>> freezedim = Y Y Y
>>> ; Isotropic pressure coupling is now on
>>> ;Pcoupl = berendsen
>>> ;Pcoupltype = isotropic
>>> ;tau_p = 0.5
>>> ;compressibility = 4.5e-5
>>> ;ref_p = 1.0
>>> annealing = single single
>>> annealing-npoints = 20 20
>>> annealing-time = 0 200 400 800 1200 1600 2000 2400 2800 3200 3600
>>> 4000 4400 4800 5200 5600 6000 6400 6800 7200 0 200 400 800 1200 1600
>> 2000
>>> 2400 2800 3200 3600 4000 4400 4800 5200 5600 6000 6400 6800 7200
>>> annealing-temp = 100 200 230 240 250 260 270 280 290 300 310 320
>> 330
>>> 340 350 360 370 380 390 400 100 200 230 240 250 260 270 280 290 300 310
>> 320
>>> 330 340 350 360 370 380 390 400
>>> ;Generate velocites is off at 300 K.
>>> gen_vel = yes
>>> gen_temp = 230.0
>>> ;gen_seed = 173529
>>>
>>> Velocities are generated at 230 (which is kind of strange, but changing
>>> that doesn't do anything) and the system cools to 100K and then stays
>>> there. The output in the md.log file shows that the correct ref_t is
>> being
>>> read, but the actual temperature of the system does not increase. The
>> same
>>> input using the md integrator and the V-rescaling thermostat does what
>> it's
>>> supposed to.
>>> Will
>>> --
>>> 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: 5
>> Date: Mon, 3 Feb 2014 21:56:25 +0100
>> From: Albert <mailmd2011 at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: [gmx-users] intel GPU acceleration?
>> Message-ID:
>> <
>> CAO2eAcuOpzoBv4kaVmw5EbZVaC2xhUc_pRRxq9vvipXU1N-qqw at mail.gmail.com>
>> Content-Type: text/plain; charset=GB2312
>>
>> Hello?
>>
>> I noticed that Intel also have GPU such as: Intel(R) Xeon Phi(tm)
>> coprocessor
>> 3120A. I am just wondering is the latest version of Gromacs support such
>> kind of GPU calculation?
>>
>> thank you very much.
>>
>> Albert
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Mon, 3 Feb 2014 22:35:27 +0100
>> From: Tamas Horvath <hotafin at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] intel GPU acceleration?
>> Message-ID:
>> <
>> CAFNqVghxugeG88aLb549vsQmcv_yy7AmELOB8cngxtXt67r9Vg at mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> It's actually more like a cluster on a card than a gpu. It has x86 cores
>> (albeit very simple ones). Theoretically any x86 code compiled with the
>> xeon phi compiler can run on it without any further modification, though
>> further optimizations are possible.
>>
>>
>> On 3 February 2014 21:56, Albert <mailmd2011 at gmail.com> wrote:
>>
>>> Hello?
>>>
>>> I noticed that Intel also have GPU such as: Intel(R) Xeon Phi(tm)
>>> coprocessor
>>> 3120A. I am just wondering is the latest version of Gromacs support such
>>> kind of GPU calculation?
>>>
>>> thank you very much.
>>>
>>> Albert
>>> --
>>> 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.
>>
>>
>> End of gromacs.org_gmx-users Digest, Vol 118, Issue 10
>> ******************************************************
>>
More information about the gromacs.org_gmx-users
mailing list