[gmx-users] Ree: Gromacs: Cloud Vs. Boinc Server

lloyd riggs lloyd.riggs at gmx.ch
Fri Oct 14 12:02:49 CEST 2011


You right (gromacs). and your right (50 not 500 Gf), just a quick response.

No you need the funky aluminum coupled fans, especially if you use more than one for anything (graphics or other).  The ATI's get really hot, for real I have used them for other things from graphics to cheese.

I have tested them with the freeware on scientific computing so they do run around that speed, as there supposed too.  In addition, CUDA and OpenCL are supposed to be merging (or more specifically CUDA is supposed to be going to OpenCL instead of a platform/device specific code simply for product based competition rather than logical application, according to online CUDA publications circa over a year or 2 old).

As only mdrun and a couple core modules work, it prbably wouldn't be too hard to convert the modules to pure openCL with one of the online porting/language tables for CUDA Vs. OpenCL.  That or the OpenMPI version.

Software I am targetting, well I started writting something when OpenCL just came out which was an extension on automated/rational drug design and protein design, in the hopes to get out of an economic hole, and then all the sudden was finally allowed to attend a PhD program, so put it off for a year or 4.

Besides, I am sure you know the price differences for ATI Vs. Nvidia ( Nvidia being 3 times the price of an ATI GPU).

Anhd when I do specific things, such as massive docking, gromacs, etc...I usually look mostly at the usage stats, including time which in the end is the most important thing.

Thank you for the advice, points.  I was just trying to point out to the origional posting what is available, off the top of my head.

For gromacs I use a cluster system at the Uni.

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Wed, 12 Oct 2011 18:23:50 +0200 (CEST)
> Von: gmx-users-request at gromacs.org
> An: gmx-users at gromacs.org
> Betreff: gmx-users Digest, Vol 90, Issue 48

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> Today's Topics:
> 
>    1. Re: Gromacs: Cloud Vs. Boinc Server? (Szil?rd P?ll)
>    2. Uniform Distribution of drug molecules inside water	spc216
>       (meisam valizadeh kiamahalleh)
>    3. Potential Energy Landscape (Natalie Stephenson)
>    4. Re: FEP (Fabian Casteblanco)
>    5. Re: Uniform Distribution of drug molecules inside water
>       spc216 (Justin A. Lemkul)
>    6. Re: Gromacs: Cloud Vs. Boinc Server? (Matt Larson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 12 Oct 2011 16:54:23 +0200
> From: Szil?rd P?ll <szilard.pall at cbr.su.se>
> Subject: Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CANnYEw5UQLKo2SFEzW9Z0JZDJv9qDUc6zjLBR0=F6hXX8uCLcg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear Stephan,
> 
> > Radeons work as well.  You can put a 3-4 GPU board together with the
> highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a
> day or two, but the cooling is the main problem (with 1/4 the price radeons
> Vs. GTI cards), so one has to take cooling into account (h20 cost another
> 800$, or investing in 4-6 good fans/cooling an additional 2-300$).  If you
> have a slightly higher budget you can get multi CPU boards with 4 GPU
> slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's is
> where the money is spent.
> 
> No, Radeons don't work and won't work in the near future - Gromacs
> doesn't support OpenCL. Cooling needs attention, but in reality it's
> nowhere near $2-300 extra - unless you want the fans with funky leds.
> 
> Btw, what software is the above hardware description targeting? To me
> it sounds more like a gaming rig and not something specifically aiming
> at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
> released).
> 
> > As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon
> 5900 series (double percission, single is supposed to run around 4 tera
> flops per GPU, so depends on your needs, desires as far as simulations), and
> the latest Intel 970's are around 400-500 Gflops/chip.
> 
> Again, I might be missing something, but how exactly does Gromacs run
> on Radeons? I assume when referring to the i7 970 (?) above you meant
> 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
> that Flops are not every useful, what matters is time to solution for
> the specific problem one wants to solve.
> 
> Cheers,
> --
> Szilárd
> 
> > --
> > NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
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> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 12 Oct 2011 23:13:50 +0800
> From: meisam valizadeh kiamahalleh <meisam488 at gmail.com>
> Subject: [gmx-users] Uniform Distribution of drug molecules inside
> 	water	spc216
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAOh12OE-Tibc2uXkp5oRQGOEBnTuC0yKWLqA7cKhwBODOnSO=A at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear GMX users
> Good day to you
> I have some drug molecules (cisplatin) added manually and randomly inside
> a
> system which is going to be solvated in spc216 water.  I used genbox
> command
> to add the correct number of water molecules needed to solvate the box.
> The
> drug molecules are located very closed to each other. Kindly, would you
> please let me know how I can distribute drug molecules uniformly among the
> water molecoules to obtain a certain concentration of the drug? May I know
> if there is any specific tool or script which can help me to do it?
> Thank you very much
> Kind regards
> Meisam
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> ------------------------------
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> Message: 3
> Date: Wed, 12 Oct 2011 15:34:29 +0000
> From: Natalie Stephenson
> 	<Natalie.Stephenson at postgrad.manchester.ac.uk>
> Subject: [gmx-users] Potential Energy Landscape
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> 	<037BC2AE05ACF5459BEC1ACBFC4D9142067055 at MBXP06.ds.man.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> I was recently told in passing that it would be possible to construct a
> 'potential energy landscape' from the simulations I have performed.  This way
> I could remove any loading rate differences between simulations and
> experimental force experiments I've been performing ... however I cannot find
> anywhere in which this is mentioned.
> 
> The only thing close I could find that was close was the free energy
> landscape using g_anaeig under the Dihedral PCA
> (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure
> this is what I'm looking for.
> 
> Does anyone know where I would be able to find out / read more about how
> to create potential energy landscapes from my simulation outputs?
> 
> Thanks
> Natalie
> 
> 
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> ------------------------------
> 
> Message: 4
> Date: Wed, 12 Oct 2011 11:38:34 -0400
> From: Fabian Casteblanco <fabian.casteblanco at gmail.com>
> Subject: [gmx-users] Re: FEP
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAG3KNbhgx13-jQJ0Jv9364t9yEuBK-o3xcXidWTJ8N51VvQ_FA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello Michael or others,
> 
> It seems I'm still getting errors when doing a FEP on a molecule (a
> -CH3 to a -H).  This below is for when I was charging things from a -H
> uncharged to -H charged, although it also happens when I'm actually
> converting the -CH3 to -H (at Lambdas greater than 85%).  I made sure
> to keep the charges balanced at 0 while mutating and I did it at 3
> steps like Michael Shirts suggested.
> 
> Set 1: turn R-CH3 charges off in a way that preserves the total charge.
> Set 2: change CH3 LJ to H LJ
> Set 3: Turn R-H charges on in a way that preserves the total charge.
> 
> In the portion of the error below atom 9 is -C9-(H67,H68,H66) which in
> this specific case H67 is already a dummy molecule with no mass or
> charge.  From what I can see, it seems that the atoms do not know how
> to treat the dummy molecules in terms of angles.  How should I treat
> the dummy molecules? Should I be treating them like hollow spheres
> with no charge so I would assign them angle constraints?
> 
> I think it can also be that I'm peturbing the dihedral angles
> incorrectly.  I received errors at first saying that dihedral
> multiplicities can't be peturbed so I had to equal the multiplicities
> just to get it to run.  Does anybody have any experience with this?
> 
> Thank you for your help.
> 
> -Fabian Casteblanco
> 
> Portion of Error Output:
> -----------------------------------------------------------------
> Reading file nvt0.5.tpr, VERSION 4.5.3 (single precision)
> starting mdrun 'SIMVASTATIN'
> 150000 steps,    300.0 ps.
> 
> Step 7, time 0.014 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.006111, max 0.139443 (between atoms 9 and 67)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 
> Step 8, time 0.016 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.007341, max 0.167622 (between atoms 9 and 67)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 
> Step 8, time 0.016 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.008771, max 0.201182 (between atoms 9 and 67)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 
> 
> 
> 
> 
> 
> 
> On Mon, Oct 10, 2011 at 4:10 PM, Fabian Casteblanco
> <fabian.casteblanco at gmail.com> wrote:
> > Hi all,
> >
> > I have an additional question related to what Steven Neumann was
> > mentioning.  I actually have to do a molecule mutation.  I'm trying to
> > use Michael Shirts method  1) making small
> > changes 'alchemical' changes in the molecules and computing the free
> > energies by any method (BAR, TI, etc).  I'm specifically want to try
> > to use BAR at the end once I collect all the data.  This helped a lot
> > on clarification since it seemed that Justin's tutorial is essentially
> > a FEP except its using the BAR mathematical method for computing the
> > complete decoupling of the molecule rather than using the old FEP
> > mathematics of the exponential averaging formula.  So BAR is only
> > referring to the mathematical code used to calculate the overall free
> > energy for the FEP, correct?
> >
> > My question is, for a mutation of a -CH3 group to a -H group, is it
> > better to simply run:
> > [+ from (Lambda=0 ,  R-CH3, full charges and interactions -STATE A)
> > --> (Lambda=1, R-CH, full charges and interactions -STATE B)]
> >
> > OR
> >
> > [1) from (Lambda=0 ,  R-CH3, STATE A : Charges and LJ Interactions: ON)
> > 2)  (Lambda=?, -CH3 Charges: OFF ,LJ Interactions: ON and unmutated)
> > 3)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ Interactions: OFF)
> > 4)  (Lambda=?, R-CH3, -CH3 Charges: OFF ,LJ interactions: ON and
> Mutated to -H)
> > 5)  (Lambda=1, R-CH3, -CH3  STATE B : Charges and LJ Interactions: ON)
> >
> > Reason I'm asking is because when I try the first choice to do it
> > STATE A to STATE B in one step, when I reach Lambda=0.85 and above on
> > the NVT equilibration right after EM, I receive errors saying that
> > bonds are moving way to far off their constraints which leads me to
> > believe that the system is moving too far from where it was energy
> > minimized.  Errors such as:
> >
> > Step 188, time 0.376 (ps)
> > LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.000017, max 0.000636 (between atoms 9 and 68)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >      9     68   31.2    0.1111   0.1110      0.1111
> >
> > Step 188, time 0.376 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 0.000015, max 0.000531 (between atoms 9 and 68)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >      9     68   31.0    0.1111   0.1110      0.1111
> >
> >
> > **Please, if anybody can help, I would greatly appreciate it.  Thanks.
> > --
> > Best regards,
> >
> > Fabian F. Casteblanco
> > Rutgers University --
> > Chemical Engineering
> > C: +908 917 0723
> > E:  fabian.casteblanco at gmail.com
> >
> 
> 
> 
> -- 
> Best regards,
> 
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E:  fabian.casteblanco at gmail.com
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 12 Oct 2011 11:57:47 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Uniform Distribution of drug molecules inside
> 	water	spc216
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E95B8FB.5050602 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> meisam valizadeh kiamahalleh wrote:
> > Dear GMX users
> > Good day to you
> > I have some drug molecules (cisplatin) added manually and 
> > randomly inside a system which is going to be solvated in spc216 water. 
> >  I used genbox command to add the correct number of water molecules 
> > needed to solvate the box. The drug molecules are located very closed to
> > each other. Kindly, would you please let me know how I can distribute 
> > drug molecules uniformly among the water molecoules to obtain a 
> > certain concentration of the drug? May I know if there is any specific 
> > tool or script which can help me to do it?
> 
> I don't know how you did the initial insertion, but genbox -ci -nmol will
> add 
> molecules randomly, after which you can solvate with water.  Don't combine
> these 
> steps.  Do the insertion, then add the water.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Wed, 12 Oct 2011 11:23:21 -0500
> From: Matt Larson <larsonmattr at gmail.com>
> Subject: Re: [gmx-users] Gromacs: Cloud Vs. Boinc Server?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CAFrQctPvxkJrc_sFB6JH_WjOSMMREAyTJMrE940Fu0nabhddhA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> >From the Gromacs on GPU page
> (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs)
> 
> These are the compatible GPU cards (Basically buy NVidia for now):
> 
> v2.0
> Compatible NVIDIA CUDA versions (also see OpenMM version compatibility
> above):
> 
> v3.x
> Compatible hardware (for details consult the NVIDIA CUDA GPUs list):
> 
> G92/G94:
> GeForce 9800 GX2/GTX/GTX+/GT
> GeForce 9800M GT
> GeForce GTS 150, 250
> GeForce GTX 280M, 285M
> Quadro FX 4700
> Quadro Plex 2100 D4
> GT200:
> GeForce GTX 260, 270, 280, 285, 295
> Tesla C1060, S1070, M1060
> Quadro FX 4800, 5800
> Quadro CX
> Quadro Plex 2200 D2, 2200 S4
> GF1xx (Fermi)
> GeForce GTX 460, 465, 470, 480, 570, 580
> Tesla C2050, C2070, M2050, M2070
> 
> ---
> 
>  I got an EVGA Geforce GTX 580, which is about $450 for trying out GPU
> based MD, and has 512 GPU cores and a high clock rate, 1.5 gigs of
> memory.  Having more cores and more memory are both important things
> for the GPU side of molecular dynamics (cores = more parallel, memory
> = more atoms and less memory transferring).  I think you have some
> limitations with the GPU sims, like atoms < 100,000.  It is amazing
> that with implicit solvent you can really see a huge benefit and
> perhaps that might open some new doors.
> 
> -Matt Larson
> 
> 
> On Wed, Oct 12, 2011 at 9:54 AM, Szilárd Páll <szilard.pall at cbr.su.se>
> wrote:
> > Dear Stephan,
> >
> >> Radeons work as well.  You can put a 3-4 GPU board together with the
> highest end AMD or Intel chip for 3K, plus 16G RAM if you look around for a
> day or two, but the cooling is the main problem (with 1/4 the price radeons
> Vs. GTI cards), so one has to take cooling into account (h20 cost another
> 800$, or investing in 4-6 good fans/cooling an additional 2-300$).  If you
> have a slightly higher budget you can get multi CPU boards with 4 GPU
> slots, ie 4 or 8 CPU's (direct via mail from Taiwan), but the CPU's and GPU's
> is where the money is spent.
> >
> > No, Radeons don't work and won't work in the near future - Gromacs
> > doesn't support OpenCL. Cooling needs attention, but in reality it's
> > nowhere near $2-300 extra - unless you want the fans with funky leds.
> >
> > Btw, what software is the above hardware description targeting? To me
> > it sounds more like a gaming rig and not something specifically aiming
> > at maximum performance with Gromacs 4.5 (nor 4.6 which is yet to be
> > released).
> >
> >> As far as I have seen GPU Gromacs runs at around 1 Teraflop per Radeon
> 5900 series (double percission, single is supposed to run around 4 tera
> flops per GPU, so depends on your needs, desires as far as simulations), and
> the latest Intel 970's are around 400-500 Gflops/chip.
> >
> > Again, I might be missing something, but how exactly does Gromacs run
> > on Radeons? I assume when referring to the i7 970 (?) above you meant
> > 40-50 GFlops/chip - the i7 970 should have 70 GFlops peak. Also note
> > that Flops are not every useful, what matters is time to solution for
> > the specific problem one wants to solve.
> >
> > Cheers,
> > --
> > Szilárd
> >
> >> --
> >> NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
> >> Jetzt informieren: http://www.gmx.net/de/go/freephone
> >> --
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> 
> 
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> 
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> *****************************************

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