This might help even more:
Go into gpu.cpp, and look for this line:
gpu->sim.randomSteps = MAX_RANDOM_STEPS;
Change to:
gpu->sim.randomSteps = MAX_RANDOM_STEPS / 2;
recompile...
On Sat, Aug 20, 2011 at 6:20 PM, filip fratev <filipfratev.yahoo.com> wrote:
> Hi Scott,
> >Don't believe me? Try this "nvidia-smi -q -a". With a 3.2 driver and
> toolkit, this will indicate that the system eats ~190 MB on a 32-bit OS
> and ~250 MB on a 64-bit OS. In contrast, a non-display GPU only loses
> about 10 MB
>
> I believe you because I tried "nvidia-smi -a" too and examined which option
> has the most important impact for the memory. My system eats about 230MB
> for display, thus I changed to another card, as you suggested. I will get
> some 50$ cards for the other PC's. I found out that I was able to run your
> benchmarks because you use ntt=1 instead of ntt=3 or 2 as in my inputs. This
> was the most important factor! If you use ntt=3 I have only 75MB free memory
> per one 1.5GB GPU core (it is the same with ntt=2), but using ntt=1 about
> 320MB !! NVT needs of more memory 138MB against 75MB for NPT. In the case of
> MPI run (ntt=1) I obtained 94MB for core 1 versus 333MB for the second.
> Factor IX NVE bench eats 1360MB i.e.138MB free memory. According to these
> results the people with GTX570, 470 and so on can profit from the new and
> really fast code only for smaller systems.
>
> Thus, if I want to simulate my systems with my previous parameters,and
> probably the most common, my limitation is 90K atoms (For the standard
> versions of GTX580 and GTX590). This means that I have to use only 8A water
> buffer. However, with ntt=1 will be much more. I will check this tomorrow.
>
>
>
> Hope that above will be helpful.
> Scott, thanks for that discussion and help!
>
>
> All the best,
> Filip
>
>
>
>
>
>
> ________________________________
> From: Scott Le Grand <varelse2005.gmail.com>
> To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Sunday, August 21, 2011 2:04 AM
> Subject: Re: [AMBER] Major GPU Update Released
>
>
> I already told you what to do: stop using the GTX 580 as your display
> device.
>
> I just checked out what the effect of doing so is: you'll get back about
> 200 MB. This should be enough to run your system. I would guess this is
> the difference between yours and Ross's results. My main work system has a
> $50 CUDA 1.1 display GPU with 512 MB for this very reason.
>
> Don't believe me? Try this "nvidia-smi -q -a". With a 3.2 driver and
> toolkit, this will indicate that the system eats ~190 MB on a 32-bit OS and
> ~250 MB on a 64-bit OS. In contrast, a non-display GPU only loses about 10
> MB.
>
> So why did this work before for you? First, performance costs memory.
> This is a massively parallel calculation and it needs lots of memory to keep
> the threads in the GPU from colliding into each other. Remember, one $500
> GTX 580 performs on par with a $20,000 PC cluster. And that PC cluster will
> need far more than 3 GB to keep up. It's the calculation itself that needs
> space. I've nearly doubled performance and upped memory usage maybe 30%.
> That's just how the cookie crumbles.
>
> Further, AMBER is in some ways a victim of its own success. As more and
> more previous corner cases go mainstream, I have had to write more and more
> custom kernels to handle these cases in a combinatorial kernel compilation
> conundrum. It appears the CUDA runtime loads *all* of them into GPU memory
> upon initialization. This is a fixed cost regardless of system size and
> it's not possible to calculate how much because it's all under the hood.
> This is why a 3 GB GTX 580 can run cellulose and your 1.5 GB GTX 580 is now
> stuck stuck in the mud.
>
> All that said, I'm happy to hire myself out as a professional AMBER
> consultant to build you a special version of AMBER for your specific cases
> with all the offending kernels removed at my usual consulting rate (whatever
> the heck that is but it's probably a lot more than buying yourself a $50
> display GPU or running your machine headless).
>
> Scott
>
>
>
>
>
> On Sat, Aug 20, 2011 at 2:15 PM, filip fratev <filipfratev.yahoo.com>
> wrote:
>
> Farid,
> >It look obvious yes, but can you EXPLAIN how Ross performed Factor IX
> benchmark (90K atoms) using GTX295 ( 896MB per GPU, i.e. nearly 2x less
> )???
> >I can perform in a "realistic" case only about 80K atoms. Thus, if it is
> so obvious, please explain me the above and provide some useful tricks/guide
> how and what must be done before pmemd.cuda to be used.....
> >
> >This is of course not ONLY for you!
> >
> >Filip
> >
> >
> >
> >
> >________________________________
> >From: "Ismail, Mohd F." <farid.ou.edu>
> >
> >To: filip fratev <filipfratev.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> >Sent: Saturday, August 20, 2011 9:13 PM
> >
> >Subject: RE: [AMBER] Major GPU Update Released
> >
> >Filip,
> >
> >I think it's obvious, that the new optimization uses more GPU memory than
> the older code. That's why you were getting the out of memory error with
> 1.5GB, and no error with 3GB GPU RAM. You might need to use a smaller
> system with the GTX590 or just use the 580 only for the bigger system that
> you have.
> >
> >
> >--Farid
> >
> >________________________________________
> >From: filip fratev [filipfratev.yahoo.com]
> >Sent: Saturday, August 20, 2011 12:32 PM
> >To: Ross Walker
> >Cc: AMBER Mailing List
> >Subject: Re: [AMBER] Major GPU Update Released
> >
> >Hi Ross,
> >Thanks for your guide. However, as I wrote in my last post, something
> going
> >wrong with cuda.MPI even with 89K atoms. Because, there were no problems
> with the older code and the same input files and settings, I thing and
> >report that it could be
> >some bug. Indeed it could be also something in my settings. I have no
> >problems with Factor IX bench, but the system was very well
> >equilibrated, thus this is another indication.
> >
> >Because you have at least 2 GTX580 with 1.5GB memory could you test
> please, when you have time, whats going wrong?
> >
> >If some one other can try/help (I saw that there are a lot of people with
> GTX590 and GTX580's) I will be very tankful!
> >
> >All the best,
> >Filip
> >
> >
> >________________________________
> >From: Ross Walker <ross.rosswalker.co.uk>
> >To: 'filip fratev' <filipfratev.yahoo.com>; 'AMBER Mailing List' <
> amber.ambermd.org>
> >Sent: Saturday, August 20, 2011 6:40 PM
> >Subject: RE: [AMBER] Major GPU Update Released
> >
> >Hi Filip.
> >
> >Unfortunately some of the new optimizations come at the expense of memory.
> The GPU memory in use is a lower bounds on the amount of memory being used,
> the actual amount may be higher and can change during a run if density
> changes etc. You could switch to NVT which will use less memory. Also using
> things like the Berendsen thermostat should use less memory than langevin.
> Finally avoiding the use of restraints (which always seemed a little bogus
> to me in NPT simulations anyway) could also help reduce memory usage.
> >
> >You could also ensure that your machine is in runlevel 3 so that no X
> server is running and also try it from a fresh boot into runlevel 3 since it
> is possible there are memory leaks in some of the graphics drivers.
> >
> >All the best
> >Ross
> >
> >> -----Original Message-----
> >> From: filip fratev [mailto:filipfratev.yahoo.com]
> >> Sent: Saturday, August 20, 2011 7:17 AM
> >> To: filip fratev; AMBER Mailing List
> >> Subject: Re: [AMBER] Major GPU Update Released
> >>
> >> Hi Scott and Ross,
> >>
> >> > For NPT:
> >> > | GPU memory information:
> >> > | KB of GPU memory in use: 882413
> >> > | KB of CPU memory in use: 104090
> >> >
> >> >
> >> > | GPU memory information:
> >> > | KB of GPU memory in use: 1006146
> >> > | KB of CPU memory in use: 99724
> >>
> >> So, the above values are from the older code and for the new are about
> >> 2x more? Just to be clear.
> >>
> >>
> >> Indeed that the update is great! I've wrote about that! Just need some
> >> more information and help.
> >>
> >>
> >> Regards,
> >> Filip
> >>
> >>
> >>
> >>
> >>
> >> ________________________________
> >> From: filip fratev <filipfratev.yahoo.com>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Sent: Saturday, August 20, 2011 5:02 PM
> >> Subject: Re: [AMBER] Major GPU Update Released
> >>
> >> I performed some tests last night.
> >> All were NPT simulations. The test system was AMD 1090T.3.9Ghz, GTX590
> >> (Asus) and 3GB GTX580 (Palit). Suse11.3.
> >>
> >>
> >> JAC:
> >> GTX590 1GPU= 32.61 ns/day
> >>
> >> GTX590 2GPU =42.19 ns/day
> >>
> >> GTX580 1GPU= 40.73 ns/day
> >>
> >> GTX580 plus GTX590=50.21 ns/day
> >>
> >> Factor IX:
> >> GTX590 1GPU= 9.54 ns/day
> >>
> >> GTX590 2GPU =12.24 ns/day
> >>
> >> GTX580 1GPU= 11.72 ns/day
> >>
> >> GTX580 plus GTX590=14.69 ns/day
> >>
> >> Cellulose:
> >> GTX580 (3GB) =2.67 ns/day
> >>
> >>
> >>
> >> Regards,
> >> Filip
> >>
> >> P.S. My 1.5GB memory issue was still not solved...I will reduce waters
> >> from 12A to 10A. Not good but seems the only way for now...hope to
> >> work...
> >>
> >>
> >>
> >>
> >>
> >>
> >> ________________________________
> >> From: Levi Pierce <levipierce.gmail.com>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Sent: Saturday, August 20, 2011 10:20 AM
> >> Subject: Re: [AMBER] Major GPU Update Released
> >>
> >> Had a chance to sit down and test out the new patch. Wow! Very
> >> impressive performance boost on a variety of systems I have been
> >> running
> >> pmemd.cuda on. Great work!
> >>
> >> On Fri, Aug 19, 2011 at 4:37 PM, Scott Le Grand
> >> <varelse2005.gmail.com>wrote:
> >>
> >> > Use a different gpu foe display I suspect
> >> > On Aug 19, 2011 4:09 PM, "filip fratev" <filipfratev.yahoo.com>
> >> wrote:
> >> > > Hi Ross,
> >> > > I compiled the new code and performed many tests and the results
> >> are
> >> > really impressive! I will post later.
> >> > >
> >> > > However, I am in a big trouble with my systems (116K atoms) and
> >> hope that
> >> > you will be able to help me.
> >> > > The problem is that with the new code I am not able to simulate
> >> these
> >> > proteins (116K) with GTX590 (1.5GB per core), because of some memory
> >> > issue/bug:
> >> > > cudaMalloc GpuBuffer::Allocate failed out of memory
> >> > >
> >> > > With the older code I had no any problems with same input files and
> >> > configuration. I tried both NPT and NVT but the same problem...
> >> > > Then I use GTX580 3GB and it works fine. From output you can see
> >> that the
> >> > requested memory is just 882MB:
> >> > > For NPT:
> >> > > | GPU memory information:
> >> > > | KB of GPU memory in use: 882413
> >> > > | KB of CPU memory in use: 104090
> >> > >
> >> > > and for restrained NVT:
> >> > >
> >> > > | GPU memory information:
> >> > > | KB of GPU memory in use: 1006146
> >> > > | KB of CPU memory in use: 99724
> >> > > Thus I shouldn’t have any problem.
> >> > >
> >> > > What could be the issue and how I can solve it?
> >> > >
> >> > > Regards,
> >> > > Filip
> >> > >
> >> > > Below is the output file (my NPT density.out) and heat.in:
> >> > >
> >> > > -------------------------------------------------------
> >> > > Amber 11 SANDER 2010
> >> > > -------------------------------------------------------
> >> > >
> >> > > | PMEMD implementation of SANDER, Release 11
> >> > >
> >> > > | Run on 08/20/2011 at 01:42:20
> >> > >
> >> > > [-O]verwriting output
> >> > >
> >> > > File Assignments:
> >> > > | MDIN:
> >> > densityF.in
> >> > > | MDOUT:
> >> > 0densitytest580Karti.out
> >> > > | INPCRD:
> >> > heattest.rst
> >> > > | PARM:
> >> > MyosinWT.prmtop
> >> > > | RESTRT:
> >> > density1test.rst
> >> > > | REFC:
> >> > heattest.rst
> >> > > | MDVEL:
> >> > mdvel
> >> > > | MDEN:
> >> > mden
> >> > > | MDCRD:
> >> > density1test.mdcrd
> >> > > | MDINFO:
> >> > mdinfo
> >> > >
> >> > >
> >> > > Here is the input file:
> >> > >
> >> > > Ligand9
> >> > density
> >> > >
> >> > &cntrl
> >> >
> >> > > imin=0,irest=1,
> >> > ntx=5,
> >> > >
> >> > nstlim=5000,dt=0.002,
> >> >
> >> > > ntc=2,ntf=2, ig=-1,
> >> > iwrap=1,
> >> > > cut=8.0, ntb=2, ntp=1,
> >> > taup=1.0,
> >> > > ntpr=5000, ntwx=5000,
> >> > ntwr=10000,
> >> > > ntt=3,
> >> > gamma_ln=2.0,
> >> > >
> >> > temp0=300.0,
> >> >
> >> > >
> >> > /
> >> >
> >> > >
> >> >
> >> >
> >> > >
> >> >
> >> >
> >> > >
> >> >
> >> >
> >> > >
> >> >
> >> >
> >> > >
> >> > >
> >> > > Note: ig = -1. Setting random seed based on wallclock time in
> >> > microseconds.
> >> > >
> >> > > |--------------------- INFORMATION ----------------------
> >> > > | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >> > > | Version 2.2
> >> > > |
> >> > > | 08/16/2011
> >> > > |
> >> > > |
> >> > > | Implementation by:
> >> > > | Ross C. Walker (SDSC)
> >> > > | Scott Le Grand (nVIDIA)
> >> > > | Duncan Poole (nVIDIA)
> >> > > |
> >> > > | CAUTION: The CUDA code is currently experimental.
> >> > > | You use it at your own risk. Be sure to
> >> > > | check ALL results carefully.
> >> > > |
> >> > > | Precision model in use:
> >> > > | [SPDP] - Hybrid Single/Double Precision (Default).
> >> > > |
> >> > > |--------------------------------------------------------
> >> > >
> >> > > |------------------- GPU DEVICE INFO --------------------
> >> > > |
> >> > > | CUDA Capable Devices Detected: 1
> >> > > | CUDA Device ID in use: 0
> >> > > | CUDA Device Name: GeForce GTX 580
> >> > > | CUDA Device Global Mem Size: 3071 MB
> >> > > | CUDA Device Num Multiprocessors: 16
> >> > > | CUDA Device Core Freq: 1.57 GHz
> >> > > |
> >> > > |--------------------------------------------------------
> >> > >
> >> > >
> >> > > | Conditional Compilation Defines Used:
> >> > > | DIRFRC_COMTRANS
> >> > > | DIRFRC_EFS
> >> > > | DIRFRC_NOVEC
> >> > > | PUBFFT
> >> > > | FFTLOADBAL_2PROC
> >> > > | BINTRAJ
> >> > > | CUDA
> >> > >
> >> > > | Largest sphere to fit in unit cell has radius = 48.492
> >> > >
> >> > > | New format PARM file being parsed.
> >> > > | Version = 1.000 Date = 05/27/11 Time = 11:50:53
> >> > >
> >> > > | Note: 1-4 EEL scale factors were NOT found in the topology file.
> >> > > | Using default value of 1.2.
> >> > >
> >> > > | Note: 1-4 VDW scale factors were NOT found in the topology file.
> >> > > | Using default value of 2.0.
> >> > > | Duplicated 0 dihedrals
> >> > >
> >> > > | Duplicated 0 dihedrals
> >> > >
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > > 1. RESOURCE USE:
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > >
> >> > > getting new box info from bottom of inpcrd
> >> > >
> >> > > NATOM = 116271 NTYPES = 21 NBONH = 109977 MBONA = 6423
> >> > > NTHETH = 14190 MTHETA = 8659 NPHIH = 27033 MPHIA = 21543
> >> > > NHPARM = 0 NPARM = 0 NNB = 207403 NRES = 35368
> >> > > NBONA = 6423 NTHETA = 8659 NPHIA = 21543 NUMBND = 59
> >> > > NUMANG = 124 NPTRA = 64 NATYP = 40 NPHB = 1
> >> > > IFBOX = 2 NMXRS = 43 IFCAP = 0 NEXTRA = 0
> >> > > NCOPY = 0
> >> > >
> >> > > | Coordinate Index Table dimensions: 23 23 23
> >> > > | Direct force subcell size = 5.1644 5.1644 5.1644
> >> > >
> >> > > BOX TYPE: TRUNCATED OCTAHEDRON
> >> > >
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > > 2. CONTROL DATA FOR THE RUN
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > >
> >> > >
> >> >
> >> >
> >> > >
> >> > > General flags:
> >> > > imin = 0, nmropt = 0
> >> > >
> >> > > Nature and format of input:
> >> > > ntx = 5, irest = 1, ntrx = 1
> >> > >
> >> > > Nature and format of output:
> >> > > ntxo = 1, ntpr = 5000, ntrx = 1,
> >> ntwr =
> >> > 10000
> >> > > iwrap = 1, ntwx = 5000, ntwv = 0, ntwe
> >> > = 0
> >> > > ioutfm = 0, ntwprt = 0, idecomp = 0,
> >> > rbornstat= 0
> >> > >
> >> > > Potential function:
> >> > > ntf = 2, ntb = 2, igb = 0, nsnb
> >> > = 25
> >> > > ipol = 0, gbsa = 0, iesp = 0
> >> > > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> >> > >
> >> > > Frozen or restrained atoms:
> >> > > ibelly = 0, ntr = 0
> >> > >
> >> > > Molecular dynamics:
> >> > > nstlim = 5000, nscm = 1000, nrespa = 1
> >> > > t = 0.00000, dt = 0.00200, vlimit = -1.00000
> >> > >
> >> > > Langevin dynamics temperature regulation:
> >> > > ig = 974683
> >> > > temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
> >> > >
> >> > > Pressure regulation:
> >> > > ntp = 1
> >> > > pres0 = 1.00000, comp = 44.60000, taup = 1.00000
> >> > >
> >> > > SHAKE:
> >> > > ntc = 2, jfastw = 0
> >> > > tol = 0.00001
> >> > >
> >> > > | Intermolecular bonds treatment:
> >> > > | no_intermolecular_bonds = 1
> >> > >
> >> > > | Energy averages sample interval:
> >> > > | ene_avg_sampling = 5000
> >> > >
> >> > > Ewald parameters:
> >> > > verbose = 0, ew_type = 0, nbflag = 1,
> >> use_pme
> >> > = 1
> >> > > vdwmeth = 1, eedmeth = 1, netfrc = 1
> >> > > Box X = 118.781 Box Y = 118.781 Box Z = 118.781
> >> > > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >> > > NFFT1 = 128 NFFT2 = 128 NFFT3 = 128
> >> > > Cutoff= 8.000 Tol =0.100E-04
> >> > > Ewald Coefficient = 0.34864
> >> > > Interpolation order = 4
> >> > >
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > > 3. ATOMIC COORDINATES AND VELOCITIES
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > >
> >> > >
> >> >
> >> >
> >> > > begin time read from input coords = 10.000 ps
> >> > >
> >> > >
> >> > > Number of triangulated 3-point waters found: 34583
> >> > >
> >> > > Sum of charges from parm topology file = -0.00000040
> >> > > Forcing neutrality...
> >> > >
> >> > > | Dynamic Memory, Types Used:
> >> > > | Reals 3524690
> >> > > | Integers 3800219
> >> > >
> >> > > | Nonbonded Pairs Initial Allocation: 19420163
> >> > >
> >> > > | GPU memory information:
> >> > > | KB of GPU memory in use: 882413
> >> > > | KB of CPU memory in use: 104090
> >> > >
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > > 4. RESULTS
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > >
> >> > > ---------------------------------------------------
> >> > > APPROXIMATING switch and d/dx switch using CUBIC SPLINE
> >> INTERPOLATION
> >> > > using 5000.0 points per unit in tabled values
> >> > > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> >> > > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> >> > > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> >> > > ---------------------------------------------------
> >> > > |---------------------------------------------------
> >> > > | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> >> > > | with 50.0 points per unit in tabled values
> >> > > | Relative Error Limit not exceeded for r .gt. 2.47
> >> > > | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> >> > > | with 50.0 points per unit in tabled values
> >> > > | Relative Error Limit not exceeded for r .gt. 2.89
> >> > > |---------------------------------------------------
> >> > > wrapping first mol.: 38.333512154956900
> >> > 54.211771142609109 93.897534410964738
> >> > > wrapping first mol.: 38.333512154956900
> >> > 54.211771142609109 93.897534410964738
> >> > >
> >> > > NSTEP = 5000 TIME(PS) = 20.000 TEMP(K)
> >> = 300.01 PRESS =
> >> > -23.7
> >> > > Etot = -281399.8069 EKtot = 71193.9609 EPtot =
> >> > -352593.7679
> >> > > BOND = 2490.5718 ANGLE = 6429.0655 DIHED =
> >> > 8582.5720
> >> > > 1-4 NB = 2942.3115 1-4 EEL = 32655.1879 VDWAALS =
> >> > 42104.9713
> >> > > EELEC = -447798.4479 EHBOND = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > > EKCMT = 30939.5460 VIRIAL = 31538.3575 VOLUME =
> >> > 1170788.5879
> >> > > Density =
> >> > 1.0106
> >> > >
> >> >
> >> > --------------------------------------------------------------------
> >> ----------
> >> > >
> >> > >
> >> > > A V E R A G E S O V E R 1 S T E P S
> >> > >
> >> > >
> >> > > NSTEP = 5000 TIME(PS) = 20.000 TEMP(K)
> >> = 300.01 PRESS =
> >> > -23.7
> >> > > Etot = -281399.8069 EKtot = 71193.9609 EPtot =
> >> > -352593.7679
> >> > > BOND = 2490.5718 ANGLE = 6429.0655 DIHED =
> >> > 8582.5720
> >> > > 1-4 NB = 2942.3115 1-4 EEL = 32655.1879 VDWAALS =
> >> > 42104.9713
> >> > > EELEC = -447798.4479 EHBOND = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > > EKCMT = 30939.5460 VIRIAL = 31538.3575 VOLUME =
> >> > 1170788.5879
> >> > > Density =
> >> > 1.0106
> >> > >
> >> >
> >> > --------------------------------------------------------------------
> >> ----------
> >> > >
> >> > >
> >> > > R M S F L U C T U A T I O N S
> >> > >
> >> > >
> >> > > NSTEP = 5000 TIME(PS) = 20.000 TEMP(K)
> >> = 0.00 PRESS
> >> > = 0.0
> >> > > Etot = 0.0000 EKtot = 0.0000 EPtot =
> >> > 0.0000
> >> > > BOND = 0.0000 ANGLE = 0.0000 DIHED =
> >> > 0.0000
> >> > > 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> >> > 0.0000
> >> > > EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
> >> > 0.0000
> >> > >
> >> >
> >> > --------------------------------------------------------------------
> >> ----------
> >> > >
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > > 5. TIMINGS
> >> > >
> >> >
> >> > ---------------------------------------------------------------------
> >> -----------
> >> > >
> >> > > | NonSetup CPU Time in Major Routines:
> >> > > |
> >> > > | Routine Sec %
> >> > > | ------------------------------
> >> > > | Nonbond 97.05 92.22
> >> > > | Bond 0.00 0.00
> >> > > | Angle 0.00 0.00
> >> > > | Dihedral 0.00 0.00
> >> > > | Shake 2.47 2.34
> >> > > | RunMD 5.71 5.43
> >> > > | Other 0.00 0.00
> >> > > | ------------------------------
> >> > > | Total 105.24
> >> > >
> >> > > | PME Nonbond Pairlist CPU Time:
> >> > > |
> >> > > | Routine Sec %
> >> > > | ---------------------------------
> >> > > | Set Up Cit 0.00 0.00
> >> > > | Build List 0.00 0.00
> >> > > | ---------------------------------
> >> > > | Total 0.00 0.00
> >> > >
> >> > > | PME Direct Force CPU Time:
> >> > > |
> >> > > | Routine Sec %
> >> > > | ---------------------------------
> >> > > | NonBonded Calc 0.00 0.00
> >> > > | Exclude Masked 0.00 0.00
> >> > > | Other 0.00 0.00
> >> > > | ---------------------------------
> >> > > | Total 0.00 0.00
> >> > >
> >> > > | PME Reciprocal Force CPU Time:
> >> > > |
> >> > > | Routine Sec %
> >> > > | ---------------------------------
> >> > > | 1D bspline 0.00 0.00
> >> > > | Grid Charges 0.00 0.00
> >> > > | Scalar Sum 0.00 0.00
> >> > > | Gradient Sum 0.00 0.00
> >> > > | FFT 0.00 0.00
> >> > > | ---------------------------------
> >> > > | Total 0.00 0.00
> >> > >
> >> > > | Final Performance Info:
> >> > > | -----------------------------------------------------
> >> > > | Average timings for last 0 steps:
> >> > > | Elapsed(s) = 0.00 Per Step(ms) = +Infinity
> >> > > | ns/day = 0.00 seconds/ns = +Infinity
> >> > > |
> >> > > | Average timings for all steps:
> >> > > | Elapsed(s) = 105.26 Per Step(ms) = 21.05
> >> > > | ns/day = 8.21 seconds/ns = 10525.53
> >> > > | -----------------------------------------------------
> >> > >
> >> > > | Setup CPU time: 0.90 seconds
> >> > > | NonSetup CPU time: 105.24 seconds
> >> > > | Total CPU time: 106.13 seconds 0.03 hours
> >> > >
> >> > > | Setup wall time: 1 seconds
> >> > > | NonSetup wall time: 105 seconds
> >> > > | Total wall time: 106 seconds 0.03 hours
> >> > >
> >> > >
> >> > > heat Ligand9
> >> > > &cntrl
> >> > > irest=0, ntx=1,
> >> > > nstlim=5000, dt=0.002,
> >> > > ntc=2,ntf=2, iwrap=1,
> >> > > cut=8.0, ntb=1, ig=-1,
> >> > > ntpr=1000, ntwx=1000, ntwr=10000,
> >> > > ntt=3, gamma_ln=2.0,
> >> > > tempi=0.0, temp0=300.0,
> >> > > ioutfm=1, ntr=1,
> >> > > ntr=1,
> >> > > /
> >> > > Group input for restrained atoms
> >> > > 2.0
> >> > > RES 1 790
> >> > > END
> >> > > END
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
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> >> > >
> >> > >
> >> > > _______________________________________________
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> >> > AMBER mailing list
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> >> >
> >>
> >>
> >>
> >> --
> >> --
> >> ==
> >> Levi C.T. Pierce, UCSD Graduate Student
> >> McCammon Laboratory
> >> http://mccammon.ucsd.edu/
> >> w: 858-534-2916
> >> _______________________________________________
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> >_______________________________________________
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Received on Sat Aug 20 2011 - 19:30:03 PDT
