Sir,
Thank you very much for the support.
with regards
mary
On Tue, Mar 19, 2013 at 5:04 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mary,
>
> What do you mean by 'going the right way'? This is a VERY subject
> question. If you mean is the calculation as setup proceeding as it should?
> If you installed the latest updates, and the test cases passed then yes
> your calculation is running as it should, eyeballing the temperature,
> density etc in your output file it looks good to me.
>
> Now if you mean is it simulating reality? Now there are a few tens of
> thousands of PhD's written on that subject and that is probably beyond the
> scope of this mailing list, as good as it is.
>
> All the best
> Ross
>
>
> On 3/18/13 10:58 AM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
>
> >Sir,
> >We do the patch and it worked highly satisfactorily. the output file is
> >attached. What should i check to know the calcualtion are going in the
> >right way.
> >
> >Thanking you for the valuable suggestions and time
> >
> >mary varughese
> >
> >
> >On Fri, Mar 15, 2013 at 10:31 PM, Mary Varughese
> ><maryvj1985.gmail.com>wrote:
> >
> >> Ok sir
> >> I am not any familiar to GPU and cuda.
> >> I will do the patch as you said.
> >> Thank you very much sir.
> >> I will report as early as possible.
> >>
> >> thanking you
> >>
> >> On Fri, Mar 15, 2013 at 9:57 PM, Ross Walker
> >><ross.rosswalker.co.uk>wrote:
> >>
> >>> Dear Mary,
> >>>
> >>> Ok, firstly you have not listened to the advice and updated the
> >>>software
> >>> hence you are still running with the original release version, bugs and
> >>> all.
> >>>
> >>> In terms of running calculations for just running on 1 GPU you do not
> >>>need
> >>> mpirun at all. So you would do:
> >>>
> >>> $AMBERHOME/pmemd.cuda -O -i ..
> >>>
> >>> Note the 'pmemd.cuda' does NOT have the .MPI here.
> >>>
> >>> All the best
> >>> Ross
> >>>
> >>>
> >>>
> >>>
> >>> On 3/15/13 9:23 AM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
> >>>
> >>> >Sir,
> >>> >
> >>> >
> >>> >
> >>> >The input of the .out file i have sent is
> >>> >
> >>> >mpirun -n 8 pmemd.cuda.MPI -O -i TbNrb_md9.in -p TbNrb.prmtop -c
> >>> >TbNrb_md8.rst -o TbNrb_md9.out -r TbNrb_md9.rst -x TbNrb_md9.mdcrd
> >>> >
> >>> >
> >>> >
> >>> >*The system i am using has 24 CPU's and a single GPU with 512 cores. *
> >>> >
> >>> >*As i understand now, in single GPU there is no need of mpdboot, no
> >>>need
> >>> >to
> >>> >specify no of cores to be used, as in accordance with % of utilization
> >>> >load
> >>> >two or more programs and its all thread base.*
> >>> >
> >>> >
> >>> >
> >>> >So i tried this command since .MPI work only with more than 1 GPU
> >>> >
> >>> >
> >>> >
> >>> >mpirun -n 1 pmemd.cuda -O -i TbNrb_md9.in -p TbNrb.prmtop -c
> >>> TbNrb_md8.rst
> >>> >-o TbNrb_md9.out -r TbNrb_md9.rst -x TbNrb_md9.mdcrd
> >>> >
> >>> >
> >>> >
> >>> >the output got waited at the last step for more than half hour and i
> >>> >terminated the program.
> >>> >
> >>> >
> >>> >
> >>> > -------------------------------------------------------
> >>> >
> >>> > Amber 11 SANDER 2010
> >>> >
> >>> > -------------------------------------------------------
> >>> >
> >>> >| PMEMD implementation of SANDER, Release 11
> >>> >
> >>> >| Run on 03/15/2013 at 18:50:47
> >>> >
> >>> > [-O]verwriting output
> >>> >
> >>> >File Assignments:
> >>> >
> >>> >| MDIN: TbNrb_md9.in
> >>> >
> >>> >
> >>> >| MDOUT: TbNrb_md9.out
> >>> >
> >>> >
> >>> >| INPCRD: TbNrb_md8.rst
> >>> >
> >>> >
> >>> >| PARM: TbNrb.prmtop
> >>> >
> >>> >
> >>> >| RESTRT: TbNrb_md9.rst
> >>> >
> >>> >
> >>> >| REFC: refc
> >>> >
> >>> >
> >>> >| MDVEL: mdvel
> >>> >
> >>> >
> >>> >| MDEN: mden
> >>> >
> >>> >
> >>> >| MDCRD: TbNrb_md9.mdcrd
> >>> >
> >>> >
> >>> >| MDINFO: mdinfo
> >>> >
> >>> >
> >>> > Here is the input file:
> >>> >
> >>> >Tb-Ntr complex : 200ps MD (production run in NPT)
> >>> >
> >>> >
> >>> > &cntrl
> >>> >
> >>> >
> >>> > imin = 0,
> >>> >
> >>> >
> >>> > irest = 1,
> >>> >
> >>> >
> >>> > ntx = 5,
> >>> >
> >>> >
> >>> > ntb = 2, ntp = 1, pres0 = 1.0,
> >>> >
> >>> >
> >>> > cut = 10,
> >>> >
> >>> >
> >>> > ntr = 0,
> >>> >
> >>> >
> >>> > ntc = 2,
> >>> >
> >>> >
> >>> > ntf = 2,
> >>> >
> >>> >
> >>> > tempi = 300.0,
> >>> >
> >>> >
> >>> > temp0 = 300.0,
> >>> >
> >>> >
> >>> > ntt = 3,
> >>> >
> >>> >
> >>> > gamma_ln = 1,
> >>> >
> >>> >
> >>> > nstlim = 1000, dt = 0.002,
> >>> >
> >>> >
> >>> > ntpr = 500, ntwx = 500, ntwr = 1000,
> >>> >
> >>> >
> >>> > /
> >>> >
> >>> >
> >>> >|--------------------- INFORMATION ----------------------
> >>> >
> >>> >| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >>> >
> >>> >| Version 12.0
> >>> >
> >>> >| 03/19/2012
> >>> >
> >>> >| 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: Tesla M2090
> >>> >
> >>> >| CUDA Device Global Mem Size: 5375 MB
> >>> >
> >>> >| CUDA Device Num Multiprocessors: 16
> >>> >
> >>> >| CUDA Device Core Freq: 1.30 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 = 47.238
> >>> >
> >>> >| New format PARM file being parsed.
> >>> >
> >>> >| Version = 1.000 Date = 10/04/12 Time = 11:18:48
> >>> >
> >>> >| Note: 1-4 EEL scale factors are being read from the topology file.
> >>> >
> >>> >| Note: 1-4 VDW scale factors are being read from the topology file.
> >>> >
> >>> >| Duplicated 0 dihedrals
> >>> >
> >>> >| Duplicated 0 dihedrals
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > 1. RESOURCE USE:
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > getting new box info from bottom of inpcrd
> >>> >
> >>> > NATOM = 119092 NTYPES = 20 NBONH = 112233 MBONA = 6978
> >>> >
> >>> > NTHETH = 14955 MTHETA = 9471 NPHIH = 29675 MPHIA = 23498
> >>> >
> >>> > NHPARM = 0 NPARM = 0 NNB = 214731 NRES = 36118
> >>> >
> >>> > NBONA = 6978 NTHETA = 9471 NPHIA = 23498 NUMBND = 78
> >>> >
> >>> > NUMANG = 158 NPTRA = 71 NATYP = 52 NPHB = 1
> >>> >
> >>> > IFBOX = 2 NMXRS = 44 IFCAP = 0 NEXTRA = 0
> >>> >
> >>> > NCOPY = 0
> >>> >
> >>> >| Coordinate Index Table dimensions: 18 18 18
> >>> >
> >>> >| Direct force subcell size = 6.4283 6.4283 6.4283
> >>> >
> >>> > 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 = 500, ntrx = 1, ntwr
> >>>=
> >>> >1000
> >>> >
> >>> > iwrap = 0, ntwx = 500, 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 = 10.00000, intdiel = 1.00000
> >>> >
> >>> >Frozen or restrained atoms:
> >>> >
> >>> > ibelly = 0, ntr = 0
> >>> >
> >>> >Molecular dynamics:
> >>> >
> >>> > nstlim = 1000, nscm = 1000, nrespa = 1
> >>> >
> >>> > t = 0.00000, dt = 0.00200, vlimit = -1.00000
> >>> >
> >>> >Langevin dynamics temperature regulation:
> >>> >
> >>> > ig = 71277
> >>> >
> >>> > temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
> >>> >
> >>> >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 = 500
> >>> >
> >>> > Ewald parameters:
> >>> >
> >>> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> >>>=
> >>> >1
> >>> >
> >>> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> >>> >
> >>> > Box X = 115.709 Box Y = 115.709 Box Z = 115.709
> >>> >
> >>> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >>> >
> >>> > NFFT1 = 120 NFFT2 = 120 NFFT3 = 120
> >>> >
> >>> > Cutoff= 10.000 Tol =0.100E-04
> >>> >
> >>> > Ewald Coefficient = 0.27511
> >>> >
> >>> > Interpolation order = 4
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > 3. ATOMIC COORDINATES AND VELOCITIES
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > begin time read from input coords = 400.000 ps
> >>> >
> >>> > Number of triangulated 3-point waters found: 35215
> >>> >
> >>> > Sum of charges from parm topology file = -0.00000042
> >>> >
> >>> > Forcing neutrality...
> >>> >
> >>> >* *
> >>> >
> >>> >* *
> >>> >* *
> >>> >
> >>> >***Then i tried this: waiting at the last step, i wait for 45 minutes
> >>>and
> >>> >terminate.*
> >>> >* *
> >>> >
> >>> >
> >>> >
> >>> >pmemd.cuda -O -i TbNrb_md9.in -p TbNrb.prmtop -c TbNrb_md8.rst -o
> >>> >TbNrb_md9.out -r TbNrb_md9.rst -x TbNrb_md9.mdcrd
> >>> >
> >>> >
> >>> >
> >>> > -------------------------------------------------------
> >>> >
> >>> > Amber 11 SANDER 2010
> >>> >
> >>> > -------------------------------------------------------
> >>> >
> >>> >| PMEMD implementation of SANDER, Release 11
> >>> >
> >>> >| Run on 03/15/2013 at 19:14:46
> >>> >
> >>> > [-O]verwriting output
> >>> >
> >>> >File Assignments:
> >>> >
> >>> >| MDIN: TbNrb_md9.in
> >>> >
> >>> >
> >>> >| MDOUT: TbNrb_md9.out
> >>> >
> >>> >
> >>> >| INPCRD: TbNrb_md8.rst
> >>> >
> >>> >
> >>> >| PARM: TbNrb.prmtop
> >>> >
> >>> >
> >>> >| RESTRT: TbNrb_md9.rst
> >>> >
> >>> >
> >>> >| REFC: refc
> >>> >
> >>> >
> >>> >| MDVEL: mdvel
> >>> >
> >>> >
> >>> >| MDEN: mden
> >>> >
> >>> >
> >>> >| MDCRD: TbNrb_md9.mdcrd
> >>> >
> >>> >
> >>> >| MDINFO: mdinfo
> >>> >
> >>> >
> >>> > Here is the input file:
> >>> >
> >>> >Tb-Ntr complex : 200ps MD (production run in NPT)
> >>> >
> >>> >
> >>> > &cntrl
> >>> >
> >>> >
> >>> > imin = 0,
> >>> >
> >>> >
> >>> > irest = 1,
> >>> >
> >>> >
> >>> > ntx = 5,
> >>> >
> >>> >
> >>> > ntb = 2, ntp = 1, pres0 = 1.0,
> >>> >
> >>> >
> >>> > cut = 10,
> >>> >
> >>> >
> >>> > ntr = 0,
> >>> >
> >>> >
> >>> > ntc = 2,
> >>> >
> >>> >
> >>> > ntf = 2,
> >>> >
> >>> >
> >>> > tempi = 300.0,
> >>> >
> >>> >
> >>> > temp0 = 300.0,
> >>> >
> >>> >
> >>> > ntt = 3,
> >>> >
> >>> >
> >>> > gamma_ln = 1,
> >>> >
> >>> >
> >>> > nstlim = 1000, dt = 0.002,
> >>> >
> >>> >
> >>> > ntpr = 500, ntwx = 500, ntwr = 1000,
> >>> >
> >>> >
> >>> > /
> >>> >
> >>> >
> >>> >|--------------------- INFORMATION ----------------------
> >>> >
> >>> >| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >>> >
> >>> >| Version 12.0
> >>> >
> >>> >| 03/19/2012
> >>> >
> >>> >| 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: Tesla M2090
> >>> >
> >>> >| CUDA Device Global Mem Size: 5375 MB
> >>> >
> >>> >| CUDA Device Num Multiprocessors: 16
> >>> >
> >>> >| CUDA Device Core Freq: 1.30 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 = 47.238
> >>> >
> >>> >| New format PARM file being parsed.
> >>> >
> >>> >| Version = 1.000 Date = 10/04/12 Time = 11:18:48
> >>> >
> >>> >| Note: 1-4 EEL scale factors are being read from the topology file.
> >>> >
> >>> >| Note: 1-4 VDW scale factors are being read from the topology file.
> >>> >
> >>> >| Duplicated 0 dihedrals
> >>> >
> >>> >| Duplicated 0 dihedrals
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > 1. RESOURCE USE:
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > getting new box info from bottom of inpcrd
> >>> >
> >>> > NATOM = 119092 NTYPES = 20 NBONH = 112233 MBONA = 6978
> >>> >
> >>> > NTHETH = 14955 MTHETA = 9471 NPHIH = 29675 MPHIA = 23498
> >>> >
> >>> > NHPARM = 0 NPARM = 0 NNB = 214731 NRES = 36118
> >>> >
> >>> > NBONA = 6978 NTHETA = 9471 NPHIA = 23498 NUMBND = 78
> >>> >
> >>> > NUMANG = 158 NPTRA = 71 NATYP = 52 NPHB = 1
> >>> >
> >>> > IFBOX = 2 NMXRS = 44 IFCAP = 0 NEXTRA = 0
> >>> >
> >>> > NCOPY = 0
> >>> >
> >>> >| Coordinate Index Table dimensions: 18 18 18
> >>> >
> >>> >| Direct force subcell size = 6.4283 6.4283 6.4283
> >>> >
> >>> > 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 = 500, ntrx = 1, ntwr
> >>>=
> >>> >1000
> >>> >
> >>> > iwrap = 0, ntwx = 500, 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 = 10.00000, intdiel = 1.00000
> >>> >
> >>> >Frozen or restrained atoms:
> >>> >
> >>> > ibelly = 0, ntr = 0
> >>> >
> >>> >Molecular dynamics:
> >>> >
> >>> > nstlim = 1000, nscm = 1000, nrespa = 1
> >>> >
> >>> > t = 0.00000, dt = 0.00200, vlimit = -1.00000
> >>> >
> >>> >Langevin dynamics temperature regulation:
> >>> >
> >>> > ig = 71277
> >>> >
> >>> > temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
> >>> >
> >>> >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 = 500
> >>> >
> >>> >
> >>> >
> >>> >Ewald parameters:
> >>> >
> >>> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> >>>=
> >>> >1
> >>> >
> >>> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> >>> >
> >>> > Box X = 115.709 Box Y = 115.709 Box Z = 115.709
> >>> >
> >>> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >>> >
> >>> > NFFT1 = 120 NFFT2 = 120 NFFT3 = 120
> >>> >
> >>> > Cutoff= 10.000 Tol =0.100E-04
> >>> >
> >>> > Ewald Coefficient = 0.27511
> >>> >
> >>> > Interpolation order = 4
> >>> >
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >------
> >>> >
> >>> > 3. ATOMIC COORDINATES AND VELOCITIES
> >>> >
> >>> >*
> >>>
> >>>
> >>>>-----------------------------------------------------------------------
> >>>>---
> >>> >-----
> >>> >*
> >>> >
> >>> > begin time read from input coords = 400.000 ps
> >>> >
> >>> > Number of triangulated 3-point waters found: 35215
> >>> >
> >>> > Sum of charges from parm topology file = -0.00000042
> >>> >
> >>> > Forcing neutrality...
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >Am i doing anything wrong.
> >>> >
> >>> >Please tell me if my input has some problem.
> >>> >
> >>> >Someone says if there is only one GPU only one core will work.
> >>> >
> >>> >Please tell me the correct syntax of using pmemd.
> >>> >
> >>> >
> >>> >
> >>> >Also I donšt understand what this really meant
> >>> >
> >>> >if (igb/=0 & cut<systemsize)
> >>> >
> >>> >*GPU accelerated implicit solvent GB simulations do not support a
> >>> cutoff.*
> >>> >
> >>> >I am using the same input used for sander!
> >>> >I will work on the patch.
> >>> >
> >>> >Thanking you
> >>> >
> >>> >
> >>> >On Fri, Mar 15, 2013 at 8:57 PM, Ross Walker <ross.rosswalker.co.uk>
> >>> >wrote:
> >>> >
> >>> >> Hi Mary,
> >>> >>
> >>> >> Please read the following page: http://ambermd.org/gpus/
> >>> >>
> >>> >> This has all the information you should need for running correctly
> >>>on
> >>> >>GPUs.
> >>> >>
> >>> >> All the best
> >>> >> Ross
> >>> >>
> >>> >>
> >>> >>
> >>> >>
> >>> >> On 3/14/13 8:20 PM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
> >>> >>
> >>> >> >Sir,
> >>> >> >
> >>> >> >Infact this is a single GPU with 24 cores as i understand.
> >>> >> >bugixes have been done.
> >>> >> >But i will try the step u suggested.
> >>> >> >Also this work run without any problem in CPU workstaion.
> >>> >> >Hope the input doesnt contain any variable not compatible with
> >>>pmemd!
> >>> >> >
> >>> >> >Thanking you
> >>> >> >
> >>> >> >On Thu, Mar 14, 2013 at 9:16 PM, Ross Walker
> >>><ross.rosswalker.co.uk>
> >>> >> >wrote:
> >>> >> >
> >>> >> >> Hi Mary,
> >>> >> >>
> >>> >> >> 8 GPUs is a lot to use you probably won't get optimal scaling
> >>>unless
> >>> >>you
> >>> >> >> have very good interconnect and only 1 GPU per node. Some things
> >>>to
> >>> >>try
> >>> >> >>/
> >>> >> >> consider:
> >>> >> >>
> >>> >> >>
> >>> >> >> >|--------------------- INFORMATION ----------------------
> >>> >> >> >
> >>> >> >> >| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> >>> >> >> >
> >>> >> >> >| Version 12.0
> >>> >> >> >
> >>> >> >> >|
> >>> >> >> >
> >>> >> >> >| 03/19/2012
> >>> >> >>
> >>> >> >> You should update your copy of AMBER since there have been many
> >>> >>tweaks
> >>> >> >>and
> >>> >> >> bug fixes. Do:
> >>> >> >>
> >>> >> >> cd $AMBERHOME
> >>> >> >> ./patch_amber.py --update
> >>> >> >>
> >>> >> >> Run this until it stops saying there are updates (about 3 or 4
> >>> >>times).
> >>> >> >>Then
> >>> >> >>
> >>> >> >> make clean
> >>> >> >> ./configure gnu
> >>> >> >> make
> >>> >> >> ./configure -mpi gnu
> >>> >> >> make
> >>> >> >> ./configure -cuda gnu
> >>> >> >> make
> >>> >> >> ./configure -cuda -mpi gnu
> >>> >> >> make
> >>> >> >>
> >>> >> >> >begin time read from input coords = 400.000 ps
> >>> >> >> >Number of triangulated 3-point waters found: 35215
> >>> >> >> >Sum of charges from parm topology file = -0.00000042
> >>> >> >> >Forcing neutrality...
> >>> >> >>
> >>> >> >> This happens with the CPU code sometimes - often when the inpcrd
> >>>/
> >>> >> >>restart
> >>> >> >> file does not contain box information when a periodic simulation
> >>>is
> >>> >> >> requested. Does it run ok with the CPU code? - Alternatively it
> >>>may
> >>> >>just
> >>> >> >> be running so slow over 8 GPUs that it hasn't even got to 500
> >>>steps
> >>> >>yet
> >>> >> >>to
> >>> >> >> print anything. Try it with just one GPU and see what happens.
> >>> >> >>
> >>> >> >>
> >>> >> >> All the best
> >>> >> >> Ross
> >>> >> >>
> >>> >> >> /\
> >>> >> >> \/
> >>> >> >> |\oss Walker
> >>> >> >>
> >>> >> >> ---------------------------------------------------------
> >>> >> >> | Assistant Research Professor |
> >>> >> >> | San Diego Supercomputer Center |
> >>> >> >> | Adjunct Assistant Professor |
> >>> >> >> | Dept. of Chemistry and Biochemistry |
> >>> >> >> | University of California San Diego |
> >>> >> >> | NVIDIA Fellow |
> >>> >> >> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> >>> >> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >>> >> >> ---------------------------------------------------------
> >>> >> >>
> >>> >> >> Note: Electronic Mail is not secure, has no guarantee of
> >>>delivery,
> >>> >>may
> >>> >> >>not
> >>> >> >> be read every day, and should not be used for urgent or sensitive
> >>> >> >>issues.
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >> _______________________________________________
> >>> >> >> AMBER mailing list
> >>> >> >> AMBER.ambermd.org
> >>> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >> >>
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >> >--
> >>> >> >Mary Varughese
> >>> >> >Research Scholar
> >>> >> >School of Pure and Applied Physics
> >>> >> >Mahatma Gandhi University
> >>> >> >India
> >>> >> >_______________________________________________
> >>> >> >AMBER mailing list
> >>> >> >AMBER.ambermd.org
> >>> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>
> >>> >>
> >>> >>
> >>> >> _______________________________________________
> >>> >> AMBER mailing list
> >>> >> AMBER.ambermd.org
> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>
> >>> >
> >>> >
> >>> >
> >>> >--
> >>> >Mary Varughese
> >>> >Research Scholar
> >>> >School of Pure and Applied Physics
> >>> >Mahatma Gandhi University
> >>> >India
> >>> >_______________________________________________
> >>> >AMBER mailing list
> >>> >AMBER.ambermd.org
> >>> >http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >> --
> >> Mary Varughese
> >> Research Scholar
> >> School of Pure and Applied Physics
> >> Mahatma Gandhi University
> >> India
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 18 2013 - 23:00:03 PDT
