Use CUDA 4.2...
We haven't released the CUDA 5.0 patch yet (not that there should have had
to have been one but sigh...)
On Thu, Oct 18, 2012 at 6:39 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Please wait for a response rather than continuing to email the list.
> Knowledgeable people will respond as they have time.
>
> Also keep in mind that people around the world live in different time zones
> and have different schedules, so it's not unusual not to hear a response
> within a couple days.
>
> In case you were getting weird bounce-back messages, your emails *are*
> getting through.
>
> All the best,
> Jason
>
> P.S. -- I think I recall reading that CUDA 5.0 does not work with Amber
> yet. So try using 4.2 for the time being. But I'm not certain.
>
> On Thu, Oct 18, 2012 at 9:00 AM, Yubo Fan <pengpengtadie.gmail.com> wrote:
>
> > Hello,
> >
> > The cluster that I run pmemd.cuda.MPI has been upgraded to cuda 5.0.
> > Both Amber 11 and 12 have been recompiled with Intel and cuda
> > compilers and openmpi or mvapich2-1.8.1 compiled with Intel. The
> > pmemd.MPI works well for my jobs but both pmemd.cuda and
> > pmemd.cuda.MPI failed to output data after the upgrade. Some
> > information is listed below.
> >
> > List in my job directory:
> > -rw-r--r-- 1 yf4 ddc3 1786 Oct 17 12:39 cuda2gpu.job
> > -rw-r--r-- 1 yf4 ddc3 287 Oct 17 12:39 logfile
> > -rw-r--r-- 1 yf4 ddc3 354 Jul 27 06:00 md4ns.in
> > -rw-r--r-- 1 yf4 ddc3 1193 Oct 15 18:04 mdinfo
> > -rwxr-xr-x 1 yf4 ddc3 5630016 Oct 17 12:37 pmemd.cuda_SPDP
> > -rwxr-xr-x 1 yf4 ddc3 9033291 Oct 17 12:39 pmemd.cuda_SPDP.MPI
> > -rwxr-xr-x 1 yf4 ddc3 4200370 Oct 17 12:37 pmemd.MPI
> > -rwxr-xr-x 1 yf4 ddc3 11885653 Oct 17 12:37 sander.MPI
> > -rw-r--r-- 1 yf4 ddc3 5640959 Oct 3 08:05
> > STAT3_SH2_1bg1_dimer_noPO4_md200.rst7
> > -rw-r--r-- 1 yf4 ddc3 772 Oct 17 12:39
> > STAT3_SH2_1bg1_dimer_noPO4_md201.nc
> > -rw-r--r-- 1 yf4 ddc3 8019 Oct 17 12:39
> > STAT3_SH2_1bg1_dimer_noPO4_md201.out
> > -rw-r--r-- 1 yf4 ddc3 0 Oct 17 12:39
> > STAT3_SH2_1bg1_dimer_noPO4_md201.rst7
> > -rw-r--r-- 1 yf4 ddc3 13662681 May 8 16:57
> > STAT3_SH2_1bg1_dimer_noPO4.prmtop
> >
> > The output file, STAT3_SH2_1bg1_dimer_noPO4_md201.out, contains:
> > -------------------------------------------------------
> > Amber 11 SANDER 2010
> > -------------------------------------------------------
> >
> > | PMEMD implementation of SANDER, Release 11
> >
> > | Run on 10/17/2012 at 12:39:50
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: md4ns.in
> > | MDOUT: STAT3_SH2_1bg1_dimer_noPO4_md201.out
> > | INPCRD: STAT3_SH2_1bg1_dimer_noPO4_md200.rst7
> > | PARM: STAT3_SH2_1bg1_dimer_noPO4.prmtop
> > | RESTRT: STAT3_SH2_1bg1_dimer_noPO4_md201.rst7
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: STAT3_SH2_1bg1_dimer_noPO4_md201.nc
> > | MDINFO: mdinfo
> > |LOGFILE: logfile
> >
> >
> > Here is the input file:
> >
> > STAT3 SH2 Dimer with unphosphorylated Tyr-705: 1-ns MD &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > ig = -1,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 10, ntr = 0,
> > ntc = 2, ntf = 2,
> > tempi = 300.0, temp0 = 300.0,
> > ntt = 3, gamma_ln = 1.0,
> > nstlim = 2000000, dt = 0.002,
> > ntpr = 500, ntwx = 500, ntwr = 100000,
> > ioutfm = 1, iwrap = 1,
> > /
> >
> >
> > Note: ig = -1. Setting random seed based on wallclock time in
> microseconds
> > and disabling the synchronization of random numbers between tasks
> > to improve performance.
> >
> > |--------------------- 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 --------------------
> > |
> > | Task ID: 0
> > | CUDA Capable Devices Detected: 2
> > | CUDA Device ID in use: 0
> > | CUDA Device Name: Tesla M2050
> > | CUDA Device Global Mem Size: 2687 MB
> > | CUDA Device Num Multiprocessors: 14
> > | CUDA Device Core Freq: 1.15 GHz
> > |
> > |
> > | Task ID: 1
> > | CUDA Capable Devices Detected: 2
> > | CUDA Device ID in use: 1
> > | CUDA Device Name: Tesla M2050
> > | CUDA Device Global Mem Size: 2687 MB
> > | CUDA Device Num Multiprocessors: 14
> > | CUDA Device Core Freq: 1.15 GHz
> > |
> > |--------------------------------------------------------
> >
> >
> > | Conditional Compilation Defines Used:
> > | DIRFRC_COMTRANS
> > | DIRFRC_EFS
> > | DIRFRC_NOVEC
> > | MPI
> > | PUBFFT
> > | FFTLOADBAL_2PROC
> > | BINTRAJ
> > | CUDA
> >
> > | Largest sphere to fit in unit cell has radius = 40.866
> >
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 05/03/12 Time = 10:32:59
> >
> > | 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 = 77271 NTYPES = 16 NBONH = 73189 MBONA = 4198
> > NTHETH = 8918 MTHETA = 5780 NPHIH = 17546 MPHIA = 13412
> > NHPARM = 0 NPARM = 0 NNB = 136792 NRES = 23593
> > NBONA = 4198 NTHETA = 5780 NPHIA = 13412 NUMBND = 44
> > NUMANG = 92 NPTRA = 48 NATYP = 31 NPHB = 1
> > IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> > | Coordinate Index Table dimensions: 14 14 14
> > | Direct force subcell size = 7.1500 7.1500 7.1500
> >
> > 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 =
> > 100000
> > iwrap = 1, ntwx = 500, ntwv = 0, ntwe =
> > 0
> > ioutfm = 1, 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 = 2000000, nscm = 1000, nrespa = 1
> > t = 0.00000, dt = 0.00200, vlimit = -1.00000
> >
> > Langevin dynamics temperature regulation:
> > ig = 824075
> > temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
> >
> > Pressure regulation:
> > ntp = 1
> > pres0 = 1.00000, comp = 44.60000, taup = 2.00000
> >
> > 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 = 100.101 Box Y = 100.101 Box Z = 100.101
> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> > NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
> > Cutoff= 10.000 Tol =0.100E-04
> > Ewald Coefficient = 0.27511
> > Interpolation order = 4
> >
> > | PMEMD ewald parallel performance parameters:
> > | block_fft = 0
> > | fft_blk_y_divisor = 2
> > | excl_recip = 0
> > | excl_master = 0
> > | atm_redist_freq = 320
> >
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> >
> --------------------------------------------------------------------------------
> >
> >
> > begin time read from input coords =800170.000 ps
> >
> >
> > Number of triangulated 3-point waters found: 23091
> >
> > Sum of charges from parm topology file = -0.00001037
> > Forcing neutrality...
> >
> > =======================================================
> > There is no further output and nc trajectory stored although the job
> > is still running in the queue system.
> >
> > The job file is listed below:
> > #PBS -N Dimer_noPO4
> > #PBS -l walltime=24:00:00
> > #PBS -l nodes=1:ppn=12
> > #PBS -o cuda2gpu.err
> > #PBS -M yfan.tmhs.org
> > #PBS -m abe
> > #PBS -q graphics
> > #PBS -V
> >
> > export AMBERHOME=/work/ddc3/yf4/program/amber12
> > export MPI_HOME=/work/ddc3/yf4/program/mvapich2-1.8.1-intel
> > export filename='STAT3_SH2_1bg1_dimer_noPO4'
> >
> > export PATH=$PATH:$MPI_HOME/bin:$AMBERHOME/bin
> >
> > cd $PBS_O_WORKDIR
> >
> > cp $AMBERHOME/bin/sander.MPI .
> > cp $AMBERHOME/bin/pmemd.MPI .
> > cp $AMBERHOME/bin/pmemd.cuda_SPDP .
> > cp $AMBERHOME/bin/pmemd.cuda_SPDP.MPI .
> >
> > export n=200
> > until [ -e $filename\_md$n\.rst7 ]; do
> > let n="$n - 1"
> > done
> > let n="$n + 1"
> > let nend="$n + 1"
> >
> > while [ $n -le $nend ]; do
> > let m="$n - 1"
> > mpiexec -np 2 ./pmemd.cuda_SPDP.MPI -O -i md4ns.in -p
> > $filename\.prmtop -c $filename\_md$m.rst7 -o $filename\_md$n.out -r
> > $filename\_md$n.rst7 -x $filename\_md$n.nc let n="$n + 1"
> > done
> > =======================================================
> >
> > Suggestions?
> >
> > Thanks,
> > Yubo
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 18 2012 - 11:30:06 PDT
