Damn Intel... Do you have a copy of the compiler you can send me so I can try it out? Otherwise my advice is to stick to the tried and tested 11.1.069 version that has worked for years.
All the best
Ross
> -----Original Message-----
> From: Albert [mailto:mailmd2011.gmail.com]
> Sent: Tuesday, May 08, 2012 10:42 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] CUDA running error
>
> HI Ross:
>
> here is the output for "ifort -V"
>
> Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on
> Intel(R) 64, Version 12.1.3.293 Build 20120212
> Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
> FOR NON-COMMERCIAL USE ONLY
>
>
>
> On 05/08/2012 07:24 PM, Ross Walker wrote:
> > Hi Albert,
> >
> > So just to confirm (forget parallel for the moment - it's not of any
> use on GTX590s anyway and for now will just complicate debugging)...
> >
> > "Serial GPU does NOT work with Intel Parallel Studio XE 2011 for
> Linux?"
> >
> > What does 'ifort -V' give?
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: Albert [mailto:mailmd2011.gmail.com]
> >> Sent: Tuesday, May 08, 2012 10:12 AM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] CUDA running error
> >>
> >> Hi ROss:
> >>
> >> thanks a lot for prompt reply.
> >> I use *Intel^® Parallel Studio XE 2011 for Linux**
> >>
> <https://registrationcenter.intel.com/RegCenter/NComForm.aspx?ProductID
> >> =1540>
> >> and mpich2-1.4.1. The MPI goes well for intel compiler. neither
> series
> >> or MPI.CUDA works although I don't get any error when I compile
> tjhem.
> >> It doesn't work when I try to submit for job running.... Yes, I
> submit
> >> errors in previous thread, and here they are:
> >>
> >>
> >>
> >> mpiexec -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -i md.in -p bm.prmtop -c
> >> npt.rst -o md.out -r md.rst -x md.mdcrd&
> >>
> >>
> >> but it failed with following infomrations:
> >>
> >>
> >>
> >>
> >>
> >> --------md.out-----------
> >> -------------------------------------------------------
> >> Amber 12 SANDER 2012
> >> -------------------------------------------------------
> >>
> >> | PMEMD implementation of SANDER, Release 12
> >>
> >> | Run on 05/07/2012 at 22:26:15
> >>
> >> File Assignments:
> >> | MDIN: md.in
> >> | MDOUT: md.out
> >> | INPCRD: npt.rst
> >> | PARM: bm.prmtop
> >> | RESTRT: md.rst
> >> | REFC: refc
> >> | MDVEL: mdvel
> >> | MDEN: mden
> >> | MDCRD: md.mdcrd
> >> | MDINFO: mdinfo
> >> |LOGFILE: logfile
> >>
> >>
> >> Here is the input file:
> >>
> >> production dynamics
> >> &cntrl
> >> imin=0, irest=1, ntx=5,
> >> nstlim=10000000, dt=0.002,
> >> ntc=2, ntf=2,
> >> cut=10.0, ntb=2, ntp=1, taup=2.0,
> >> ntpr=5000, ntwx=5000, ntwr=50000,
> >> ntt=3, gamma_ln=2.0,
> >> temp0=300.0,
> >> /
> >>
> >>
> >> |--------------------- 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: 4
> >> | CUDA Device ID in use: 0
> >> | CUDA Device Name: GeForce GTX 590
> >> | CUDA Device Global Mem Size: 1535 MB
> >> | CUDA Device Num Multiprocessors: 0
> >> | CUDA Device Core Freq: 1.22 GHz
> >> |
> >> |
> >> | Task ID: 1
> >> | CUDA Capable Devices Detected: 4
> >> | CUDA Device ID in use: 1
> >> | CUDA Device Name: GeForce GTX 590
> >> | CUDA Device Global Mem Size: 1535 MB
> >> | CUDA Device Num Multiprocessors: 0
> >> | CUDA Device Core Freq: 1.22 GHz
> >> |
> >> |--------------------------------------------------------
> >>
> >>
> >> | Conditional Compilation Defines Used:
> >> | DIRFRC_COMTRANS
> >> | DIRFRC_EFS
> >> | DIRFRC_NOVEC
> >> | MPI
> >> | PUBFFT
> >> | FFTLOADBAL_2PROC
> >> | BINTRAJ
> >> | MKL
> >> | CUDA
> >>
> >> | Largest sphere to fit in unit cell has radius = 33.920
> >>
> >> | New format PARM file being parsed.
> >> | Version = 1.000 Date = 05/02/12 Time = 13:49:08
> >>
> >> | 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 = 36356 NTYPES = 19 NBONH = 33899 MBONA =
> 2451
> >> NTHETH = 5199 MTHETA = 3321 NPHIH = 10329 MPHIA =
> 8468
> >> NHPARM = 0 NPARM = 0 NNB = 67990 NRES =
> 10898
> >> NBONA = 2451 NTHETA = 3321 NPHIA = 8468 NUMBND =
> 61
> >> NUMANG = 120 NPTRA = 71 NATYP = 45 NPHB =
> 1
> >> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA =
> 0
> >> NCOPY = 0
> >>
> >> | Coordinate Index Table dimensions: 12 12 11
> >> | Direct force subcell size = 6.0700 6.1089 6.1673
> >>
> >> BOX TYPE: RECTILINEAR
> >>
> >> --------------------------------------------------------------------
> ---
> >> ---------
> >> 2. CONTROL DATA FOR THE RUN
> >> --------------------------------------------------------------------
> ---
> >> ---------
> >>
> >> default_name
> >>
> >> 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
> >> = 50000
> >> iwrap = 0, 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 = 10.00000, intdiel = 1.00000
> >>
> >> Frozen or restrained atoms:
> >> ibelly = 0, ntr = 0
> >>
> >> Molecular dynamics:
> >> nstlim = 10000000, nscm = 1000, nrespa = 1
> >> t = 0.00000, dt = 0.00200, vlimit = -1.00000
> >>
> >> Langevin dynamics temperature regulation:
> >> ig = 71277
> >> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
> >>
> >> 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 = 5000
> >>
> >> Ewald parameters:
> >> verbose = 0, ew_type = 0, nbflag = 1,
> use_pme
> >> = 1
> >> vdwmeth = 1, eedmeth = 1, netfrc = 1
> >> Box X = 72.839 Box Y = 73.307 Box Z = 67.840
> >> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> >> NFFT1 = 80 NFFT2 = 80 NFFT3 = 64
> >> 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
> >> --------------------------------------------------------------------
> ---
> >> ---------
> >>
> >> default_name
> >> begin time read from input coords = 1300.000 ps
> >>
> >>
> >> Number of triangulated 3-point waters found: 10538
> >>
> >> Sum of charges from parm topology file = -0.00000015
> >> Forcing neutrality...
> >>
> >>
> >>
> >> --------------logfile--------------------------------
> >> FFT slabs assigned to 1 tasks
> >> Maximum of 64 xy slabs per task
> >> Maximum of 80 zx slabs per task
> >> Count of FFT xy slabs assigned to each task:
> >> 0 64
> >> Count of FFT xz slabs assigned to each task:
> >> 0 80
> >>
> >>
> >> -----------terminal--------------log---------------------
> >> Image PC Routine Line
> >> Source
> >> pmemd.cuda.MPI 000000000057E4BD Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 000000000057EB62 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 0000000000555DF5 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 000000000051D5F2 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004F901E Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004057FC Unknown Unknown
> >> Unknown
> >> libc.so.6 00002B98685A8BFD Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004056F9 Unknown Unknown
> >> Unknown
> >> forrtl: severe (71): integer divide by zero
> >> Image PC Routine Line
> >> Source
> >> pmemd.cuda.MPI 000000000057E4BD Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 000000000057EB62 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 0000000000555DF5 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 000000000051D5F2 Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004F901E Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004057FC Unknown Unknown
> >> Unknown
> >> libc.so.6 00002AF6CA4B0BFD Unknown Unknown
> >> Unknown
> >> pmemd.cuda.MPI 00000000004056F9 Unknown Unknown
> >> Unknown
> >>
> >>
> >>
> >>
> >> On 05/08/2012 06:57 PM, Ross Walker wrote:
> >>> Hi Albert,
> >>>
> >>> Which version of Intel and which version of Mpich2 and which
> version
> >> of
> >>> nvcc?
> >>>
> >>> It works fine for me with Intel 11.1.069 and mpich2-1.4. Also does
> >> the CPU
> >>> version work fine with your intel and mpich2?
> >>>
> >>> Please please please make sure you isolate errors to the GPU code
> >> before
> >>> reporting them. I.e. ALWAYS test the cpu codes thoroughly first.
> >>>
> >>> I assume the serial GPU code works fine with Intel? - Also note
> that
> >> you
> >>> will see little to no performance improvement with the Intel
> >> compilers over
> >>> GNU for the GPU code.
> >>>
> >>> All the best
> >>> Ross
> >> _______________________________________________
> >> 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 Tue May 08 2012 - 11:00:03 PDT
