It is the dev master branch checked out a few days ago.
The same system works without any problem on my local machine and the
compiler was intel 11.1/mpich2 1.4.1p1. So, it is probably related to the
MPI library.
It may not be a coordinate problem. I used sander.MPI, then it worked ok.
Whenever I switch back to pmemd.MPI, the same error occurs.
It is also interesting that a very similar system but with a slight size
difference (a little more or less water/ions) works ok. I guess it is a bad
combination of this specific prmtop file and the MPI library.
I will try openmpi.
On Thu, Oct 25, 2012 at 1:19 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Insuk,
>
> A couple of questions. Is this just the dev branch (up to date) or do you
> see the same problem with Amber 12?
>
> Can you try with openMPI and see if the problem is still there.
>
> module unload mvapich2_ib
> module load openmpi_ib
>
> Put this in your .bashrc, logout and back in and then recompile.
>
> 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.
>
>
>
>
>
>
>
> On 10/25/12 8:46 AM, "InSuk Joung" <i.joung.gmail.com> wrote:
>
> >I installed amber from the master branch on Gordon(UCSD) and I have a
> >problem in running pmemd.MPI. Here is my mdout file.
> >
> > -------------------------------------------------------
> > Amber 12 SANDER 2012
> > -------------------------------------------------------
> >
> >| PMEMD implementation of SANDER, Release 12
> >
> >| Run on 10/25/2012 at 08:04:36
> >
> > [-O]verwriting output
> >
> >File Assignments:
> >| MDIN: md.in
> >
> >| MDOUT: model.eq.out
> >
> >| INPCRD: model.min.rst
> >
> >| PARM: model.prmtop
> >
> >| RESTRT: model.eq.rst
> >
> >| REFC: model.min.rst
> >
> >| MDVEL: mdvel
> >
> >| MDEN: mden
> >
> >| MDCRD: mdcrd
> >
> >| MDINFO: mdinfo
> >
> >|LOGFILE: logfile
> >
> >
> >
> > Here is the input file:
> >
> >eq1
> >
> > &cntrl
> >
> > irest=0, ntx=1,
> >
> > ntpr=2500, ntwr=25000, ntwx=0, ntwe=0,
> >
> > nscm=1250, temp0=298, tempi=0,
> >
> > ntf=2, ntc=2,
> >
> > ntb=2, ntt=3, gamma_ln=5.0, ntp=2, tautp=1.0, taup=1.0,
> >
> > nstlim=25000, dt=0.002,
> >
> > cut=9.0,
> >
> > iwrap=1,
> >
> > ntr=1, restraint_wt=50,
> >
> > restraintmask=':1-600',
> >
> > &end
> >
> >
> >
> >
> >
> >| Conditional Compilation Defines Used:
> >| DIRFRC_COMTRANS
> >| DIRFRC_EFS
> >| DIRFRC_NOVEC
> >| MPI
> >| PUBFFT
> >| FFTLOADBAL_2PROC
> >| BINTRAJ
> >| MKL
> >
> >| Largest sphere to fit in unit cell has radius = 14.100
> >
> >| New format PARM file being parsed.
> >| Version = 1.000 Date = 10/25/12 Time = 08:03:47
> >
> >| 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 = 7132 NTYPES = 4 NBONH = 6000 MBONA = 0
> > NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
> > NHPARM = 0 NPARM = 0 NNB = 9132 NRES = 3132
> > NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 2
> > NUMANG = 0 NPTRA = 0 NATYP = 4 NPHB = 1
> > IFBOX = 1 NMXRS = 3 IFCAP = 0 NEXTRA = 0
> > NCOPY = 0
> >
> >| Coordinate Index Table dimensions: 13 5 5
> >| Direct force subcell size = 5.6620 5.6400 5.6400
> >
> > BOX TYPE: RECTILINEAR
> >
> >--------------------------------------------------------------------------
> >------
> > 2. CONTROL DATA FOR THE RUN
> >--------------------------------------------------------------------------
> >------
> >
> >default_name
> >
> >
> >General flags:
> > imin = 0, nmropt = 0
> >
> >Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> >Nature and format of output:
> > ntxo = 1, ntpr = 2500, ntrx = 1, ntwr =
> >25000
> > iwrap = 1, ntwx = 0, 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 = 9.00000, intdiel = 1.00000
> >
> >Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> > restraint_wt = 50.00000
> >
> >Molecular dynamics:
> > nstlim = 25000, nscm = 0, nrespa = 1
> > t = 0.00000, dt = 0.00200, vlimit = 20.00000
> >
> >Langevin dynamics temperature regulation:
> > ig = 71277
> > temp0 = 298.00000, tempi = 0.00000, gamma_ln= 5.00000
> >
> >Pressure regulation:
> > ntp = 2
> > 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 = 2500
> >
> >Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> > 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > Box X = 73.606 Box Y = 28.200 Box Z = 28.200
> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > NFFT1 = 80 NFFT2 = 30 NFFT3 = 30
> > Cutoff= 9.000 Tol =0.100E-04
> > Ewald Coefficient = 0.30768
> > Interpolation order = 4
> >
> >| PMEMD ewald parallel performance parameters:
> >| block_fft = 1
> >| fft_blk_y_divisor = 2
> >| excl_recip = 0
> >| excl_master = 0
> >| atm_redist_freq = 320
> >
> > LOADING THE CONSTRAINED ATOMS AS GROUPS
> >
> >
> > 5. REFERENCE ATOM COORDINATES
> >
> > default_name
> >
> > Mask :1-600; matches 600 atoms
> >
> >--------------------------------------------------------------------------
> >------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >--------------------------------------------------------------------------
> >------
> >
> >default_name
> >
> > begin time read from input coords = 0.000 ps
> >
> >
> > Number of triangulated 3-point waters found: 2000
> >
> > Sum of charges from parm topology file = 0.00000000
> > Forcing neutrality...
> >
> >| Dynamic Memory, Types Used:
> >| Reals 539386
> >| Integers 329122
> >
> >| Nonbonded Pairs Initial Allocation: 269656
> >
> >| Running AMBER/MPI version on 16 nodes
> >
> >
> >--------------------------------------------------------------------------
> >------
> > 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 = 0.8314E-11 at 2.736960
> > ---------------------------------------------------
> >|---------------------------------------------------
> >| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> >| with 50.0 points per unit in tabled values
> >| Relative Error Limit not exceeded for r .gt. 2.39
> >| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> >| with 50.0 points per unit in tabled values
> >| Relative Error Limit not exceeded for r .gt. 2.84
> >|---------------------------------------------------
> >
> >Warning! Rndv Receiver is expecting 72000 Bytes But, is receiving 54000
> >Bytes
> >Warning! Rndv Receiver is expecting 75600 Bytes But, is receiving 54000
> >Bytes
> >Warning! Rndv Receiver is expecting 72000 Bytes But, is receiving 54000
> >Bytes
> >Warning! Rndv Receiver is expecting 75600 Bytes But, is receiving 54000
> >Bytes
> >
> >After the warnings, it seems that pmemd.MPI hangs.
> >
> >With sander.MPI, I don't have any problem.
> >
> >Make test.parallel.pmemd passes ok.
> >
> >The compiler was intel 12.1.1.256 Build 20111011, and the MPI library was
> >mvapich2_ib 1.8a1p1.
> >I see the same problem in Ranger(TACC) with intel 12.1 mvapich2 1.8.
> >
> >--
> >Best,
> >InSuk Joung
> >_______________________________________________
> >AMBER-Developers mailing list
> >AMBER-Developers.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Best,
InSuk Joung
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Oct 25 2012 - 12:00:02 PDT
