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 |
---------------------------------------------------------
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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
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Received on Thu Oct 25 2012 - 10:30:06 PDT
