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 - 09:00:03 PDT
