Hello
Thanks for your comments Prof. Case.
I did comment out the job line that locked up and the subsequent AMBER11 parallel tests finished without any problems. My compiler is gcc version 4.4.0 and my OS is Red Hat Enterprise Linux Client release 5. I used the freeware "openmpi-1.4.1" as my MPI.
I did check to see if there were any errors produced by AMBER11 in my PIMD files; but, there were not. Below shows the cmd_bead1.out file where basically the run appears to lock up before any trajectories are obtained etc.
What should I do from here? Is this a significant problem?
Thanks for your advice.
Cheers, Steve
Cmd_bead1.out
_______________________________________________________
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 06/29/2010 at 08:06:42
[-O]verwriting output
File Assignments:
| MDIN: cmd.in
| MDOUT: cmd_bead1.out
|INPCRD: cmd_bead1.crd
| PARM: spcfw.top
|RESTRT: cmd_bead1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: cmd_bead1.mdcrd
|MDINFO: cmd_bead1.mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
CMD: simulation of liquid water. Equilibration.
&cntrl
ipimd = 3
ntb = 1
ntx = 5, irest = 0
temp0 = 298.15
cut = 7.0
ntt = 4, nchain = 4 ! Nose'-Hoover chains
dt = 0.000050, nstlim = 10
eq_cmd = .true.
adiab_param = 0.5
ntpr = 1, ntwr = 1, ntwx = 5
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 9.387
| New format PARM file being parsed.
| Version = 1.000 Date = 09/29/05 Time = 12:33:42
NATOM = 648 NTYPES = 2 NBONH = 648 MBONA = 0
NTHETH = 216 MTHETA = 0 NPHIH = 0 MPHIA = 0
NHPARM = 0 NPARM = 0 NNB = 864 NRES = 216
NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 2
NUMANG = 1 NPTRA = 0 NATYP = 2 NPHB = 1
IFBOX = 1 NMXRS = 3 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 117848
| Hollerith 2162
| Integer 34912
| Max Pairs 78732
| nblistReal 7776
| nblist Int 31171
| Total 1555 kbytes
| 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
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
WATERBOX18
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 1
iwrap = 0, ntwx = 5, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 1, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 7.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00005, vlimit = 20.00000
Nose-Hoover chains
gamma_ln= 0.00000
number of oscillators= 4
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 18.774 Box Y = 18.774 Box Z = 18.774
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 18 NFFT2 = 18 NFFT3 = 18
Cutoff= 7.000 Tol =0.100E-04
Ewald Coefficient = 0.40167
Interpolation order = 4
| MPI Timing options:
| profile_mpi = 0
Setting ifbox to 3 for non-orthogonal unit cell
NTX / IREST inconsistency
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
WATERBOX18
begin time read from input coords = 50.000 ps
Number of triangulated 3-point waters found: 216
| Atom division among processors:
| 0 324 648
Sum of charges from parm topology file = 0.00000000
Forcing neutrality...
| Running AMBER/MPI version on 2 nodes
| MULTISANDER: 4 groups. 2 processors out of 8 total.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
THIS IS A CENTROID MD RUN
Parameters:
number of beads = 4
number of classical atoms = 648
temperature (Kelvin) = 298.15
| # of SOLUTE degrees of freedom (RNDFP): 1944.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 1944. NUM_NOSHAKE = 0 CORRECTED RNDFP = 1944.
| TOTAL # of degrees of freedom (RNDF) = 1944.
---------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 48138
| TOTAL SIZE OF NONBOND LIST = 95931
NSTEP = 0 TIME(PS) = 50.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -401.7619 EKtot = 0.0000 EPtot = -401.7619
BOND = 135.6611 ANGLE = 59.0444 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 103.9013
EELEC = -700.3688 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.2242E-03
------------------------------------------------------------------------------
IT STOPS HERE!!
-----Original Message-----
From: case [mailto:case.biomaps.rutgers.edu]
Sent: Tuesday, June 29, 2010 10:24 AM
To: AMBER Mailing List
Subject: Re: [AMBER] make test.parallel
On Tue, Jun 29, 2010, Steve Seibold wrote:
> I have never compiled AMBER ( a real newbie at this) before and I am
> probably being too concerned, but I have done a parallel compilation
> with AMBER11 and started running the test jobs. It has passed all jobs
> so far, but has been running one job (at cd
> PIMD/full_cmd_water/equilib && ./Run.full_cmd) Testing Centroid MD for
> about two hours now. I am assuming this is a large system with explicit waters.
>
>
> I am running eight processors (and they are running). Does it
> typically take this long? Should I be concerned that my machine has
> become "stuck"??
You should be concerned, and the job must be "stuck". Kill it, then comment out that line in the test/Makefile, and try other again. Also, look at the output file for the stuck job to see if there are any hints about what is going wrong.
If you can't see anything, let us know what compiler and version you are using, along with OS information, etc.
....regards...dac
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Received on Wed Jun 30 2010 - 05:30:03 PDT
