I configured without -bintraj option, but the output file says that I
reconfigure using -bintraj option, what is your opinion? The mdout file of
the bintraj directory is as the followings, as you see
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 08/03/2008 at 01:35:34
[-O]verwriting output
File Assignments:
| MDIN: mdin
| MDOUT: mdout
|INPCRD: xprmcrd
| PARM: xprmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdtrj.nc
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
netCDF output test
&cntrl
nstlim = 10, nscm=10000,ig=3261
cut=3.0, scee=1.2, igb=0
ntx=1, irest=0, ntb=1, ntpr=1,
dt=0.002, nrespa=1,
ntt=3, tempi=300.0, temp0 = 300., gamma_ln=1.0,
ntc=2, ntf=2, tol=0.000001,
ntwr = 0, ntwx=1,ntwv=-1,ntwe=0,ioutfm=1,ntwprt=28
/
--------------------------------------------------------------------------------
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 = 9.032
| New format PARM file being parsed.
| Version = 1.000 Date = 11/03/05 Time = 18:09:35
NATOM = 610 NTYPES = 11 NBONH = 597 MBONA = 12
NTHETH = 30 MTHETA = 15 NPHIH = 54 MPHIA = 23
NHPARM = 0 NPARM = 0 NNB = 906 NRES = 197
NBONA = 12 NTHETA = 15 NPHIA = 23 NUMBND = 12
NUMANG = 20 NPTRA = 19 NATYP = 11 NPHB = 1
IFBOX = 2 NMXRS = 16 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 120307
| Hollerith 3859
| Integer 34907
| Max Pairs 12708
| nblistReal 7320
| nblist Int 87739
| Total 1540 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
netCDF output test
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 = 1, ntrx = 1, ntwr =
0
iwrap = 0, ntwx = 1, ntwv = -1, ntwe =
0
ioutfm = 1, ntwprt = 28, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 3.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10, nscm = 10000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 3261
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 22.123 Box Y = 22.123 Box Z = 22.123
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 24 NFFT2 = 24 NFFT3 = 24
Cutoff= 3.000 Tol =0.100E-04
Ewald Coefficient = 0.98370
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
Xprmcrd title
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 194
No binary trajectory support in this version
reconfigure using the -bintraj flag
Dr Jaber Jahanbin Sardroodi
Department of Chemistry, Faculty of Basic Sciences, Azarbaijan
University of Tarbiat Moallem, Tabriz, Iran
-----Original Message-----
From: "David A. Case" <case.scripps.edu>
To: amber.scripps.edu
Date: Sat, 2 Aug 2008 18:37:10 -0700
Subject: Re: AMBER: error in parallel amber 9 test
On Sun, Aug 03, 2008, Jaber Jahanbin Sardroodi wrote:
> I had the following probleme in parallel test of amber 9 (my system is
> Fedora 9, on AMD Phenom quad core processor, openmpi and gfortran):
> passed all previous tests ...
> cd bintraj; ./Run.bintraj
>
> sander and ptraj: test sander netCDF output and ptraj netCDF input
> [localhost.localdomain:19636] MPI_ABORT invoked on rank 0 in communicator
> MPI_COMM_WORLD with errorcode 1
You should look at the output files in the bintraj directory to see if they
offer any clues. (I'm assuming you used the "-bintraj" option when running
the configure script.)
...dac
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Received on Wed Aug 06 2008 - 06:07:03 PDT
