AMBER Archive (2008)

Subject: Re: AMBER: error in parallel amber 9 test

From: Jaber Jahanbin Sardroodi (jsardroodi_at_azaruniv.edu)
Date: Sun Aug 03 2008 - 03:15:19 CDT

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_at_scripps.edu>

To: amber_at_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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