AMBER Archive (2008)

Subject: AMBER: Parallel Self-guided Langevin simulation

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Wed May 21 2008 - 17:23:27 CDT

I used the following input file to run a self-guided Langevin dynamics simulation:

Self-guided Langevin dynamics run
&cntrl
   ntb=0,
   imin=0, irest=0, ntx=1,
   ntt=3, tempi=300,temp0=300.0,gamma_ln=10.0
   ntc=1, ntf=1,
   nstlim=50000000,
   ntwe=100, ntwx=100, ntpr=200,
   isgld=1, tsgavg=0.2,tempsg=1.
   cut=999.,rgbmax=999.,
/

This simulation works fine when I run it serially on my machine. However when I tried to run it in parallel on a TeraGrid NCSA cluster, it crashed.
The out file look like this:

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 05/14/2008 at 21:51:20
  [-O]verwriting output

File Assignments:
| MDIN: gb1.in
| MDOUT: gb1.out
|INPCRD: gb1.crd
| PARM: gb1.top
|RESTRT: gb1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: gb1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

Self-guided Langevin dynamics run
&cntrl
   ntb=0,
   imin=0, irest=0, ntx=1,
   ntt=3, tempi=300,temp0=300.0,gamma_ln=10.0
   ntc=1, ntf=1,
   nstlim=50000000,
   ntwe=100, ntwx=100, ntpr=200,
   isgld=1, tsgavg=0.2,tempsg=1.
   cut=999.,rgbmax=999.,
/

..........................

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

BBCA
 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 4 8 12 16 20 24 28
| 32 36 40 44 48 52 56

     Sum of charges from parm topology file = 0.00000000
     Forcing neutrality...
| Running AMBER/MPI version on 14 nodes

| WARNING: The number of processors is not a power of 2
| this may be inefficient on some systems.

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

************************************
Parameters for self-guided Langevin dynamics (SGLD) simulation

  Guiding range from 1 TO 56
  Averaging over 0.2000 ps
  Guiding temperature is set at: 1.00 K
  friction constant: 10.00 1/ps
*****************************************

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 147
| TOTAL SIZE OF NONBOND LIST = 1378

Then it did nothing. I got the following errors in the error file:

Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 0x40000000008e9c60 Unknown Unknown Unknown
sander.MPI 0x400000000084e380 Unknown Unknown Unknown
sander.MPI 0x4000000000853d40 Unknown Unknown Unknown
sander.MPI 0x200000000008f4b0 Unknown Unknown Unknown
sander.MPI 0xa0000000000040c0 Unknown Unknown Unknown
sander.MPI 0x40000000002ac1f0 Unknown Unknown Unknown
sander.MPI 0x4000000000226ba0 Unknown Unknown Unknown
sander.MPI 0x40000000006aa080 Unknown Unknown Unknown
sander.MPI 0x40000000001d2580 Unknown Unknown Unknown
sander.MPI 0x4000000000182520 Unknown Unknown Unknown
sander.MPI 0x4000000000177710 Unknown Unknown Unknown
sander.MPI 0x4000000000006910 Unknown Unknown Unknown
sander.MPI 0x20000000002ac060 Unknown Unknown Unknown
sander.MPI 0x4000000000006340 Unknown Unknown Unknown

I'm not sure what's going on. Could you please help me with this problem?

Dirar Homouz
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