AMBER Archive (2007)

Subject: Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Mar 14 2007 - 19:47:23 CST

try looking at the atom with Gmax: atom O #2500. maybe you can see something
in the coordinates, or maybe the box is not large enough? have you
tried without iwrap? I have not used that in minimization.

On 3/14/07, Eric Shamay <eric.shamay_at_gmail.com> wrote:
> I've had no success in running through a minimization of a system of water
> and nitric acid molecules. 2670 atoms in a 30x30x30 cubic periodic box.
>
> I'm attaching a few files for the interested:
> -topology
> -input coords
> -mdout of the run
>
> The input (mdin) of the run is a rather simple one:
> -----
> General minimization script
> &cntrl
> IMIN = 1,
> IWRAP = 1,
> NTPR = 250,
> NTMIN = 1,
> MAXCYC = 100000, NCYC = 3500,
> /
> -----
>
>
>
> the specific error I get (when running sander.MPI) is:
> -----
> Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
> Failing at addr:0x7dfabde0
> [0] func:/usr/local/lib/libopal.so.0 [0x400f5b38]
> [1] func:[0x40000440]
> [2] func:sander.MPI(ewald_force_+0x1a63) [0x8131d83]
> [3] func:sander.MPI(force_+0x1270) [0x8254ed8]
> [4] func:sander.MPI(runmin_+0x598) [0x80fdc68]
> [5] func:sander.MPI(sander_+0x5427) [0x80f17a3]
> [6] func:sander.MPI(MAIN__+0x14ab) [0x80e8053]
> [7] func:sander.MPI(main+0x42) [0x806a4da]
> [8] func:/lib/tls/libc.so.6(__libc_start_main+0xd3)
> [0x8a5e23]
> [9] func: sander.MPI [0x806a411]
> *** End of error message ***
> -----
>
> When running a serial version (sander) the following error is produced:
> -----
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> sander 08103B3C Unknown Unknown Unknown
> sander 08102E10 Unknown Unknown Unknown
> sander 08219F37 Unknown Unknown Unknown
> sander 080D2CA7 Unknown Unknown Unknown
> sander 080C6B43 Unknown Unknown Unknown
> sander 080C36D1 Unknown Unknown Unknown
> sander 0804B1BA Unknown Unknown Unknown
> libc.so.6 008A5E23 Unknown Unknown Unknown
> sander 0804B0F1 Unknown Unknown Unknown
> -----
>
> Changing the NCYC will allow the run to proceed until that number (i.e. if
> NCYC = 500, the run crashes at 500, if NCYC = 2500, it crashes at 2500,
> etc.) What I notice is that the energies listed in the mdout are rather
> large, but I'm at a loss for how to reduce the initial values as I've got no
> overlaps of atoms, and I've checked out the force field parameters and they
> seem kosher. I've read through a number of the segfault topics on the
> reflector that come close and it doesn't seem that anyone has come up with a
> solution beyond blaming the compiler. I've been able to successfully
> minimize a different system (similar, but all water molecules without any
> nitric acid), so something tells me that this segmentation fault is indeed
> system-specific: an artifact of the initial conditions and not the compiled
> code.
>
> The system used is a dual-processor athlon (32-bit), and the amber 9 source
> was compiled with ifort 9.1.040. Openmpi 1.1.4 compiled with the same ifort.
> Intel MKL 9.0 libraries were used.
>
> Any help is greatly appreciated. I'm at a loss for whether the installation
> was done correctly or not, and would like to pinpoint where the problem may
> be. Please feel free to ask for further information on anything I've
> forgotten to include.
> --
> ~Eric Shamay
> eric.shamay_at_gmail.com
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu