AMBER: Unexpected stop of Sander run

From: Grzegorz Jezierski <>
Date: Sun, 22 May 2005 21:44:55 +0200

Dear users,
While trying to run Sander in short test simulations, I have encoutered
strange errors which stopped the execution of a program. I used to work
with AMBER package, and I think I checked all the options carefully this
time, so probably the error is non-trivial.
Here I tried several structures (peptides and nucleic acids), also with
and without MPI, with Amber6 and Amber8, and on three different machines
(#1, Opteron cluster; #'s 2 and 3, SGI).

Here is what is happening:
Machine #1 (MPI):
? FORTRAN Runtime Error:
? Variable not present in current namelist
? READ(UNIT=5,...

Machine #2 gives a lot of text (ellipsis for ommitted text):
MPI: On host flugor, Program /scratch/gj/amber6/exe/sander, Rank 0,
Process 595681 received signal SIGTRAP(5)

MPI: --------stack traceback-------
PC: 0x7165080 MPI_SGI_stacktraceback in /usr/lib32/
PC: 0x71655a8 first_arriver_handler in /usr/lib32/
PC: 0x7165858 slave_sig_handler in /usr/lib32/
PC: 0xfafcacc _sigtramp in /usr/lib32/
PC: 0x1006e3e4 pmesh_kspace_get_sizes in /scratch/gj/amber6/exe/sander
PC: 0x1006a258 ewald_mem in /scratch/gj/amber6/exe/sander
PC: 0x100376cc locmem in /scratch/gj/amber6/exe/sander
PC: 0x1002b954 RDPARM in /scratch/gj/amber6/exe/sander
PC: 0x10030600 MDREAD in /scratch/gj/amber6/exe/sander
PC: 0x10008178 SANDER in /scratch/gj/amber6/exe/sander
PC: 0xad39d74 main in /usr/lib32/
MPI: -----stack traceback ends-----
MPI: On host flugor, Program /scratch/gj/amber6/exe/sander, Rank 0,
Process 595681: Dumping core on signal SIGTRAP(5) into directory


Machine #3, when run without "mpirun", starts the simulation, starts
writing to the output file and then stops writing the following at the
end of output file:
" rdparm: a parameter array overflowed
            (e.g. the table of dihedral params)"

When MPI was on, the calculation doesn't even start :
MPI: could not run executable
MPI: No details available, no log files found (all_signal.c:203)

Can anyone tell me what is happening? I am not able to even reproduce
the simplest simulation I run several years ago, no matter what machine
I am using.
Thank you.
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Received on Mon May 23 2005 - 09:53:01 PDT
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