4 sequential jobs work on laptops, but only first one works on supercomputer

From: JT (JTibbitt_at_odu.edu)
Date: Mon Apr 13 2009 - 18:00:49 CDT

Hey NAMD community,
A little trouble here. There are four sequential jobs to be run on a
solvated polymer:
1. minimize surrounding solvent, polymer fixed
2. minimize polymer, solvent fixed
3. minimize both
4. equilibrate

The first job uses a solvated polymer built with VMD. Then each
successive job takes the output files from the previous job
(.coor, .xsc, .....) as its starting point. The thing is, these jobs
work fine under two different laptop architectures (OSX and XP). But
when trying the exact same input files on a supercomputer, only the
first minimization works. Two different supercomputers have been
tried. Serial and parallel runs were tried on both. The same thing
happens each time. Info about one of the clusters: forty compute
nodes, each with two 3-gigahertz dual-core Intel processors and 8
gigabytes of memory. When it crashes, it's like NAMD thinks the
system is exploding or something (high energies, nan written
everywhere, ...). Output from the crash is pasted in below. Also, I
placed links to the other input and output files. BTW, if it is
better to just attach files, or not to attach them (unless asked),
please let me know. I also tried running the minimizations on my
laptop, then just using the supercomputers for running equilibration.
Similar errors occur.

Thank-you for looking,
Jeff Tibbitt

Input files:
www.drclawslaboratory.com/clawup/namd_min1.tcl
www.drclawslaboratory.com/clawup/namd_min2.tcl
www.drclawslaboratory.com/clawup/namd_min3.tcl
www.drclawslaboratory.com/clawup/namd_equi.tcl

Output files (run on OSX laptop):
www.drclawslaboratory.com/clawup/namd_min1.out
www.drclawslaboratory.com/clawup/namd_min2.out
www.drclawslaboratory.com/clawup/namd_min3.out
www.drclawslaboratory.com/clawup/namd_equi.out

Output files (run on supercomputer):
www.drclawslaboratory.com/clawup/namd_min1_WORKED.out
www.drclawslaboratory.com/clawup/namd_min2_CRASHED.out

Queue submission script files (for running on supercomputer):
www.drclawslaboratory.com/clawup/s2_sp
www.drclawslaboratory.com/clawup/s2_mp

Output from minimization that crashed on supercomputer
(namd_min2_CRASHED.out):
TCL: Minimizing for 2000 steps
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL T
EMP TOTAL2 TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 491.9037 99999999.9999 76.3226
8.5673 -428179.8422 1346.5543 0.0000
0.0000 0.0000 99999999.9999 0.0
000 99999999.9999 99999999.9999 0.0000 99999999.9999
99999999.9999 272212.3858 99999999.9999 99999999.9999

INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 nan nan nan nan
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 5e-07

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