AMBER Archive (2001)

Subject: sander on SP3

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Tue Apr 24 2001 - 16:59:16 CDT

Hello,
        I run sander(AMBER6) on IBM SP3 and get a variety of problems. I
cannot comprehed the possible reasons. The important problems are:

1) Running the benchmark of AMBER6
   -------------------------------

   This runs for 2-9 processors (nodes). Gives problem for single
processor or more than ten. In fact, even for 9 processors it gave
problems and used to hang(?) after a few steps. I had to run it repeatedly
so that it completed 100 steps. This doesn't work with processors greater
than nine.

2) If I run the same benchmark (or another input of my own), it works fine
with the thin node (ie 4-node SP3 processor). With the main one (16 node)
it hangs after sometime. (This is what is written above).

3) I could even run a 16 node job on 4 node successfully, though it took
much longer time to complete of course). But when I run on the main
(thick) node using all 16 (or anything greater than 9), the following
error crops up (without shake). [Also for higher processes, it comes out
saying that it has reached maximum (3000) steps for SHAKE, IF I use
shake.]

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

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 9811.84
 Etot = -58205.0586 EKtot = 0.0000 EPtot = -58205.0586
 BOND = 8976.8757 ANGLE = 312.4856 DIHED = 759.3461
 1-4 NB = 426.9862 1-4 EEL = 3832.4532 VDWAALS = 24893.4084
 EELEC = -97406.6138 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 0.0000 VIRIAL = -50908.9538 VOLUME = 240306.6153
                                                Density = 0.7817
 Ewald error estimate: 0.3273E-03

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

 EWALD BOMB in subroutine ew_recip/grid_weights
 nmine exceeds num_ks
 System must be very inhomogeneous. Cannot continue.
ERROR: 0031-250 task 1: Terminated
ERROR: 0031-250 task 2: Terminated
ERROR: 0031-250 task 3: Terminated
ERROR: 0031-250 task 0: Terminated

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

I am totally confused with this this enigmatic behavior of this machine.

Can anyone tell me where I faltered!? I am attaching the MACHINE file that
I have used for compiling. (Also I recompiled on thick node and I am also
using unlimit command).

Thanking in advance,
-Sanjeev

Attachment Converted: "c:\eudora\attach\MACHINE1"