[gmx-users] gromacs 3.0.5 compilation on Compaq XP1000 TruUnix64

[Dr. Y. U. Sasidhar]

David van der Spoel wrote:

> Your problem really is a compiler problem, but here is a workaround:
> go to src/tools and type
> make CFLAGS=-O g_rms
> then go to the top level directory and type
> make

1) It now compiles. However demo script in gmxdemo still got stuck at
editconf, genbox level.
I found that giving -nice 0 option gets it going up to mdrun (em ). So I
gave -nice 0 to all mdrun commands in the script. Now the script goes
through. Note that during all this there were only two users on the system
and other user's job seemed to be idle. I am giving accounting below: ( This
is through telnet to our compute server; using bash shell )
=============
Computing:      M-Number      M-Flop's  % Flop's
                   LJ     30.858335    956.608385     2.0
              Coulomb     67.454933   1821.283191     3.9
           Coulomb(W)      4.961964    401.919084     0.9
         LJ + Coulomb     43.507922   1653.301036     3.5
         LJ + Coul(W)     13.927847   1281.361924     2.7
        LJ + Coul(WW)    148.600391  36407.095795    77.5
      Innerloop-Iatom    103.284824   1032.848240     2.2
             NS-Pairs     54.453665   1143.526965     2.4
         Reset In Box      0.805107      7.245963     0.0
              Shift-X     16.073214     96.439284     0.2
               CG-CoM      0.283065      8.208885     0.0
               Angles      1.045209    170.369067     0.4
              Propers      0.370074     84.746946     0.2
            Impropers      0.350070     72.814560     0.2
               Virial      8.171634    147.089412     0.3
               Update      8.036607    249.134817     0.5
              Stop-CM      8.035000     80.350000     0.2
            Calc-Ekin      8.038214    217.031778     0.5
                Lincs      0.720432     43.225920     0.1
            Lincs-Mat     12.547524     50.190096     0.1
              Shake-V      8.036607    120.549105     0.3
            Shake-Vir      8.036607    144.658926     0.3
               Settle      2.441464    788.592872     1.7
          Total                 46978.59225   100.0

               NODE (s)   Real (s)      (%)
       Time:    151.244    302.000     50.1
                       2:31
               (Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
Performance:     10.155    310.615    238.026      4.201
========================================
2) The same demo script if run under dtterm the following output results:
I am always using bash.
==========================================

The genbox program reads the peptide structure file and an input file
containing the sizes of the desired water box. The output of genbox is
a gromos structure file of a peptide solvated in a box of water. The
genbox program also changes the topology file ( .top extension ) to
include water. First we will use the program editconf to define the
right boxsize for our system.

-----------------------------------------------------------------
-----------------------------------------------------------------
The output of the genbox program should appear
": Event not found.
bash-2.02$
====================================
3) Even when we were using gromacs 2.0 on this machine we observed that our
progrmas were stopping for no apparent reason without any error messages. By
trial and error we found that -nice 0 alleviates the problem.
On another similar machine ( same hardware/OS  ) no such problem was
observed !!

Any comments on this behaviour ?


 Sasidhar