NAMD on KRAKEN

From: PAUL NEWMAN (paulclizana_at_gmail.com)
Date: Fri Oct 28 2011 - 02:04:00 CDT

Dear NAMD users,

I am running a Free Energy calculation on KRAKEN and I got the following
error. ( Sorry I don't know if it is appropriate to port here )

#############################################################################################################################
ENERGY: 400 5033.9992 13345.0199 7704.4458
0.0000 -1781977.4449 211831.2980 0.0000 0.0000
301202.1718 -1242860.5102 309.7946 -1544062.6820
-1242026.2916 310.0217 36.8877 67.6739
4928733.5188 28.9856 28.9725

[0] MPICH has run out of unexpected buffer space.
Try increasing the value of env var MPICH_UNEX_BUFFER_SIZE (cur value is
62914560),
and/or reducing the size of MPICH_MAX_SHORT_MSG_SIZE (cur value is 128000).
aborting job:
out of unexpected buffer space
FreeEnergy: 500 1.000 Stop 1.00000 0.00000 ( 40.701,
63.777, 113.334) ( 40.718, 63.932, 113.375) 0.161 |
SMD 500 44.5049 73.3361 141.589 0 0 0.298436
[NID 10569] 2011-10-27 20:24:16 Apid 7553654: initiated application
termination
Application 7553654 exit codes: 255
Application 7553654 exit signals: Killed
Application 7553654 resources: utime 33496, stime 298
############################################################################################################################

I also add the following lines in the running script after the aprun but I
still got the same error.

aprun -n \$PBS_NNODES -cc cpu
/lustre/scratch/jphillip/NAMD_2.7_CRAY-XT-Kraken/namd2 $CONFFILE >& $LOGFILE

setenv MPICH_PTL_SEND_CREDITS -1
setenv MPICH_MAX_SHORT_MSG_SIZE 8000
setenv MPICH_PTL_UNEX_EVENTS 100M
setenv MPICH_UNEX_BUFFER_SIZE 500M

It seems that it is not changing the default values. Any help will be highly
appreciate it.

Thanks

-- 
Cheers,
Paul

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