From: Michael Galloway (gallowaymd_at_ornl.gov)
Date: Thu Sep 13 2012 - 10:30:09 CDT
ok, i've been experimenting with namd built with openmpi and running
binaries over IPoIB and its not going so well.
my namd2.9 built with gcc 4.7.1 and the apoa1 test data with 4 nodes by
12 cores per node is:
[mgx_at_cmbcluster namd]$ mpirun -np 48 -machinefile nodes
/shared/namd-2.9-gcc471/Linux-x86_64-g++/namd2 apoa1/apoa1.namd
Info: Benchmark time: 48 CPUs 0.0357351 s/step 0.413601 days/ns 309.887
MB memory
TIMING: 500 CPU: 19.0964, 0.0354278/step Wall: 19.0964,
0.0354278/step, 0 hours remaining, 309.886719 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 500 20974.8940 19756.6571 5724.4523
179.8271 -337741.4155 23251.1001 0.0000 0.0000
45359.0760 -222495.4090 165.0039 -267854.4849
-222061.0908 165.0039 -3197.5171 -2425.4142
921491.4634 -3197.5171 -2425.4142
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
WRITING COORDINATES TO OUTPUT FILE AT STEP 500
The last position output (seq=-2) takes 0.002 seconds, 315.496 MB of
memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
The last velocity output (seq=-2) takes 0.002 seconds, 315.496 MB of
memory in use
====================================================
WallClock: 20.894575 CPUTime: 20.894575 Memory: 315.496094 MB
End of program
same dataset, same node processor count for the NAMD_2.9_Linux-x86_64
binary run over IBoIP:
[mgx_at_cmbcluster NAMD_2.9_Linux-x86_64]$ ./charmrun ./namd2 +p48
++nodelist ./nodelist ++remote-shell ssh apoa1/apoa1.namd
Info: Benchmark time: 48 CPUs 0.278276 s/step 3.22078 days/ns 54.4712 MB
memory
TIMING: 500 CPU: 17.0394, 0.0332949/step Wall: 120.797, 0.246653/step,
0 hours remaining, 54.471237 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 500 20974.8941 19756.6576 5724.4523
179.8271 -337741.4179 23251.1005 0.0000 0.0000
45359.0770 -222495.4094 165.0039 -267854.4864
-222061.0912 165.0039 -3197.5171 -2425.4143
921491.4634 -3197.5171 -2425.4143
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
WRITING COORDINATES TO OUTPUT FILE AT STEP 500
The last position output (seq=-2) takes 0.003 seconds, 59.168 MB of
memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
The last velocity output (seq=-2) takes 0.004 seconds, 59.014 MB of
memory in use
====================================================
WallClock: 141.985214 CPUTime: 21.389748 Memory: 59.014664 MB
i still get random segfaults with my compiled namd :-\
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:04 CST