MBG wiki | RecentChanges | Blog | 2024-03-29 | 2024-03-28

Running NAMD on the cluster via SGE

There are two ways to run NAMD on the cluster : the old way, and the new way.

The old way

Is to submit a batch job via unix's 'at' command :
at -q z now
/bin/mosrun -L /usr/local/NAMD_2.5/charmrun /bin/mosrun -L /usr/local/NAMD_2.5/namd2 +p9 heat.namd > LOG
<CTRL-D>
where '+p9' defines the number of processors to use (9 in this case).

But, there were problems with the old way :

The new way

Enter SGE :


The advantages of using a proper queuing system are too many to discuss (see the SGE documentation). What is worth noting is that all this additional functionality comes at virtually no cost in terms of speed of execution. Compare the minimisation speed for the same identical job submitted via 'at' and 'qsub':

at timing statistics

TIMING:  200  CPU: 178.66,  0.8836/step   Wall: 181.67,  0.896849/step, 0.448424  hours remaining, 13975 kB of memory in use.
TIMING:  400  CPU: 345.77,  0.83555/step  Wall: 351.351, 0.848402/step, 0.377068  hours remaining, 13975 kB of memory in use.
TIMING:  600  CPU: 512.58,  0.83405/step  Wall: 520.755, 0.847025/step, 0.329398  hours remaining, 13975 kB of memory in use.
TIMING:  800  CPU: 679.38,  0.834/step    Wall: 696.912, 0.880784/step, 0.293595  hours remaining, 13975 kB of memory in use.
TIMING: 1000  CPU: 846.07,  0.83345/step  Wall: 866.847, 0.849677/step, 0.236021  hours remaining, 15687 kB of memory in use.
TIMING: 1200  CPU: 1013.13, 0.8353/step   Wall: 1037.54, 0.853481/step, 0.189662  hours remaining, 15687 kB of memory in use.
TIMING: 1400  CPU: 1180,    0.83435/step  Wall: 1208.06, 0.852557/step, 0.142093  hours remaining, 15687 kB of memory in use.
TIMING: 1600  CPU: 1347.06, 0.8353/step   Wall: 1377.96, 0.849509/step, 0.0943899 hours remaining, 15687 kB of memory in use.

SGE timing statistics

TIMING:  200  CPU: 178.57,  0.8832/step   Wall: 183.282, 0.904775/step, 0.452388 hours remaining, 13973 kB of memory in use.
TIMING:  400  CPU: 345.51,  0.8347/step   Wall: 354.533, 0.856257/step, 0.380559 hours remaining, 13973 kB of memory in use.
TIMING:  600  CPU: 512.48,  0.83485/step  Wall: 525.369, 0.85418/step,  0.332181 hours remaining, 13973 kB of memory in use.
TIMING:  800  CPU: 678.87,  0.83195/step  Wall: 696.738, 0.856846/step, 0.285615 hours remaining, 13973 kB of memory in use.
TIMING: 1000  CPU: 845.37,  0.8325/step   Wall: 867.586, 0.854238/step, 0.237288 hours remaining, 15685 kB of memory in use.
TIMING: 1200  CPU: 1012.03, 0.8333/step   Wall: 1039.36, 0.858858/step, 0.190857 hours remaining, 15685 kB of memory in use.
TIMING: 1400  CPU: 1178.78, 0.83375/step  Wall: 1210.17, 0.854063/step, 0.142344 hours remaining, 15685 kB of memory in use.
TIMING: 1600  CPU: 1345.85, 0.83535/step  Wall: 1383.31, 0.865716/step, 0.096190 hours remaining, 15685 kB of memory in use.