Hi Jason,
Thanks for the response. The reason we would like to use the previously
mentioned mask is because the whole system entropy calculation takes a long
time. The same setting entropy calculation (48 frames for the whole
system 10 A of water and 260 a.a.) become a lot slower than before. Before
it can be finished using 4 nodes/ 48 CPUs/ large memory nodes (1 TB RAM )
in 48 hours and now 4 nodes/ 48 CPUs/ large memory nodes ((1 TB RAM ))
cannot be finished even im 96 hours (wall limit) . We wonder the
possible explanation is perhaps the node communication might become slower?
We also notice that during the entropy calculation, some parts run
faster/update constantly than the others, as following. Wonder this
phenomena is normal or it suggests that something is wrong so the parts are
not coordinated? Thanks.
-rw-rw-r-- 1 user user 6769040 Dec 14 02:30
LIGAND_preparation/_MMPBSA_receptor_nm.out.0
-rw-rw-r-- 1 user user 3818948 Dec 13 10:09
LIGAND_preparation/_MMPBSA_receptor_nm.out.10
-rw-rw-r-- 1 user user 5419009 Dec 13 20:01
LIGAND_preparation/_MMPBSA_receptor_nm.out.11
-rw-rw-r-- 1 user user 29974 *Dec 15 22:39 *
LIGAND_preparation/_MMPBSA_receptor_nm.out.2
-rw-rw-r-- 1 user user 4185838 *Dec 13 17:48 *
LIGAND_preparation/_MMPBSA_receptor_nm.out.3
-rw-rw-r-- 1 user user 21907213*Dec 15 22:39*
LIGAND_preparation/_MMPBSA_receptor_nm.out.4
-rw-rw-r-- 1 user user 21944257*Dec 15 22:39*
LIGAND_preparation/_MMPBSA_receptor_nm.out.5
-rw-rw-r-- 1 user user 4762318 Dec 13 17:34
LIGAND_preparation/_MMPBSA_receptor_nm.out.6
-rw-rw-r-- 1 user user 3960067 Dec 13 19:01
LIGAND_preparation/_MMPBSA_receptor_nm.out.7
-rw-rw-r-- 1 user user 49692 *Dec 15 22:39 *
LIGAND_preparation/_MMPBSA_receptor_nm.out.8
-rw-rw-r-- 1 user user 3492151 Dec 13 14:33
LIGAND_preparation/_MMPBSA_receptor_nm.out.9
Cheers,
Henry
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Received on Sun Dec 15 2013 - 21:00:02 PST
