From NWChem
Viewed 3463 times, With a total of 2 Posts
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Just Got Here
Threads 2
Posts 4
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| 1:30:15 AM PST - Sat, Mar 3rd 2012 |
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Dear all,
I need to ab intio calculations with where no. of basis functions ~ 1000 at MP2 l.o. theory with basis sets such as aug-cc-pvtz.
My hardware is a beowulf cluster with 7x intel i7 @ 3.40GHz machines with 16gb memory each.
Nwchem is compiled with openmpi. The jobs run fine in parallel, and with ~500-600 basis fns the performance is good. But with larger systems, the scf takes too long. Both direct and semidirect.
The disk I/O is very slow so i need to to direct scf calculationsfor the integral computation or semidirect with very limited disk I/O.
But direct seems very expensive
f.e. water cluster of 11 units takes 2hrs for a S.P.E. at MP2/aug-cc-pvtz on the given hardware. Of this the SCF takes 45 mins!
1. Is the time reasonable?
2. Are there some optimal values for stack, heap and global memory (other than default to maximize chacing)?
Thanks in advance!
Jonathan
Some relevant info :
The scf options were :
scf
semidirect filesize 10000000
end
mp2
freeze atomic
end
task mp2
Memory information
------------------
heap = 129602401 doubles = 988.8 Mbytes
stack = 129602401 doubles = 988.8 Mbytes
global = 259204800 doubles = 1977.6 Mbytes (distinct from heap & stack)
total = 518409602 doubles = 3955.2 Mbytes
verify = yes
hardfail = no
Superposition of Atomic Density Guess
-------------------------------------
Sum of atomic energies: -833.58996280
Integral file = ./scr/test.aoints.00
Record size in doubles = 65536 No. of integs per rec = 32766
Max. records in memory = 0 Max. records in file = 2478
No. of bits per label = 16 No. of bits per value = 64
#quartets = 9.885D+08 #integrals = 3.954D+10 #direct = 94.2% #cached = 5.8%
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Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Forum Vet
Threads 4
Posts 597
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| 1:08:24 PM PST - Wed, Mar 7th 2012 |
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In direct mode each two-electron integral is recomputed every time it is needed. In semidirect the SCF will try to store as much as it can, either in memory or on disk. If you do not want to use disk for caching you should use "semidirect filesize 0". The calculation will try to store as much in memory as it can. The memory it uses is the stack. I see you specify about 4 Gbyte of memory per core in your input. Standard, memory will be allocated 25% heap + 25% stack + 50% global. To store more integrals in memory, you want to maximize stack. I would try reducing the heap to maybe 100 mb and up the stack to 1900 mb. You may be able to reduce the global space and move that to stack too.
Alternatively, adding more processors gives you more memory to work with. In all reality, recomputing these integrals every time is expensive. One could fiddle with the threshold for the integrals, to reduce the number of integrals being recomputed if you really want.
Bert
Quote:Jonathan Mar 3rd 8:30 amDear all,
I need to ab intio calculations with where no. of basis functions ~ 1000 at MP2 l.o. theory with basis sets such as aug-cc-pvtz.
My hardware is a beowulf cluster with 7x intel i7 @ 3.40GHz machines with 16gb memory each.
Nwchem is compiled with openmpi. The jobs run fine in parallel, and with ~500-600 basis fns the performance is good. But with larger systems, the scf takes too long. Both direct and semidirect.
The disk I/O is very slow so i need to to direct scf calculationsfor the integral computation or semidirect with very limited disk I/O.
But direct seems very expensive
f.e. water cluster of 11 units takes 2hrs for a S.P.E. at MP2/aug-cc-pvtz on the given hardware. Of this the SCF takes 45 mins!
1. Is the time reasonable?
2. Are there some optimal values for stack, heap and global memory (other than default to maximize chacing)?
Thanks in advance!
Jonathan
Some relevant info :
The scf options were :
scf
semidirect filesize 10000000
end
mp2
freeze atomic
end
task mp2
Memory information
------------------
heap = 129602401 doubles = 988.8 Mbytes
stack = 129602401 doubles = 988.8 Mbytes
global = 259204800 doubles = 1977.6 Mbytes (distinct from heap & stack)
total = 518409602 doubles = 3955.2 Mbytes
verify = yes
hardfail = no
Superposition of Atomic Density Guess
-------------------------------------
Sum of atomic energies: -833.58996280
Integral file = ./scr/test.aoints.00
Record size in doubles = 65536 No. of integs per rec = 32766
Max. records in memory = 0 Max. records in file = 2478
No. of bits per label = 16 No. of bits per value = 64
#quartets = 9.885D+08 #integrals = 3.954D+10 #direct = 94.2% #cached = 5.8%[/quote]
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Just Got Here
Threads 2
Posts 4
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| 11:39:01 AM PDT - Sun, Mar 11th 2012 |
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Bert,
Thanks. Maximizing stack does help. Will try and fiddle with threshold
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