QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: Jahangiri on July 7, 2010, 08:26
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Dear users and Developers
I have a question. Maximum for how many atoms for two probe system atk can work ?
I am asking because I faced an error which I think is due to memory allocation .
I am having this error:
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/opt/mpich2/bin/mpiexec -n 8 /opt/vnl-2008.10.0/atk/bin/atk twoprobe_configuration_script.py > OUT1.out
Traceback (most recent call last):
File "<string>", line 1139, in ?
ATKError: St9bad_alloc
=======================================================================
I should mention the job gets over after one day ( by getting the error ) , and the number of atoms are 749.
Could any one give any suggestion?
Thank you.
Best regards
Akbar
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Over 700 atoms is certainly pushing the limit. There is no strict limit, since it depends on your parameters. The memory consumption depends critically on the k-point sampling, the basis set size (and of course the number of atoms), and the grid size (total simulation volume, taking the mesh cut-off into account).
Also the parallelization strategy is important. I see you use -n 8, but do you have 8 computers, or one machine with two quad-cores? Each MPI processes uses the same amount of memory, so if you run 8 processes on one single machine, each process can max use 1/8 of the machine RAM. In this case, you can only run small systems - or use fewer MPI processes.
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Dear Anders Blom
We have one machine with 8 cores. But by referring to the system configuration. I think 16GB RAM would be sufficient !
Am I right?
The system Information is as following :
===============================================================
MemTotal: 16461608 kB
MemFree: 15317608 kB
Buffers: 19184 kB
Cached: 231664 kB
SwapCached: 106636 kB
Active: 28292 kB
Inactive: 714956 kB
Active(anon): 12044 kB
Inactive(anon): 480364 kB
Active(file): 16248 kB
Inactive(file): 234592 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 5119992 kB
SwapFree: 4829652 kB
Dirty: 0 kB
Writeback: 0 kB
AnonPages: 422284 kB
Mapped: 20444 kB
Slab: 56960 kB
SReclaimable: 25944 kB
SUnreclaim: 31016 kB
PageTables: 15456 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 13350796 kB
Committed_AS: 930184 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 368876 kB
VmallocChunk: 34359339227 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 7680 kB
DirectMap2M: 16760832 kB
=======================================================================
Thank you very much.
Best regards
Akbar
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That gives you 2 Gb per MPI process. 2 Gb for 700 atoms is tight, esp. if you want something better than SingleZeta basis set (and you do), and a couple of k-points.
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Dear Anders Blom
Thank you very much.
Best regards
Akbar