QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: serhan on April 20, 2009, 18:38

Title: St9_badalloc error
Post by: serhan on April 20, 2009, 18:38
Hi,

I'm trying to calculate scf of a (6,6) carbon nanotube but ATK gives the error:

Code
master@node01:~$ mpiexec -n 12 /home/master/atk-2008.10.0/bin/atk /home/master/6/6_6_nanotube_script.py > /home/master/6.dat &
[1] 10244
master@node01:~$ Traceback (most recent call last):
  File "<string>", line 916, in ?
ATKError: St9bad_alloc

I searched google, some say that this is caused from insufficient memory. My simulation includes 480 carbon atoms. I'm using LDA with 150 Ry cut-off. Each machine uses 2GB RAM with 64-bit Ubuntu and I'm using 6 PCs in parallel.

Cheers,
Serhan
Title: Re: St9_badalloc error
Post by: Anders Blom on April 20, 2009, 20:21
Yes, it means out of memory (searching on this Forum would give you that answer too ;) )

480 C atoms can fit into 2 Gb, but it depends a bit on the parameters. For instance, if you have a DoubleZetaPolarized basis set, it naturally requires more memory than SingleZeta. Also, a bit hidden, is the number of k-points.

However, in your case there seems to be a simpler way to reduce the memory used per machine. You have 6 PCs yet you run 12 MPI processes. That means each PC will receive 2 MPI jobs, and thus only 1 Gb is available for each process. If you instead run "mpiexec -n 6" each MPI process will have 2 Gb.
Title: Re: St9_badalloc error
Post by: serhan on April 21, 2009, 03:39
Thank you very much :)

Cheers,
Serhan
Title: Re: St9_badalloc error
Post by: Nordland on April 21, 2009, 08:17
Totally unrelated question:

Is your avatar picture the band structure for Graphene?
Title: Re: St9_badalloc error
Post by: serhan on April 21, 2009, 20:39
Yes, it is said to be the band structure of graphene. I've taken it after some googling from the Internet.

Cheers,
Serhan
Title: Re: St9_badalloc error
Post by: serhan on April 25, 2009, 15:06
Hi,

Can I use swap space if RAM is not enough?

Cheers,
Serhan
Title: Re: St9_badalloc error
Post by: Nordland on April 25, 2009, 16:23
It depends alot on your machine, however you are limited by the maximum amount of memory your operating system can assign, so if you are on 32bit, then it will be maximum 3.5 Gb...
Title: Re: St9_badalloc error
Post by: serhan on April 25, 2009, 16:40
I'm using on 64-bit Ubuntu. Does ATK automatically tries to assign swap space, or is it dependent on th OS?

Cheers,
Serhan
Title: Re: St9_badalloc error
Post by: Nordland on April 25, 2009, 16:58
It depends on the OS.

What version of Ubuntu are you running, because I am trying to install VNL on 64bit ubuntu and I am having a little trouble with it.
Title: Re: St9_badalloc error
Post by: serhan on April 26, 2009, 06:01
I'm using Ubuntu 9.0.4. However, I could not install VNL on it, it gives some library errors, that may be corrected by installing libraries. I'm using only ATK on it.