[gmx-users] g_cluster - Cannot allocate memory

Nuno R. L. Ferreira nunolf at ci.uc.pt
Sat Mar 12 01:35:09 CET 2005

Hi *

I run g_cluster on a set of 44k frames (each with 48 atoms), and I got the

g_cluster -f ../../trimers_build/trimers_strands_EG.pdb  -s
./trimers_set1_00001.pdb -n ../strands_EG.ndx -dist -sz -clid -nice 0


Select group for least squares fit and RMSD calculation:
Group     0 (  strands_EG) has    48 elements
There is one group in the index
Reading frame       0 time    1.000    '', 48 atoms
Last frame      39999 time 40000.000   
Allocated 23040000 bytes for frames
Read 40000 frames from trajectory ../../trimers_build/trimers_strands_EG.pdb
Program g_cluster, VERSION 3.3_beta_20050202
Source code file: smalloc.c, line: 113

Fatal error:
calloc for m[i] (nelem=40000, elsize=4, file matio.c, line 70)

"Hold On Like Cliffhanger" (Urban Dance Squad)
: Cannot allocate memory

Obviously my machine does not have suficient memory.
>From the warning, it tells me that aprox. 22 MB were
allocated to the frames. But I have 1 GB of RAM. Perhaps
the remaining goes to the matrix building?

The trajectory I'm feeding to g_cluster does not come from MD,
that's way I do not want to skip every dt frame. 

How can I know a priori, if a certain trajectory with x frames is able to be
clustered in a machine with y of RAM?

Best regards,

Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
" Do not worry about your dificulties in mathematics.
   I can assure you that mine are still greater."

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