It happens using both 3.2 and trunk version. The program runs both on a local cluster and on a supercomputing cluster.the last one has only 2 GB of memory per node and 16 cpu per node and I have verified that it works using only 2cpu per node,I.e.,with memory per process of about 8 GB (the same holds in the local cluster) The code has been compiled by different teams in the two clusters so I'm curious about the possible mistake in the compilation. Thanks for your support Simona Il 30/ott/2015 16:11, "Nick Papior" <[email protected]> ha scritto:
> siesta version? > are you on a cluster? If so, have you asked your local administrator for > memory exhausts? > those outputs suggests relatively small systems so perhaps you have > compiled the program erroneously? > > 2015-10-30 16:00 GMT+01:00 Simona Achilli <[email protected]>: > >> Dear SIESTA users, >> I’ve currently some problem to run SIESTA for metal surfaces because >> often the program crashes with segmentation fault. >> It happens mainly with large systems (more than 400 atoms) but also with >> cells containing few atomic layers (40 atoms). In general in these >> calculations the number of orbitals is quite large. >> I was thinking it can be a problem related to memory requirement. In fact >> I’ve verified that allowing an higher memory per MPI process SOMETIMES I >> can overcome the problem. >> >> Nevertheless, being the segmentation fault always at the same point, i.e. >> after the initialization of the DM and the definition of the mesh, I was >> wandering if it can be due to a different problem, may be related to the >> mesh. >> In fact it seems quite strange that problem of memory occurs using only >> 40 atoms…. >> I have attached below the last lines before the program stop, the first >> for large simulation cell, the second for a smaller one. >> >> If you have encountered the same problem and solved, please give me ad >> advise. >> I’ve also tried to use the DirectPhi .true. parameter but never changed. >> >> >> Thank you in advance >> >> Simona Achilli >> >> >> *************************************************************************************** >> InitMesh: MESH = 240 x 240 x 360 = 20736000 >> InitMesh: (bp) = 120 x 120 x 180 = 2592000 >> InitMesh: Mesh cutoff (required, used) = 250.000 267.995 Ry >> ExtMesh (bp) on 0 = 192 x 132 x 158 = 4004352 >> New grid distribution: 2 >> 1 1: 120 1: 60 1: 32 >> 2 1: 120 1: 60 33: 180 >> 3 1: 120 61: 120 1: 32 >> 4 1: 120 61: 120 33: 180 >> New grid distribution: 3 >> 1 1: 120 1: 60 1: 35 >> 2 1: 120 1: 60 36: 180 >> 3 1: 120 61: 120 1: 35 >> 4 1: 120 61: 120 36: 180 >> Setting up quadratic distribution... >> ExtMesh (bp) on 0 = 192 x 132 x 100 = 2534400 >> >> *************************************************************************************** >> >> New_DM. Step: 1 >> Initializing Density Matrix... >> >> InitMesh: MESH = 50 x 50 x 1200 = 3000000 >> InitMesh: Mesh cutoff (required, used) = 300.000 312.872 Ry >> >> * Maximum dynamic memory allocated = 115 MB >> > > > > -- > Kind regards Nick >
