simtk.org

Hello,

I'm trying to do the simulation with "http://simvascular.github.io/clinicalCase4.html" (Healthy Pulmonary). Everything went well until the simulation :

Error! ***Memory allocation failed for SetUpGraph: gdata. Requested size: -1364245688 bytes
(please see attached the whole error message).

Does it mean that my computer doesn't have enough memory (and the memory requested is so big that the value overflowed ?). If it is the case is there a way to do the simulation anyway ?

Thank you in advance,
Have a nice day,

Ruiyi

Hi Ruiyi,

This error is from the Metis mesh partitioning code used by the solver and means that your computer does not have enough memory. How large is your mesh? Are you trying to run this simulation on a workstation?

Cheers,
Dave

Hello Dave,

Here are the characteristics of my mesh :

Nb of nodes : 19741690
Nb of Elems : 122558419
Nb of Edges : 4005168
Nb de Faces : 2670112

I'm working on my laptop (Intel Core i7-4712HQ Processor), I have 158 Go of free memory. My question may be a bit naive but it isn't enough ? If it is the case, could you have an estimation of how much I need ?

Thank you in advance,
Have a nice day,

Ruiyi

Hi Ruiyi,

This is a huge mesh, you can't run a simulation for this size mesh on your laptop. You will need to run the simulation on a high-performance computer cluster and even then it will take a lot of resources, a few hundred processors I would think.

You should try to decrease the size of the mesh to a few million elements. You would still not be able to run the simulation on your laptop but it would easy to run on an HPC cluster.

Cheers,
Dave

Hello,

It seems that it works fine with less elements in the mesh. Thank you very much !

Have a nice day,
Ruiyi