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Bug #41

How to change the Memory allocation function in Gromacs-3.3

Added by Richard Wong almost 14 years ago. Updated almost 14 years ago.

Status:
Closed
Priority:
Low
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

I have installed the MPI version of Gromacs-3.3 on a cluster system running
LINUX 2.4.21-37.ELsmp.
The version of MPI on our system is MPICH-1.2.5..10
The network software is Myrinet GM 2.0.8.
The gcc version is gcc-3.2.3.

My problem is that the MPICH-GM does not like MPI application software using
its own malloc library and so I am not able to run the MPI Gromacs-3.3 on our
system. Is it possible to turn off the Gromacs' malloc library in
the 'configure' command and use the default Myrinet-GM malloc library?

Richard

History

#1 Updated by Richard Wong almost 14 years ago

I have found out the mistake I made in the execution of configure command.
To generate a MPICH-GM version of gromacs-3.3, the options 'enable-mpi'
and 'enable-share' are mutually exclusive in the configure command. Otherwise,
the executable 'mdrun_mpi' would not run successfully in MPICH-1.2.5..10,
GM/2.0.8 environment.

#2 Updated by Erik Lindahl almost 14 years ago

Hi,

Great, I take it that means it's closed.

The MPI standard doesn't allow for MPI implementations requiring their own allocation routines, so we
don't want to change that. In many cases (Altivec, SSE, etc) there are other libraries (e.g. FFTW) that DO
require their own allocation, which would otherwise make them mutually exclusive.

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