How to change the Memory allocation function in Gromacs-3.3
I have installed the MPI version of Gromacs-3.3 on a cluster system running
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?
#1 Updated by Richard Wong over 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,
#2 Updated by Erik Lindahl over 14 years ago
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.