[gmx-users] lamboot command problem

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 13 11:39:39 CET 2008

sarbani chattopadhyay wrote:
> Hi everybody,
>                     I am facing problem while running parallel runs. 
> Ours is a single Mac Os X
> machine with 2 dual core processors.
> Thus the hostfile taht I made was
> mac-pros-computer.local cpu=2
> mac-pros-computer.local cpu=2
> When I use the command "lamboot" I get the message
> LAM 7.0.6/MPI 2 C++/ROMIO - Indiana University
> n-1<21286> ssi:boot:base:linear: booting n0 (mac-pros-computer.local)
> n-1<21286> ssi:boot:base:linear: finished
> Then when i try to run mdrun_mpi on 4 processors with the command
> nohup mdrun_mpi -v -s 4cpu_3rdvel.tpr -np 4 -N 4 -deffnm 4cpu_3rdvel &
> I get the error message:
> "run input file 4cpu_3rdvel.tpr was made for 4 nodes,
>             while mdrun_mpi expected it to be for 1 nodes"
> That means my hostfile could not specify that there are 4 processors. 
> Then how to write the
> hostfile correctly so as to fix this problem?

There need be nothing wrong with your hostfile. The hostfile describes 
the layout and range of MPI possibilities. When you run an MPI program, 
the default is to use only one MPI process. If you want more, use mpirun 
properly, e.g. mpirun -np 4 mdrun_mpi. These days one doesn't need to 
give -np 4 to mdrun_mpi, but the converse is not true.


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