AMBER Archive (2009)

Subject: RE: [AMBER] mpirun problem in HPC

From: Ross Walker (
Date: Fri Feb 06 2009 - 02:05:37 CST

Dear Vijay,

> Dear sir I have problem in installing amber9 in HPC and I get the out put
> as below::
> prob in HPC for mpirun
> vijay_at_ptmlxclus:~/Simulation> mpirun -np 16 pmemd -O -i MD-betaMalto-
> -p -c betaMalto-lyoHIGH-MD18-
> run0700.rst_100000 -o betaMalto-lyoHIGH-MD18-run0700.out -x betaMalto-
> lyoHIGH-MD18-run0700.traj -r betaMalto-lyoHIGH-MD18-run0800.rst
> You can't run mpdboot on ['cl1n003'] version of python must be >= 2.4,
> current ['']
> You can't run mpdboot on ['cl1n002'] version of python must be >= 2.4,
> current ['']
> You can't run mpdboot on ['cl1n001'] version of python must be >= 2.4,
> current ['']
> You can't run mpdboot on ['cl1n004'] version of python must be >= 2.4,
> current ['']
> mpiexec: unable to use -nolocal for mpd ring with size 1
> vijay_at_ptmlxclus:~/Simulation>

This is not a problem with AMBER it is a problem with your MPI installation and will affect all mpi programs not just AMBER. This suggests to me that you probably did not build this version of MPI on the machine and operating system you are trying to run it on. It could also be that your OS does not meet the minimum requirements for the version of MPI you are using. You should check the docs for your MPI implementation and see what the requirements are - then upgrade the OS on your nodes to match this. This is the cleanest way to do it. Since you don't specify which version of MPI you are using, your architecture, operating system or any other information that is necessary to understand exactly what is going on it is a little difficult to help here.

However, as an undocumented and 'unsupported!!!' hack you could try editing $MPI_HOME/bin/mpdboot (you probably need to be root to do this) and look for something like:

#!/usr/bin/env python2.4

at the top of the file. Try changing that to python2.3 and see if it helps. If that doesn't work try searching through the file for where the check is made on the version of python (if you don't know python now would be a good time to learn since you'll probably need it at some point if you plan to do computational chemistry). Once you find the check (searching for the error message is always a good start) then just disable the check and see if mpdboot now runs...

If you are lucky the people who wrote your MPI were just over cautious on the version of python needed and it will run fine with an older version of python. If you are not lucky then they will have used features only found in python >=2.4 and then you will need to upgrade the version of python on your machines.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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