AMBER Archive (2002)

Subject: RE: Sander multiprocessors running problem with MPI

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 02 2002 - 12:52:27 CDT

Dear William,

This is the essential line you need to focus on:

> rsh: host.utoronto.ca: not found

It is telling you that host.utoronto.ca cannot be found. The problem is
thus with your mpi configuration. You need to check the mpi machine
definition file for your system.

- Does it list the correct machine names and number of processors.

Try typing "uname" to get the correct hostname for your machine and
correct the mpi definition file as necessary.
You will also need to add this host and all other hosts you want to run
the mpi job over to .rhosts in your home directory in order to allow rsh
to these machines without a password.

Without more detailed information on your system set up and mpi
configuration it is a little hard to offer a detailed solution.

All the best
Ross

/\
\/
|\oss Walker

| Imperial College of Science, Technology & Medicine |
| Department of Chemistry | Theoretical Division |
| Tel:- +44 20 759(45851) |
| EMail:- ross_at_rosswalker.co.uk | http://www.rosswalker.co.uk/ |
| PGP Key available on request |

> -----Original Message-----
> From: William Wei [mailto:william_at_phm.utoronto.ca]
> Sent: 02 October 2002 19:10
> To: Amber List
> Subject: Sander multiprocessors running problem with MPI
>
>
> Hi all,
>
> Now I met a problem with multi processor sander running.
> Before I can run it
> with MPI, and actually, it had run for 1ns dynamics
> simulation. Several days
> ago, while I send it for longer dynamics simulation, it told me:
> rsh: host.utoronto.ca: not found
> p0_243143: p4_error: Timeout in making connection to remote process on
> host.utoronto.ca:0
>
> And gave me a file named PIXXXX:
> host.utoronto.ca 0 /usr/people/soft/amber/exe/sander
> host.utoronto.ca 1 /usr/people/soft/amber/exe/sander
> host.utoronto.ca 1 /usr/people/soft/amber/exe/sander
> .......
>
>
> Could you help me to figure out, what is wrong with my system
> (sgi Onyx
> multiprocessor super computer). Thanks a lot.
>
> William
>
> -------------------------
> William Wei
> Faculty of Pharmacy
> 19 Russell Street
> Toronto, ON. M5S 2S2
> Tel: 1-416-946-8469
> Fax: 1-416-978-8511
> Email: william_at_phm.utoronto.ca
> william.wei_at_utoronto.ca
>
>
>
>
>