AMBER Archive (2009)

Subject: RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8%

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Mon Jun 22 2009 - 14:54:17 CDT

Dear Amber Users,
 
My thanks, first of all, to Drs. Grignani and Case for your responses to my questions. I should have mentioned in my initial request for help that I had followed the instructions in the Amber 10 manual, as carefully as possible, using the -lamsource option. I then ran the ./configure_lam file and finally tried to do the parallel Amber 10 install which appeared to be running correctly. However, I then tried to test lam and it would not boot -- thus, I was unable to use the mpirun command. In working backwards, it appears that the source of the problem lies in the CygIPC software which offers no up-to-date install instructions. The result was that during the lam installation, the warnings that "SYSV semaphore and shared memory support could not be detected on my system" must have been fatal.
 
Just "for kicks" I also tried to do the complete installation using the -lamsource option without having CygIPC running -- the resulting failure was essentially identical. I'll try to contact the lam-mpi folks to see if they have any suggestions since a Google search doesn't reveal any help available for CygIPC. Thanks again.
 
Bob Hopkins
 

________________________________

From: amber-bounces_at_ambermd.org on behalf of case
Sent: Sat 6/20/2009 5:04 PM
To: AMBER Mailing List
Subject: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8%

On Sat, Jun 20, 2009, Hopkins, Robert wrote:
>
>
> 1.) Is it reasonable to try to install Amber 10 in parallel in a
> Cygwin environment on a machine with dual processors?

Yes.

>
> 2.) If anyone has done this, could you offer any suggestions as
> to how one might install LAM under Cygwin

Use the -lamsource option to configure, then run the configure_lam script that
is created. The point of shipping the lam sources with Amber was that lam
was the only popular MPI that seemed to build nicely under cygwin.

Having said that, it could be that the machine I tested this on had cygIPC
installed in a useful fashion that might be hard to replicate. But if you
haven't tried using the sources we provide, that is certainly a good thing to
try.

...dac

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