Re: [AMBER-Developers] [AMBER] Error initiating H-REMD

From: Jason Swails <>
Date: Fri, 1 Feb 2013 21:56:40 -0500

On Fri, Feb 1, 2013 at 6:52 PM, Brian Radak <> wrote:

> Hi all,
> I am trying to run QM/MM umbrella sampling using HREMD. However, all of the
> simulations crash and the first replica in the groupfile gives the
> following error:
> Creation of partners array failed! Bad REMD setup!

Since this is an error that's only possible in the developers version I'm
moving it to the developer list instead.

> Here's an example line from the groupfile:
> -O -i r0/QMMM_1.inp -o r0/QMMM_1.out -p
> ../initial/ets_C41pC75p_Mg_QMMM_initial.prmtop -c r0/QMMM_0.rst7 -r
> r0/QMMM_1.rst7 -x r0/ -rem 3 -remlog QMMM_1.remlog
> Poking around in the source code it looks like the error message is
> triggered when checking that all replicas have 2 defined replicas. Under
> what circumstances would/should this check fail? It seems like a pretty
> foolproof process based off of reading the groupfile.

So what's really happening here is that the replica index is grabbed for
the current dimension (this is how I know it's Amber developer only), the
neighbors (or partners) of the array are determined by the replica one
higher and one lower (as defined in the groupfile for H-REMD), and then all
indices are gathered into a table so each replica can pick out the ranks
that its partners are in the REMD communicator.

The only way I can really see this failing in one dimension is if the index
array (either index_list or replica_indexes) is corrupted at some point --
I've seen weird behavior with specific compiler/MPI combinations in rare
instances (OpenMPI with ifort comes to mind). Can you modify the code to
print out these tables on each thread? Printing them to a different file
(something like write(666+remd_rank, *) blah) will help narrow down what
data isn't correct on which replica.

Also, do the test cases pass?

Worst case scenario we can debug it next week.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Fri Feb 01 2013 - 19:00:04 PST
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