AMBER Archive (2008)

Subject: Re: AMBER: Compilation of amber8 patched with ramd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 25 2008 - 03:17:59 CDT

This is especially directed to Vlad and Stefen, as they know ramd:

For the parallel compilation I made recourse to tricks as the flag
-openmpi was not recognized. Having MPICH_HOME pointing where MPI_HOME
is (although I have only openmpi) I used the flag -mpich.

The test "make test.sander" was met with failure for tgtmd only. I
believe it can be forgotten.

The test ./Run.ramd (while still having the env var DO_PARALLEL for 4
processors) only reported some diff that seem to me acceptable given
the different platform (the serial test was completed in 5 sec against
the 14 sec used in 2005 on your platform). Could you please have
acursory view at the attached files to confirm my impression and
giving me the imprimatur to use ramd? Thanks (thousand)

francesco

On Wed, Jun 25, 2008 at 12:06 AM, David A. Case <case_at_scripps.edu> wrote:
> On Tue, Jun 24, 2008, Francesco Pietra wrote:
>
>> Running the general serial test for amber8, all PASSED except
>> newton_raph (forrtl: severe (174) segmentation fault). That likely
>> because no bugfix was applied (and it can't) to amber8 before patching
>> with ramd. I was unable to trace what newton_raph is expected to do,
>> so that may I ask whether this is a problem for running ramd?
>
> As I understand it, RAMD is a modification to *sander*, and newton_raph
> is an *nmode* test. They are complete separate executables.
>
> ...dac
>
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-- 
Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)
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