Hi Ross and Wei,
The PIMD/CMD stuff has been updated and slightly modified a couple of
months ago. Therefore, the old PIMD/CMD test cases are not meaningful
anymore. The new test cases are in test/PIMD.
cheers,
Francesco
Ross Walker wrote:
> Hi Wei,
>
>
>> In amber 10, you need to use sander.MPI to do NEB simulation.
>>
>
> This is good but I have a number of concerns...
>
>
>> There is a test case showing how to do this in
>> amber10/test/full_pimd/Run.full_pimd.
>>
>
> These test cases appear nowhere in the standard test Makefile so I assume
> haven't been run for ages and none of the other developers would be aware if
> they are trampling on this code with their updates.
>
> The Centroid test case fails with a namelist error:
>
> Testing Centroid MD
> forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
> 5, file /usr/local/amber10/mpich2/test/full_pimd/cmd.in, line 21, position
> 11
>
> All other test cases run but fail. The errors are reasonably innocuous in
> that it appears that the saved files all just need updating. The save files
> all have a zero temperature and in addition all new runs print the time to 5
> decimal places instead of 3. E.g:
>
> < NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0. PRESS =
> 0.
> ---
>
>> NSTEP = 1 TIME(PS) = 0.00100 TEMP(K) = 179.57 PRESS =
>>
> 0.
> 13c13
> < NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 0. PRESS =
> 0.
> ---
>
>> NSTEP = 2 TIME(PS) = 0.00200 TEMP(K) = 341.05 PRESS =
>>
> 0.
>
> So the problems with testing here concern me - have you validated that the
> current tree indeed gets the correct results? You should really update the
> test cases and have it run as part of the standard testing ASAP otherwise
> there could be serious problems with other people updating the CVS tree.
>
> So you might want to fix the printing of the time and update the test cases
> with the correct temperatures. Meanwhile I'll run alanine dipeptide with the
> new NEB and make sure it gets the correct pathway.
>
> Also are there any qmmm NEB test cases?
>
> On another note the following from numprocs.awk:
>
> BEGIN{i=0}
> {while ( i < NF ){if( $i == "-np" || $i == "-n"){i++;print $i; exit}; i++;}}
>
> is not transferable. Not all mpi implementations have -n or -np followed by
> the number of processors. For example on AIX the environment variables
> MP_NODES and MP_TASKS_PER_NODE are used to define the number of processors
> to run and then "poe" with no extra command line options is used to launch
> the mpi job.
>
> Hence we need to rethink how the test cases detect the number of processors.
> While it isn't so much of a problem with Amber 10 while under development
> once it is released I can just hear all the complaints on the amber mailing
> list... :-(. So either we write a single centralized (probably in
> $AMBERHOME/test/) numprocs.awk script that works for all mpi implementations
> we can find or we find a more graceful way for the test case scripts to
> handle sander quiting due to incompatible processor counts. Comments?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
Received on Wed Apr 25 2007 - 06:07:34 PDT
