Dear Ross,
When I created this test case, I compared the NEB result of the old and new
implementation. They are identical.
Later Francesco updated the code and fixed output format and temperature,
Maybe he forget to update the test case or moved it to somewhere else. I
need
check with him, since the energy is still identical I think we are safe
to say the
code is correct.
I haven't got time to test QMMM/NEB yet, but since it is now running in
multi-sander
mode, I don't see any problem while cause error.
I agree with you that we need a more general way to get number of
processor during
test.
Sincerely,
Wei
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
