One more question regarding the "parallel" section:
AmberTools
1) Configure for the MPI build:
cd $AMBERHOME/src
make clean
./configure -mpi gnu
I am not sure where to clean, but the configure should definitely happen
in $AMBERHOME/AmberTools/src and not in $AMBERHOME/src, right?
Jan-Philip
On 01/13/2012 03:34 PM, Jan-Philip Gehrcke wrote:
> Hey,
>
> I've read and followed
>
> http://ambermd.org/HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html
>
>
> Under "Serial compilation", section "AMBER", there is no configure step
> mentioned. Also, according to that manual, it is not necessary to
> execute AT15_Amber11.py.
>
> I exactly followed this manual. Hence, I incorporated all bugfixes.
> During `make serial` in $AMBERHOME/src, I got an error like
>
> cannot stat: ../../AmberTools/src/netcdf/include/*.mod -- no such file
> or directory
>
> (I lost the original message.) In fact, I verified that there was no
> directory $AMBERHOME/AmberTools/src/netcdf/include. I've then executed
> AT15_Amber11.py, because I've seen that one of its patches deals with
> exactly this directory. I invoked `make serial` again and it finished
> properly.
>
> AT15 bugfix 24 should "automagically" apply the AT15_Amber11.py script.
> However, following the steps of the manual it does not seem to work
> properly. I believe that either the AT15_Amber11.py step should be added
> to the manual or the bugfix 24 is not working correctly.
>
> Thanks,
>
> Jan-Philip
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 13 2012 - 07:00:05 PST
