Mario Valle Web

STM3 development ideas

Here are, without any order, some ideas I have tried and collected during STM3 development. This page serves only as a repository, for now.

The user environment was Linux 7.2 with gcc 2.96 and AVS/Express 6.2 – RH7

Optimization

Use the profiler to understand where to focalize the efforts

Tune gcc options

Builtin function usage

The real optimizations

But anyway the best optimization has been to change the DrawBonds algorithm! The brute force approach was ok for small molecules, but the time is O(n2). The real lesson is to test with varying load levels after the code is working.

Also I have provided various rendering options to balance visual quality with speed.

Another optimization is not to execute unneeded operations (like compute H bonds if no H are present in the input file).

Another AVS/Express performance killer

To allocate a dynamic list I was doing something like this inside a loop:

num_bonds = num_bonds + 1;
int *bond_type_lst_arr = (int *)bond_type_lst.ret_array_ptr(OM_GET_ARRAY_RW);
bond_type_lst_arr[num_bonds-1] = H_BOND;
ARRfree(bond_type_lst_arr);

This was a real performance killer. Then I changed it to:

bond_type_lst_vect.push_back(int(H_BOND));
followed by a copy to bond_type_lst_arr outside the loop

And, together with the search algorithm change, my timing went from 48 sec to 0.7 sec. Amazing!

Esoteric options

--file-ordering map_file
The --file-ordering option causes "gprof" to print a suggested .o link line ordering for the program based on profiling data. This option suggests an ordering which may improve paging, tlb and cache behavior for the program on systems which do not support arbitrary ordering of functions in an executable.
Use of the -a argument is highly recommended with this option.
The map_file argument is a pathname to a file which provides function name to object file mappings. The format of the file is similar to the output of the program "nm".
To create a map_file with GNU "nm", type a command like:
"nm --extern-only --defined-only -v --print-file-name program-name"

Not tried yet.

Code cleaning

Compiling with:

-Wall -pedantic

is really too much. So it is better to use (-O to catch uninitializated variables usage):

-Wall -0

Another exercise is to compile both on Linux and Windows.

Use lint, splint, indent to catch dubious code format.