[SOSlib-discuss] FW: AIX, Re: SOSlib: arithmetic compiler issues

[Eric F. <efe...@ph...>]

> > Rainer Machne wrote:
> > this might be a general problem with current gcc
> compilation. For some
> > other reason I have just integrated a quite large model and can 
> > confirm that gcc compilation also on my machine takes surprisingly 
> > long. We should investigate this problem, but currently we
> don't have
> > much time unfortunately.
> 
> Ok, I have just analyzed this a bit. Most time is indeed spent by the 
> compiler, and not e.g. in loading the .so/library file.
> 
> This model has 93 ODEs, and the resulting c file is 1.2 MB big! Is 
> this file size a bottle-neck for gcc file parsing?
> 
> Some ways to decrease file size:
> The majority of this file are 0 entries of the Jacobian. If CVODE 
> initializes these correctly (DENSE_ELEM makro), then we could just 
> skip all these equations. Also the whole adjoint stuff is co-compiled,

> even if not requested. This is another big part of the file, and the 
> according functions could be compiled separately, on request.
> 
> what do you think?

Hi,

I am coming back to you regarding the issues I get using model
compilation on AIX (old method, using gcc) and would like to share my
findings.

I previously reported how slow gcc was to compile models, taking
sometime almost 2 minutes. This time was proportional to the size of the
value array in the c file, and not the overall "complexity" of the model
(nb of species and events for instance). Also, it is very dependent on
the level of optimization the compiler is set.

I tried compiling bhalla_02.xml MAPK model with gcc and xlc_r (IBM
compiler on AIX) and got those results (in seconds):

For gcc I used something like:
time gcc -I/hpc/work/fernandz/local/include
-I/hpc/work/fernandz/local/include -I../src -pipe -shared -fPIC -o ./out
./model.c -L../src -L/hpc/work/fernandz/local/lib -lODES -lsbml -lm
-lstdc++ -O0

For xlc_r I used something like:
time xlc_r -I/hpc/work/fernandz/local/include
-I/hpc/work/fernandz/local/include -I../src -G -o out ./model.c -L../src
-L/hpc/work/fernandz/local/lib -lODES -lsbml -lm

gcc
-O0 15.4
-O1 108
-O3 334

xlc_r
-O0 1.7
-O1 1.7
-O2 20
-O3 21
-O5 fails with unresolved references

I share your opinion Rainer: if we can drop the 0 entries it might
significantly accelerate the compilation time. Obviously gcc has some
issues on AIX to compile such kind of code, but xlc_r does not shine
either at higher optimization levels.
Also, I replaced gcc with xlc_r in compiler.c (and replaced -shared with
-G, removed other options like -pipe, -fPIC, -lstdc++), set -O0 and it
works very well. Maybe that would be nice to have a compile_with_xlc_r
function for AIX users. I'll try to send a patch when I do it cleanly.

Eric