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David Nickerson wrote:
> Alan Garny wrote:
>
>> As you know, there is a CellML 1.0 version of the epicardial version of the
>> ten Tusscher model, which we have. I computed that model for one-second
>> worth of cardiac activity, plotting the trans-membrane potential. From
>> there, we could extrapolate to 70 minutes by saying that the frequency of
>> the stimulus is 1 Hz. Like David, I have set the maximum time step to 0.1
>> ms. Here are some rough figures:
>>
>> Simulation time: 1037.4 s (i.e. ~17 min 17 sec)
>> Computation time: 684.6 s (i.e. ~11 min 24 sec)
>>
>
>
Hi Andre,

I have now added support for CVODE into CIS, and have run your benchmark
using the command-line test program RunCellML. I note that you didn't
specify error control parameters, so I chose 1E-6 for both absolute and
relative error control (with a maximum step size of 0.1).
This command line used was...
time ../../../../CellML_DOM_API/RunCellML
file:///people/amil082/code/Andres_Benchmark/model/2004_tenTusscher/experiments/increasing-frequency-epicardial.xml

step_type BDF15SIMP range 0,4200000,1 step_size_control 1E-6,1E-6,1,0.1

This was run on the following processor...
processor : 0
vendor_id : GenuineIntel
cpu family : 15
model : 6
model name : Intel(R) Pentium(R) D CPU 3.20GHz
stepping : 2
cpu MHz : 3192.180
cache size : 2048 KB
physical id : 0
siblings : 1
core id : 255
cpu cores : 1
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 6
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm
pni monitor ds_cpl vmx cid cx16 xtpr lahf_lm
bogomips : 6390.23
The processor has hyperthreading turned on, but the integrator is
entirely serial, so only used one hyper-thread. The process was able to
take up an entire hyper-thread, running at 100% CPU.

Note that RunCellML times include model loading and parsing, code
generation, compilation, and model run (but that isn't really a big
deal, because it is insignificant compared to the time it took to run
the model).

I get:
real 25m49.238s
user 25m46.581s
sys 0m0.684s

This is with the main program / SUNDIALS compiled with -O2, and the
generated code compiled with -O3 -ffast-math. I have disassembled the
computation functions in the -O3 -ffast-math code, and it looks
reasonable, there are no CALL instructions anymore (the built-in exp and
log from gcc get inlined). I therefore doubt that differences in the
quality of the generated code is the cause of the problem. It is
possible that Alan has managed to get the better benchmark by compiling
CVODE with -O3 -ffast-math or other optimisations. Another possibility
would be that his CellML 1.0 Ten Tuscher model behaves differently. Yet
another possibility would be that the differences could be arising from
the structure of the CVODE stepping loop, or differences in some
parameters given to the solver. My stepping loop looks like this:
https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/CIS/sources/CISSolve.cxx,

see function SolveODEProblemCVODE.
> so the total (predicted) wall clock run time is 17minutes? or 28minutes?
> any chance you could run something longer than a 1s simulation and
> extrapolate from there, if not run a whole 70minutes worth? If not, I
> guess I can run it next time I'm on a windows machine ;)
>
BTW, it would be useful if I could also have Alan's CellML 1.0 ten
Tuscher model (with the embedded stimulus protocol), to see if this
makes any difference.

Best regards,
Andrew
>
>> The computer on which I have run this is an IBM ThinkPad T42p (2 GHZ
>> processor with 2 GB of RAM). These figures can obviously vary quite a bit,
>> since it's based on a one-second simulation and is subject to whatever my
>> system does at the time... Still, that should give you a rough idea
>> indeed...
>>
>> Alan.
>>

---

• [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
  • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/30/2006
    • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Alan Garny, 10/30/2006
    • [cellml-discussion] pcenv development priorities, Poul Nielsen, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/30/2006
    • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
      • [cellml-discussion] pcenv development priorities, Alan Garny, 10/30/2006
        • [cellml-discussion] pcenv development priorities, David Nickerson, 10/30/2006
          • [cellml-discussion] pcenv development priorities, Alan Garny, 10/31/2006
          • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/31/2006
            • [cellml-discussion] pcenv development priorities, David Nickerson, 10/31/2006
              • [cellml-discussion] pcenv development priorities, Andrew Miller, 10/31/2006
              • [cellml-discussion] pcenv development priorities, Alan Garny, 10/31/2006

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