[Gate-users] GATE: Voxelized source/phantom speed issue on CPU and error cut off values

[David Boersma]

Hi Jennifer,

I am confused. In the first sentence you mention that you have speed 
issues, which implies that it is running normally, only slow. But in the 
last sentence you mention that you get an error message (missing 
phantom) which implies it is *not* running normally, the run gets 
aborted already during the initialization phase. I must be 
misunderstanding your question.

I have not yet used the job splitter myself (the one in 
"cluster_tools"). But I would recommend to first try running things 
first without the job splitter, and to verify that the output is 
correct. Only after you are confident that you are getting correct 
results you should try to make it faster. (And after you did that, you 
need to check again that the result is still correct...)

One way to get errors regarding the missing phantom is by forgetting to 
download the examples and benchmark data. In order to get them you need 
to set the corresponding flags from OFF to ON during the cmake step. 
(This is assuming that you are indeed running one of the examples. If 
you run your own code on your own data then you do not need these 
example/benchmark data.)

Some practical questions:

(1) Which script are you trying to run? If it is not one of the 
examples, could you send your "mac" file to this mailing list?

(2) Are you sure that the input data is present on your system? 
Specifically, if you are running e.g. 
examples/example_PHANTOM_SOURCE/Voxelized_Phantom_Source/VoxelizedPhantom.mac, 
which uses brain_phantom.h33, could you check that brain_phantom.h33 
exists and is not a broken link?

(3) If you still get errors after check (2): please quote the full error 
output.

(4) If you do not get errors any more, Gate produces a sensible output 
file but it's just slow: please tell us how long it took, and on what 
kind of a system you are running (how much RAM, what kind of CPU with 
what kind of clock speed, do you run everything on a local disk or are 
there network disks involved?).

Good luck,
David Boersma

Den 15/12/2016 kl. 16:36, skrev Gottwald, Jennifer:
> Hi,
>
>
>
> I am a new user of GATE 7.2 and have speed issues on running PET
> voxelized source/phantom simulations on CPU
>
>
>
> I already use the option to split jobs.
>
>
>
> Does someone has experience with that? I would be very grateful for any
> advice
>
>
>
> I try to set cut of values in the physics mac but I get error messages
> that the voxelized phantom can’t be found.
>
>
>
> Thanks
>
> Jennifer
>
>
>
>
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