Comments (10)
futianfan
commented on May 20, 2024
1
You are right. In the current version, both variables are set as global
variables. If you set a large number, the memory would increase. We will
fix it soon. Thanks!
…On Sun, Dec 13, 2020 at 9:35 PM Po-Yu Kao ***@***.***> wrote:
I got the same issue and I double the size of MAX_ATOM and MAX_BOND. It
solved this issue but I think it takes more GPU memories on both training
and test phases, right?
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Sunlab, http://sunlab.org/
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hima111997
commented on May 20, 2024
i added two print statements to print fbonds.shape[0] and fatoms.shape[0]
and they gave me these numbers:
fbonds.shape[0] --> 403
fatoms.shape[0] --> 183
when I checked MAX_ATOM and MAX_BOND variables they were 200 and 400, respectively.
So should I increase MAX_BOND value to 500 for example?
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futianfan
commented on May 20, 2024
Yeah. You can increase MAX_ATOM and MAX_BOND. The current setting is only
for small molecules. Thanks!
…On Thu, Dec 10, 2020 at 11:13 AM hima111997 ***@***.***> wrote:
i added two print statements to print fbonds.shape[0] and fatoms.shape[0]
and they gave me these numbers:
fbonds.shape[0] --> 403
fatoms.shape[0] --> 183
when I checked MAX_ATOM and MAX_BOND variables they were 200 and 400,
respectively.
So should I increase MAX_BOND value to 500 for example?
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Tianfan Fu
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futianfan.github.io
Sunlab, http://sunlab.org/
College of Computing
Georgia Institute of Technology
266 Ferst Dr NW, Atlanta, GA 30332
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pykao
commented on May 20, 2024
I got the same issue and I double the size of MAX_ATOM and MAX_BOND. It solved this issue but I think it takes more GPU memories on both training and test phases, right?
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pykao
commented on May 20, 2024
For KIBA database, I increased MAX_ATOM=270 and MAX_BOND=600 that solved the issue. :)
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futianfan
commented on May 20, 2024
Thanks for letting us know!
…On Sun, Dec 13, 2020 at 10:03 PM Po-Yu Kao ***@***.***> wrote:
For KIBA database, I increased MAX_ATOM=270 and MAX_BOND=600 that solved
the issue. :)
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Sunlab, http://sunlab.org/
College of Computing
Georgia Institute of Technology
266 Ferst Dr NW, Atlanta, GA 30332
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xuzhang5788
commented on May 20, 2024
Sorry, I can't find "MAX_ATOM" and "MAX_BOND" in utils.py
I don't understand why it was okay in "MPNN_CNN_Kiba.ipynb"? It also used Kiba dataset
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futianfan
commented on May 20, 2024
Sorry, I can't find "MAX_ATOM" and "MAX_BOND" in utils.py
I don't understand why it was okay in "MPNN_CNN_Kiba.ipynb"? It also used Kiba dataset
Please see
DeepPurpose/DeepPurpose/utils.py
Line 27 in 5300269
Can you increase them, and try again?
We change the setting for support of multi-GPU. The tutorial may be out-of-date.
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xuzhang5788
commented on May 20, 2024
It doesn't work. Do I need to reinstall deeppurpose? Actually, I installed it again, but it still doesn't work, even I increased the numbers.
Have my own dataset to be under the folder of DeepPurpose? I created a new folder for my own experiments. Is it okay?
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kexinhuang12345
commented on May 20, 2024
I think this is resolved in #74
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