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jvlehtonen / brutenib

Rather brute optimizer for negative image-based models
MIT License
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new ShaEP version vs multithreading #1

Closed CLG68 closed 1 month ago

CLG68 commented 1 month ago

Hi,

I tried the new ShaEP version (1.4.0) with Brutenib. As the new ShaEP version is taking care of multi-threading, natively, it is not compatible with the way Brutenib is dealing with parallel jobs... the version 1.4.0 is slowing down brutenib to 50% as the system gets overwhelmed. Maybe you should indicate in your Read.me file that Brutenib was optimized for version 1.3.1 and not for 1.4.0

I also changed the way a formula was defined in brutenib, to be compatible with newer Bash versions: NUM=$(tail -n +$((1 + HEADER)) "${NIB}" | grep -c -v "^$")

Best, Christian

jvlehtonen commented 1 month ago

The new ShaEP does indeed default to use all cores, which leads to overallocation when Brutenib starts multiple instances (as is the default). Use -c 1 as a workaround. We should probably pass explicit --njobs to ShaEP in order to retain control on how much resources it gets.

Thanks for note about the deprecation of the square bracket notation. I had missed that.

CLG68 commented 1 month ago

Hi,

For screening 1.4.0 is faster than the previous version but I'm not sure for rescoring. For Brutenib, I end up reverting to 1.3.1 so I could use all threads with rocker. Using 1.3.1 is not really a problem but it would be a good to add this info to the read.me file.

Best, Christian

CLG68 commented 1 month ago

I just realized that you already updated your Read.me.

Thanks, Christian

CLG68 commented 1 month ago

also, just a small correction in brutenib:

ITERATIONS="300" ACTIVENAME=""

should be

ITERATIONS="100" ACTIVENAME="CHEMBL"

to match: echo "-g number, Maximum iterations. Optional. Defaults to 100." echo "-a REGEXP, Sets ACTIVENAME for rocker. Optional. Defaults to 'CHEMBL'."

It is facultative but I also added this code to brutenib as Panther sometimes creates multiple negative-image models and saves them all in the same mol2 file. This obviously creates problems with brutenib:

MODEL_COUNT=$(grep -c "@ATOM" "$MODEL") if [ "$MODEL_COUNT" -ne 1 ]; then echo "Error: The negative image file contains $MODEL_COUNT models." echo "Please edit the negative image file to keep only one model." exit 1 fi