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Use all cores in distrobuted search #694

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5137d62
use all available CPU cores in distributed search scripts
mschwoer Sep 30, 2025
82daf0e
adapt to latest alphadia
mschwoer Sep 30, 2025
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6 changes: 4 additions & 2 deletions misc/distributed_search/inner.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,13 @@ cd $chunk_directory || exit
# config file fixed as config.yaml
config_filename="config.yaml"

N_THREADS=$N_CPUS

# run with or without custom quant_dir
if [ -z "${quant_dir}" ]; then
alphadia --config ${config_filename}
alphadia --config ${config_filename} --config-dict "{\"general\": {\"thread_count\": $N_THREADS}}"
else
alphadia --config ${config_filename} --quant-dir ${quant_dir}
alphadia --config ${config_filename} --config-dict "{\"general\": {\"thread_count\": $N_THREADS}}" --quant-dir ${quant_dir}
fi

echo "AlphaDIA completed successfully"
14 changes: 7 additions & 7 deletions misc/distributed_search/outer.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@
#SBATCH --output=./logs/%j-%x-slurm.out

# Set behavior when errors are encountered
# # TODO: unresolved issues with failing on error due to library generation steps expecting AlphaDIA to fail since there are no rawfiles.
set -u -x
# add -x for debugging
set -u -e

# Default search parameters
nnodes=1
Expand Down Expand Up @@ -119,7 +119,7 @@ if [[ "$predict_library" -eq 1 ]]; then
--cpus-per-task=${cpus} \
--mem=${mem} \
--output="${home_directory}/logs/%j-%x-speclib-slurm.out" \
--export=ALL --wrap="alphadia --config=speclib_config.yaml"
--export=ALL,N_CPUS=$cpus --wrap="alphadia --config=speclib_config.yaml"

# navigate back to home directory
cd "${home_directory}"
Expand Down Expand Up @@ -156,7 +156,7 @@ if [[ "$first_search" -eq 1 ]]; then
--ntasks-per-node=${ntasks_per_node} \
--cpus-per-task=${cpus} \
--mem=${mem} \
--export=ALL,target_directory=${first_search_directory},quant_dir=${mbr_progress_directory} ./inner.sh
--export=ALL,N_CPUS=$cpus,target_directory=${first_search_directory},quant_dir=${mbr_progress_directory} ./inner.sh
else
echo "Skipping first search"
fi
Expand Down Expand Up @@ -187,7 +187,7 @@ if [[ "$mbr_library" -eq 1 ]]; then
--ntasks-per-node=${ntasks_per_node} \
--cpus-per-task=${cpus} \
--mem=${mem} \
--export=ALL,target_directory=${mbr_library_directory} ./inner.sh
--export=ALL,N_CPUS=$cpus,target_directory=${mbr_library_directory} ./inner.sh
else
echo "Skipping MBR library building"
fi
Expand Down Expand Up @@ -217,7 +217,7 @@ if [[ "$second_search" -eq 1 ]]; then
--ntasks-per-node=${ntasks_per_node} \
--cpus-per-task=${cpus} \
--mem=${mem} \
--export=ALL,target_directory=${second_search_directory},quant_dir=${lfq_progress_directory} ./inner.sh
--export=ALL,N_CPUS=$cpus,target_directory=${second_search_directory},quant_dir=${lfq_progress_directory} ./inner.sh
else
echo "Skipping second search"
fi
Expand Down Expand Up @@ -248,7 +248,7 @@ if [[ "$lfq" -eq 1 ]]; then
--ntasks-per-node=${ntasks_per_node} \
--cpus-per-task=${cpus} \
--mem=${mem} \
--export=ALL,target_directory=${lfq_directory} ./inner.sh
--export=ALL,N_CPUS=$cpus,target_directory=${lfq_directory} ./inner.sh
else
echo "Skipping LFQ"
fi
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