Merge pull request #51 from eseiler/misc/util_scripts

[MISC] Add and fix util scripts

util/README.md

@@ -74,6 +74,7 @@ bin/
 $ tree src/bash_scripts/
 src/bash_scripts/
 ├── benchmark.sh           # Runs benchmarks for Raptor
+├── benchmark_wk.sh        # Runs different w/k combinations for Raptor
 ├── count_minimisers.sh    # Counts a variety of different minimizers for a data set
 ├── dream_yara.sh          # Runs benchmarks for DREAM-Yara
 ├── original_dream_yara.sh # Runs benchmarks for the original DREAM-Yara

util/src/bash_scripts/benchmark.sh

@@ -1,73 +1,89 @@
 #!/bin/bash
 set -e
 
-READ_LENGTH=250
+READ_LENGTH=100
+W=23
+K=19
 ERRORS=2
 HASH=2
-SIZE="4096m"
+SIZES="1g 2g 4g"
 THREADS=4
 BIN_NUMBER=1024
 BINARY_DIR="<path to built binaries>" # containing the raptor binary
-BIN_DIR="<bin path>" # output directory of simulation. the directory that contains the BIN_NUMBER directory
-BENCHMARK_DIR="<path>" # directory where the benchmarks should be run. Input data will be copied here. e.g. /dev/shm/username; BIN_NUMBER directory will be created.
+INPUT_DIR="<bin path>" # output directory of simulation. the directory that contains the BIN_NUMBER directory
+BENCHMARK_DIR="<path>" # directory where results should be stored. E.g., /dev/shm/username; BIN_NUMBER directory will be created.
+COPY_INPUT=false # If true, input data will be copied from INPUT_DIR to BENCHMARK_DIR.
+EVAL_ENERGY=true # If true, use perf to measure power/energy-pkg/ and power/energy-ram/.
 
 working_directory=$BENCHMARK_DIR/$BIN_NUMBER
-mkdir -p $working_directory/bins/
-mkdir -p $working_directory/reads/
+mkdir -p $working_directory
 
-for i in $(seq -f "$BIN_DIR/$BIN_NUMBER/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)))
-do
-    cp $i $working_directory/bins/
-done
-seq -f "$working_directory/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)) > $working_directory/bins.list
+if [ "$COPY_INPUT" = true ] ; then
+    echo -n "Copying input..."
+    mkdir -p $working_directory/bins/
+    mkdir -p $working_directory/reads/
 
-cp $BIN_DIR/$BIN_NUMBER/reads_e$ERRORS\_$READ_LENGTH/all.fastq $working_directory/reads/
+    for i in $(seq -f "$INPUT_DIR/$BIN_NUMBER/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)))
+    do
+        cp $i $working_directory/bins/
+    done
+    seq -f "$working_directory/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)) > $working_directory/bins.list
 
-do_task () {
-    ibf_filename=$working_directory/$w\_$k\_$SIZE.ibf # Does not contain HASH
-    build_log=$working_directory/$w\_$k\_$SIZE\_build.log
-    echo "Building IBF with ($w, $k)-minimisers with $HASH hashes and of size $SIZE"
-    /usr/bin/time -o $build_log -v \
-        $BINARY_DIR/raptor build \
-            --output $ibf_filename \
-            --kmer $k \
-            --window $w \
-            --size $SIZE \
-            --threads $THREADS \
-            --hash $HASH \
-            $working_directory/bins.list
+    cp $INPUT_DIR/$BIN_NUMBER/reads_e$ERRORS\_$READ_LENGTH/all.fastq $working_directory/reads/
+    read_file=$working_directory/reads/all.fastq
+    echo "Done."
+else
+    seq -f "$INPUT_DIR/$BIN_NUMBER/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)) > $working_directory/bins.list
+    read_file=$INPUT_DIR/$BIN_NUMBER/reads_e$ERRORS\_$READ_LENGTH/all.fastq
+fi
 
-    query_log=$working_directory/$w\_$k\_$SIZE\_query.log # Does not contain HASH
-    query_out=$working_directory/$w\_$k\_$SIZE.out
-    echo "Searching IBF for reads of length $READ_LENGTH containing $ERRORS errors"
-    /usr/bin/time -o $query_log -v \
-        $BINARY_DIR/raptor search \
-            --query $working_directory/reads/all.fastq \
-            --index $ibf_filename \
-            --output $query_out \
-            --threads $THREADS \
-            --error $ERRORS \
-            --pattern $READ_LENGTH \
-            --tau 0.9999 \
-            --time
+launch_build() {
+    if [ "$EVAL_ENERGY" = true ] ; then
+        perf stat -o $build_perf -e power/energy-pkg/,power/energy-ram/ "$@"
+    else
+        "$@"
+    fi
+}
 
-    rm $ibf_filename
+launch_query() {
+    if [ "$EVAL_ENERGY" = true ] ; then
+        perf stat -o $query_perf -e power/energy-pkg/,power/energy-ram/ "$@"
+    else
+        "$@"
+    fi
 }
 
-pidlist=""
+for size in $SIZES; do
+    ibf_filename=$working_directory/$W\_$K\_$size.ibf # Does not contain HASH
+    build_log=$working_directory/$W\_$K\_$size\_build.log
+    build_perf=$working_directory/$W\_$K\_$size\_build.perf
+    echo "Building IBF with ($W, $K)-minimisers with $HASH hashes and of size $size"
+    launch_build    /usr/bin/time -o $build_log -v \
+                        $BINARY_DIR/raptor build \
+                            --output $ibf_filename \
+                            --kmer $K \
+                            --window $W \
+                            --size $size \
+                            --threads $THREADS \
+                            --hash $HASH \
+                            $working_directory/bins.list
 
-for w in $(seq 23 2 32 && seq 32 2 80)
-do
-    for k in 16 17 18 19 20
-    do
-        if [[ $w != 23 ]] || [[ $k != 20 ]]; then # Segfault for READ_LENGTH = 150
-            do_task & pidlist="$pidlist $!"
-        fi
-    done
-    for job in $pidlist
-    do
-        wait $job
-    done
+    query_log=$working_directory/$W\_$K\_$size\_query.log # Does not contain HASH
+    query_perf=$working_directory/$W\_$K\_$size\_query.perf
+    query_out=$working_directory/$W\_$K\_$size.out
+    echo "Searching IBF for reads of length $READ_LENGTH containing $ERRORS errors"
+    launch_query    /usr/bin/time -o $query_log -v \
+                            $BINARY_DIR/raptor search \
+                                --query $read_file \
+                                --index $ibf_filename \
+                                --output $query_out \
+                                --threads $THREADS \
+                                --error $ERRORS \
+                                --pattern $READ_LENGTH \
+                                --tau 0.9999 \
+                                --time
+
+    rm $ibf_filename
 done
 
 # Uncomment for basic cleanup, does not delete results

util/src/bash_scripts/benchmark_wk.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+set -e
+
+READ_LENGTH=250
+ERRORS=2
+HASH=2
+SIZE="4096m"
+THREADS=4
+BIN_NUMBER=1024
+BINARY_DIR="<path to built binaries>" # containing the raptor binary
+INPUT_DIR="<bin path>" # output directory of simulation. the directory that contains the BIN_NUMBER directory
+BENCHMARK_DIR="<path>" # directory where results should be stored. E.g., /dev/shm/username; BIN_NUMBER directory will be created.
+COPY_INPUT=false # If true, input data will be copied from INPUT_DIR to BENCHMARK_DIR.
+
+working_directory=$BENCHMARK_DIR/$BIN_NUMBER
+mkdir -p $working_directory
+
+if [ "$COPY_INPUT" = true ] ; then
+    echo -n "Copying input..."
+    mkdir -p $working_directory/bins/
+    mkdir -p $working_directory/reads/
+
+    for i in $(seq -f "$INPUT_DIR/$BIN_NUMBER/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)))
+    do
+        cp $i $working_directory/bins/
+    done
+    seq -f "$working_directory/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)) > $working_directory/bins.list
+
+    cp $INPUT_DIR/$BIN_NUMBER/reads_e$ERRORS\_$READ_LENGTH/all.fastq $working_directory/reads/
+    read_file=$working_directory/reads/all.fastq
+    echo "Done."
+else
+    seq -f "$INPUT_DIR/$BIN_NUMBER/bins/bin_%0${#BIN_NUMBER}g.fasta" 0 1 $((BIN_NUMBER-1)) > $working_directory/bins.list
+    read_file=$INPUT_DIR/$BIN_NUMBER/reads_e$ERRORS\_$READ_LENGTH/all.fastq
+fi
+
+do_task () {
+    ibf_filename=$working_directory/$w\_$k\_$SIZE.ibf # Does not contain HASH
+    build_log=$working_directory/$w\_$k\_$SIZE\_build.log
+    echo "Building IBF with ($w, $k)-minimisers with $HASH hashes and of size $SIZE"
+    /usr/bin/time -o $build_log -v \
+        $BINARY_DIR/raptor build \
+            --output $ibf_filename \
+            --kmer $k \
+            --window $w \
+            --size $SIZE \
+            --threads $THREADS \
+            --hash $HASH \
+            $working_directory/bins.list
+
+    query_log=$working_directory/$w\_$k\_$SIZE\_query.log # Does not contain HASH
+    query_out=$working_directory/$w\_$k\_$SIZE.out
+    echo "Searching IBF for reads of length $READ_LENGTH containing $ERRORS errors"
+    /usr/bin/time -o $query_log -v \
+        $BINARY_DIR/raptor search \
+            --query $read_file \
+            --index $ibf_filename \
+            --output $query_out \
+            --threads $THREADS \
+            --error $ERRORS \
+            --pattern $READ_LENGTH \
+            --tau 0.9999 \
+            --time
+
+    rm $ibf_filename
+}
+
+pidlist=""
+
+# 5 jobs in parallel
+for w in $(seq 23 2 32 && seq 32 2 80) # w=23,25,27,29,31,32,34,36,38,...,80
+do
+    for k in 16 17 18 19 20
+    do
+        if [[ $w != 23 ]] || [[ $k != 20 ]]; then # Segfault for READ_LENGTH = 150
+            do_task & pidlist="$pidlist $!"
+        fi
+    done
+    for job in $pidlist
+    do
+        wait $job
+    done
+done
+
+# Uncomment for basic cleanup, does not delete results
+# chmod -R 744 $working_directory/bins
+# chmod -R 744 $working_directory/reads
+# rm -f $working_directory/bins/*.fasta
+# rm -d $working_directory/bins
+# rm -f $working_directory/reads/all.fastq
+# rm -d $working_directory/reads

util/src/bash_scripts/simulate.sh

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 set -e
 
-BINARY_DIR="<path to built binaries>"
-OUT_DIR="<output path>"
+BINARY_DIR="<path to built binaries>" # Dir containing "mason_genome", "split_sequence", etc.
+OUT_DIR="<output path>" # Where simulated data should be stored
 LENGTH=4294967296 # 4*2^30 =  4GiB
 SEED=42 # was 20181406 before, but was hardcoded to 42 in seqan
 BIN_NUMBER=1024