Merge branch 'feature-a/918-profiling' into 'dev'

profiling c++

Closes #918

See merge request !686

.gitlab-ci.yml

@@ -56,6 +56,7 @@ test_germlines:
 include:
   - local: '/doc/.gitlab-ci.yml'
   - local: 'algo/.gitlab-ci-compilers.yml' # Stage multiple_tests
+  - local: 'algo/.gitlab-ci.yml' # Vidjil-algo pipelines
 
 # Algorithm
 
@@ -372,9 +373,7 @@ ff45-server-functional:
 
 benchmark_algo:
   image:  gcc:6.3
-  before_script:
-    - apt-get update
-    - apt-get install -y time valgrind python3 wget tar
+  extends: .install-algo-dependencies
   stage: benchmark
   script:
     - cd algo/tests ; python3 benchmark-releases.py -r 3 -bIc

algo/.gitlab-ci-compilers.yml

+.install-algo-dependencies:
+  before_script:
+    - apt-get update
+    - apt-get install -y time valgrind python3 wget tar
+    
+
 .testing-compilers:
+  extends: .install-algo-dependencies
   stage: multiple_tests
   tags:
     - cidocker
-  before_script:
-    - apt-get update
-    - apt-get install -y time valgrind python3 wget tar
   script:
     - $CXX --version
     - make demo data germline

algo/.gitlab-ci.yml

+profiling_algo:
+  stage: benchmark
+  image: gcc:9
+  before_script:
+    - apt-get update
+    - apt-get install -y wget python3 tar libgoogle-perftools4 libgoogle-perftools-dev google-perftools graphviz
+  script:
+    - make demo data germline
+    - make DEBUG="-g"
+    - LIB_PROFILE=$(find /usr/lib -name libprofiler.so)
+    - CPUPROFILE=vidjil.cpu LD_PRELOAD="$LIB_PROFILE" ./vidjil-algo -g germline -r 1 demo/LIL-L4.fastq.gz
+    - LIB_MALLOC=$(find /usr/lib -name libtcmalloc.so)
+    - HEAPPROFILE=vidjil.mem LD_PRELOAD="$LIB_MALLOC" ./vidjil-algo -g germline -r 1 demo/LIL-L4.fastq.gz
+
+    - google-pprof --lines --text vidjil-algo vidjil.cpu
+    - echo "###########################################"
+    - google-pprof --lines --text vidjil-algo vidjil.mem.*
+    - google-pprof --lines --pdf vidjil-algo vidjil.cpu > vidjil-cpu.pdf
+    - google-pprof --lines --pdf vidjil-algo vidjil.mem.* > vidjil-mem.pdf
+  artifacts:
+    paths:
+      - vidjil-*.pdf
+      - vidjil.cpu
+      - vidjil.mem.*
+  when: manual
+  tags:
+    - cidocker
+