From 311c5c078a9fc8ec6bb449fa685dbb1657d75d39 Mon Sep 17 00:00:00 2001 From: Benjamin Auder Date: Mon, 17 Oct 2016 00:23:23 +0200 Subject: [PATCH] fix CGDS usage, compilation, check usability --- .gitignore | 3 ++- README.md | 2 +- code/README | 8 +++++--- code/{ => src}/main.sh | 0 code/src/stage1/Algorithm/pam.c | 2 +- code/src/stage1/CMakeLists.txt | 12 +++++++----- code/src/stage1/TimeSeries/serialize.c | 4 ++-- code/src/stage1/Util/utils.c | 2 +- code/src/stage1/main.c | 2 +- 9 files changed, 20 insertions(+), 15 deletions(-) rename code/{ => src}/main.sh (100%) diff --git a/.gitignore b/.gitignore index 112c581..0372ddc 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ -/code/build/* +/code/src/build/* +/code/test/build/* /code/data/src/ *.aux diff --git a/README.md b/README.md index d510f69..2b103b2 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ Joint work with [Jairo Cugliari](http://eric.univ-lyon2.fr/~jcugliari/), --- This program takes n time-series in input and is divided in two stages: - 1) (Heuristic) k-medoids algorithm in parallel to obtain K centers, K << n + 1) (Heuristic) k-medoids algorithm in parallel to obtain K centers, K << n 2) Filtering WER(?) to obtain the final k < K group representations. --- diff --git a/code/README b/code/README index ccb3a0f..5546cf6 100644 --- a/code/README +++ b/code/README @@ -1,14 +1,16 @@ To compile source code : - cd build - cmake ../src + (mkdir -p (src|test)/build + cd (src|test)/build + cmake .. make Usage : - ppam-mpi cluster ifilename nbSeriesInChunk nbClusters randomize p_for_dissims + mpirun -np nbProcess ppam.exe cluster ifilename nbSeriesInChunk nbClusters randomize p_for_dissims Where : + nbProcess = number of simultaneous processes ifilename = path to serialized dataset (read below) nbSeriesInChunk = number of time-series to process sequentially nbClusters = number of clusters diff --git a/code/main.sh b/code/src/main.sh similarity index 100% rename from code/main.sh rename to code/src/main.sh diff --git a/code/src/stage1/Algorithm/pam.c b/code/src/stage1/Algorithm/pam.c index 4e3dfac..7cde367 100644 --- a/code/src/stage1/Algorithm/pam.c +++ b/code/src/stage1/Algorithm/pam.c @@ -1,6 +1,6 @@ #include "Util/types.h" #include "Util/rng.h" -#include +#include #include #include diff --git a/code/src/stage1/CMakeLists.txt b/code/src/stage1/CMakeLists.txt index e69ca5d..b69602f 100644 --- a/code/src/stage1/CMakeLists.txt +++ b/code/src/stage1/CMakeLists.txt @@ -11,9 +11,11 @@ include_directories("${CMAKE_SOURCE_DIR}") #ppam executable (serialize, cluster, classif) #cds -find_path(CDS_INCLUDE_PATH "cds/cds.h") -find_library(CDS_LIBRARY cds) -include_directories(${CDS_INCLUDE_PATH}) +set(CGDS_INCLUDE_PATH "/usr/local/include/cgds") +#set(CGDS_LIBRARY "/usr/local/lib/libcgds.so") +#find_path(CDS_INCLUDE_PATH "cgds/cgds.h") +#find_library(CGDS_LIBRARY cgds) +include_directories(${CGDS_INCLUDE_PATH}) #GSL: standard location find_path(GSL_INCLUDE_PATH "gsl/gsl_linalg.h") @@ -33,8 +35,8 @@ include_directories(${LIBXML2_INCLUDE_DIR}) file(GLOB_RECURSE ppam_src "${CMAKE_SOURCE_DIR}/*.c") add_executable(ppam.exe ${ppam_src}) add_library(ppam SHARED ${ppam_src}) -target_link_libraries(ppam.exe m cds ${MPI_LIBRARIES} ${LIBXML2_LIBRARIES} ${GSL_LIBRARIES} ${CDS_LIBRARY}) -target_link_libraries(ppam m cds ${MPI_LIBRARIES} ${LIBXML2_LIBRARIES} ${GSL_LIBRARIES} ${CDS_LIBRARY}) +target_link_libraries(ppam.exe m cgds ${MPI_LIBRARIES} ${LIBXML2_LIBRARIES} ${GSL_LIBRARIES})# ${CGDS_LIBRARY}) +target_link_libraries(ppam m cgds ${MPI_LIBRARIES} ${LIBXML2_LIBRARIES} ${GSL_LIBRARIES})# ${CGDS_LIBRARY}) if (MPI_COMPILE_FLAGS) set_target_properties(ppam.exe PROPERTIES diff --git a/code/src/stage1/TimeSeries/serialize.c b/code/src/stage1/TimeSeries/serialize.c index ab552c9..88b15f1 100644 --- a/code/src/stage1/TimeSeries/serialize.c +++ b/code/src/stage1/TimeSeries/serialize.c @@ -4,7 +4,7 @@ #include #include "Util/types.h" #include "Util/utils.h" -#include +#include #include // parse a line into two integers (ID, raw power) @@ -156,7 +156,7 @@ void serialize_byCols(const char* ifileName, const char* ofileName, uint32_t nbI { //just starting a new time-series: must process the last one (if there is a last one !) if (lastID > 0) - { + { if (tsLength == refTsLength && !overflow) { seriesCount++; diff --git a/code/src/stage1/Util/utils.c b/code/src/stage1/Util/utils.c index 3786eda..9713e30 100644 --- a/code/src/stage1/Util/utils.c +++ b/code/src/stage1/Util/utils.c @@ -1,6 +1,6 @@ #include "Util/utils.h" #include -#include +#include void free_work(Work_t* work) { diff --git a/code/src/stage1/main.c b/code/src/stage1/main.c index bb4bd46..992b97c 100644 --- a/code/src/stage1/main.c +++ b/code/src/stage1/main.c @@ -10,7 +10,7 @@ #include "TimeSeries/deserialize.h" #include "Classification/getClass.h" #include -#include +#include #include // serialize text file argv[1] into a binary file argv[2] -- 2.44.0