improve project structure

diff --git a/.gitignore b/.gitignore
deleted file mode 100644 (file)
index 0372ddc..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,10 +0,0 @@
-/code/src/build/*
-/code/test/build/*
-/code/data/src/
-
-*.aux
-*.log
-*.nav
-*.snm
-*.toc
-*.out

diff --git a/code/.gitignore b/code/.gitignore
new file mode 100644 (file)
index 0000000..f8a6218
--- /dev/null
+++ b/code/.gitignore
@@ -0,0 +1,2 @@
+#ignore "real" data (way too large)
+data/

diff --git a/code/README b/code/README
index 5546cf6..fa76933 100644 (file)
--- a/code/README
+++ b/code/README
@@ -1,8 +1,7 @@
 To compile source code :
 
-   (mkdir -p (src|test)/build
-   cd (src|test)/build
-   cmake ..
+   cd build/stage1/src #and then stage2
+   cmake ../../../stage1/src
    make
 
 Usage :

diff --git a/code/src/stage1/Algorithm/compute_coefficients.c b/code/stage1/src/Algorithm/compute_coefficients.c
similarity index 100%
rename from code/src/stage1/Algorithm/compute_coefficients.c
rename to code/stage1/src/Algorithm/compute_coefficients.c

diff --git a/code/src/stage1/Algorithm/compute_coefficients.h b/code/stage1/src/Algorithm/compute_coefficients.h
similarity index 100%
rename from code/src/stage1/Algorithm/compute_coefficients.h
rename to code/stage1/src/Algorithm/compute_coefficients.h

diff --git a/code/src/stage1/Algorithm/get_dissimilarities.c b/code/stage1/src/Algorithm/get_dissimilarities.c
similarity index 100%
rename from code/src/stage1/Algorithm/get_dissimilarities.c
rename to code/stage1/src/Algorithm/get_dissimilarities.c

diff --git a/code/src/stage1/Algorithm/get_dissimilarities.h b/code/stage1/src/Algorithm/get_dissimilarities.h
similarity index 100%
rename from code/src/stage1/Algorithm/get_dissimilarities.h
rename to code/stage1/src/Algorithm/get_dissimilarities.h

diff --git a/code/src/stage1/Algorithm/pam.c b/code/stage1/src/Algorithm/pam.c
similarity index 100%
rename from code/src/stage1/Algorithm/pam.c
rename to code/stage1/src/Algorithm/pam.c

diff --git a/code/src/stage1/Algorithm/pam.h b/code/stage1/src/Algorithm/pam.h
similarity index 100%
rename from code/src/stage1/Algorithm/pam.h
rename to code/stage1/src/Algorithm/pam.h

diff --git a/code/src/stage1/CMakeLists.txt b/code/stage1/src/CMakeLists.txt
similarity index 100%
rename from code/src/stage1/CMakeLists.txt
rename to code/stage1/src/CMakeLists.txt

diff --git a/code/src/stage1/Classification/_Readme b/code/stage1/src/Classification/_Readme
similarity index 100%
rename from code/src/stage1/Classification/_Readme
rename to code/stage1/src/Classification/_Readme

diff --git a/code/src/stage1/Classification/getClass.c b/code/stage1/src/Classification/getClass.c
similarity index 100%
rename from code/src/stage1/Classification/getClass.c
rename to code/stage1/src/Classification/getClass.c

diff --git a/code/src/stage1/Classification/getClass.h b/code/stage1/src/Classification/getClass.h
similarity index 100%
rename from code/src/stage1/Classification/getClass.h
rename to code/stage1/src/Classification/getClass.h

diff --git a/code/src/stage1/MPI_Communication/pack.c b/code/stage1/src/MPI_Communication/pack.c
similarity index 100%
rename from code/src/stage1/MPI_Communication/pack.c
rename to code/stage1/src/MPI_Communication/pack.c

diff --git a/code/src/stage1/MPI_Communication/pack.h b/code/stage1/src/MPI_Communication/pack.h
similarity index 100%
rename from code/src/stage1/MPI_Communication/pack.h
rename to code/stage1/src/MPI_Communication/pack.h

diff --git a/code/src/stage1/MPI_Communication/unpack.c b/code/stage1/src/MPI_Communication/unpack.c
similarity index 100%
rename from code/src/stage1/MPI_Communication/unpack.c
rename to code/stage1/src/MPI_Communication/unpack.c

diff --git a/code/src/stage1/MPI_Communication/unpack.h b/code/stage1/src/MPI_Communication/unpack.h
similarity index 100%
rename from code/src/stage1/MPI_Communication/unpack.h
rename to code/stage1/src/MPI_Communication/unpack.h

diff --git a/code/src/stage1/MPI_Main/master.c b/code/stage1/src/MPI_Main/master.c
similarity index 100%
rename from code/src/stage1/MPI_Main/master.c
rename to code/stage1/src/MPI_Main/master.c

diff --git a/code/src/stage1/MPI_Main/master.h b/code/stage1/src/MPI_Main/master.h
similarity index 100%
rename from code/src/stage1/MPI_Main/master.h
rename to code/stage1/src/MPI_Main/master.h

diff --git a/code/src/stage1/MPI_Main/slave.c b/code/stage1/src/MPI_Main/slave.c
similarity index 100%
rename from code/src/stage1/MPI_Main/slave.c
rename to code/stage1/src/MPI_Main/slave.c

diff --git a/code/src/stage1/MPI_Main/slave.h b/code/stage1/src/MPI_Main/slave.h
similarity index 100%
rename from code/src/stage1/MPI_Main/slave.h
rename to code/stage1/src/MPI_Main/slave.h

diff --git a/code/src/stage1/TimeSeries/deserialize.c b/code/stage1/src/TimeSeries/deserialize.c
similarity index 100%
rename from code/src/stage1/TimeSeries/deserialize.c
rename to code/stage1/src/TimeSeries/deserialize.c

diff --git a/code/src/stage1/TimeSeries/deserialize.h b/code/stage1/src/TimeSeries/deserialize.h
similarity index 100%
rename from code/src/stage1/TimeSeries/deserialize.h
rename to code/stage1/src/TimeSeries/deserialize.h

diff --git a/code/src/stage1/TimeSeries/serialize.c b/code/stage1/src/TimeSeries/serialize.c
similarity index 100%
rename from code/src/stage1/TimeSeries/serialize.c
rename to code/stage1/src/TimeSeries/serialize.c

diff --git a/code/src/stage1/TimeSeries/serialize.h b/code/stage1/src/TimeSeries/serialize.h
similarity index 100%
rename from code/src/stage1/TimeSeries/serialize.h
rename to code/stage1/src/TimeSeries/serialize.h

diff --git a/code/src/stage1/Util/rng.c b/code/stage1/src/Util/rng.c
similarity index 100%
rename from code/src/stage1/Util/rng.c
rename to code/stage1/src/Util/rng.c

diff --git a/code/src/stage1/Util/rng.h b/code/stage1/src/Util/rng.h
similarity index 100%
rename from code/src/stage1/Util/rng.h
rename to code/stage1/src/Util/rng.h

diff --git a/code/src/stage1/Util/types.h b/code/stage1/src/Util/types.h
similarity index 100%
rename from code/src/stage1/Util/types.h
rename to code/stage1/src/Util/types.h

diff --git a/code/src/stage1/Util/utils.c b/code/stage1/src/Util/utils.c
similarity index 100%
rename from code/src/stage1/Util/utils.c
rename to code/stage1/src/Util/utils.c

diff --git a/code/src/stage1/Util/utils.h b/code/stage1/src/Util/utils.h
similarity index 100%
rename from code/src/stage1/Util/utils.h
rename to code/stage1/src/Util/utils.h

diff --git a/code/src/stage1/main.c b/code/stage1/src/main.c
similarity index 100%
rename from code/src/stage1/main.c
rename to code/stage1/src/main.c

diff --git a/code/src/main.sh b/code/stage1/src/main.sh
similarity index 100%
rename from code/src/main.sh
rename to code/stage1/src/main.sh

diff --git a/code/test/stage1/Algorithm/t.compute_coefficients.c b/code/stage1/test/Algorithm/t.compute_coefficients.c
similarity index 100%
rename from code/test/stage1/Algorithm/t.compute_coefficients.c
rename to code/stage1/test/Algorithm/t.compute_coefficients.c

diff --git a/code/test/stage1/Algorithm/t.pam.c b/code/stage1/test/Algorithm/t.pam.c
similarity index 100%
rename from code/test/stage1/Algorithm/t.pam.c
rename to code/stage1/test/Algorithm/t.pam.c

diff --git a/code/test/stage1/CMakeLists.txt b/code/stage1/test/CMakeLists.txt
similarity index 100%
rename from code/test/stage1/CMakeLists.txt
rename to code/stage1/test/CMakeLists.txt

diff --git a/code/test/stage1/MPI_Communication/t.pack.c b/code/stage1/test/MPI_Communication/t.pack.c
similarity index 94%
rename from code/test/stage1/MPI_Communication/t.pack.c
rename to code/stage1/test/MPI_Communication/t.pack.c
index 125fd47..6692af5 100644 (file)
--- a/code/test/stage1/MPI_Communication/t.pack.c
+++ b/code/stage1/test/MPI_Communication/t.pack.c
@@ -9,7 +9,7 @@
 void t_pack1()
 {
        Work_t* work = (Work_t*)malloc(sizeof(Work_t));
-       work->inputFileName = "../data/inputTest.bin";
+       work->inputFileName = "../tdata/inputTest.bin";
        work->nbSeries = 5;
        uint32_t ranks[] =
        {
@@ -27,9 +27,9 @@ void t_pack1()
        // Hard-coded expected packed work
        unsigned char expectedPackedWork[] =
        {
-               // --> ../data/inputTest.bin
+               // --> ../tdata/inputTest.bin
                46,46,47,100,97,116,97,47,105,110,112,117,116,84,101,115,116,46,98,105,110,
-               // continue with 256 - strlen("../data/inputTest.bin") zeros...
+               // continue with 256 - strlen("../tdata/inputTest.bin") zeros...
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

diff --git a/code/test/stage1/MPI_Communication/t.unpack.c b/code/stage1/test/MPI_Communication/t.unpack.c
similarity index 93%
rename from code/test/stage1/MPI_Communication/t.unpack.c
rename to code/stage1/test/MPI_Communication/t.unpack.c
index 90e5ae1..caf0e8d 100644 (file)
--- a/code/test/stage1/MPI_Communication/t.unpack.c
+++ b/code/stage1/test/MPI_Communication/t.unpack.c
@@ -12,9 +12,9 @@ void t_unpack1()
        // Hard-coded packed work
        unsigned char packedWork[] =
        {
-               // --> ../data/inputTest.bin
+               // --> ../tdata/inputTest.bin
                46,46,47,100,97,116,97,47,105,110,112,117,116,84,101,115,116,46,98,105,110,
-               // continue with 256 - strlen("../data/inputTest.bin") zeros...
+               // continue with 256 - strlen("../tdata/inputTest.bin") zeros...
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
                0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
@@ -35,7 +35,7 @@ void t_unpack1()
        uint32_t nbSeriesInChunk = 7;
        Work_t* work = unpack_work(packedWork, nbSeriesInChunk);
 
-       LUT_ASSERT(strcmp(work->inputFileName, "../data/inputTest.bin") == 0);
+       LUT_ASSERT(strcmp(work->inputFileName, "../tdata/inputTest.bin") == 0);
        LUT_ASSERT(work->nbSeries == 5);
        uint32_t ranks[] =
        {

diff --git a/code/test/stage1/TimeSeries/t.deserialize.c b/code/stage1/test/TimeSeries/t.deserialize.c
similarity index 96%
rename from code/test/stage1/TimeSeries/t.deserialize.c
rename to code/stage1/test/TimeSeries/t.deserialize.c
index 22e0956..3a6413d 100644 (file)
--- a/code/test/stage1/TimeSeries/t.deserialize.c
+++ b/code/stage1/test/TimeSeries/t.deserialize.c
@@ -8,7 +8,7 @@
 void t_deserialize1()
 {
        // decode sample_byCols.bin into the toy dataset (4 customers, 3 sample points)
-       const char* ifName = "../data/test/sample_byCols.bin";
+       const char* ifName = "../tdata/test/sample_byCols.bin";
        
        // check 'header'
        uint32_t nbSeries = get_nbSeries(ifName);
@@ -52,7 +52,7 @@ void t_deserialize1()
 void t_deserialize2()
 {
        // decode sample_byRows.bin into the toy dataset (4 customers, 3 sample points)
-       const char* ifName = "../data/test/sample_byRows.bin";
+       const char* ifName = "../tdata/test/sample_byRows.bin";
        
        // check 'header'
        uint32_t nbSeries = get_nbSeries(ifName);

diff --git a/code/test/stage1/TimeSeries/t.serialize.c b/code/stage1/test/TimeSeries/t.serialize.c
similarity index 71%
rename from code/test/stage1/TimeSeries/t.serialize.c
rename to code/stage1/test/TimeSeries/t.serialize.c
index 1dda321..6003c67 100644 (file)
--- a/code/test/stage1/TimeSeries/t.serialize.c
+++ b/code/stage1/test/TimeSeries/t.serialize.c
@@ -16,9 +16,9 @@ static void checkFilesEqual(const char* fileName1, const char* fileName2)
 
 void t_serialize1()
 {
-       const char* csvIfName = "../data/test/sample_byCols.csv";
-       const char* binaryIfName = "../data/test/sample_byCols.bin";
-       const char* tmpBinaryIfName = "../data/test/sample_byCols.tmp.bin";
+       const char* csvIfName = "../tdata/test/sample_byCols.csv";
+       const char* binaryIfName = "../tdata/test/sample_byCols.bin";
+       const char* tmpBinaryIfName = "../tdata/test/sample_byCols.tmp.bin";
        
        // serialize text file into a temporary binary file
        serialize_byCols(csvIfName, tmpBinaryIfName, 0);
@@ -32,9 +32,9 @@ void t_serialize1()
 
 void t_serialize2()
 {
-       const char* csvIfName = "../data/test/sample_byRows.csv";
-       const char* binaryIfName = "../data/test/sample_byRows.bin";
-       const char* tmpBinaryIfName = "../data/test/sample_byRows.tmp.bin";
+       const char* csvIfName = "../tdata/test/sample_byRows.csv";
+       const char* binaryIfName = "../tdata/test/sample_byRows.bin";
+       const char* tmpBinaryIfName = "../tdata/test/sample_byRows.tmp.bin";
        
        // serialize text file into a temporary binary file
        serialize_byRows(csvIfName, tmpBinaryIfName, 0);

diff --git a/code/test/stage1/Util/t.rng.c b/code/stage1/test/Util/t.rng.c
similarity index 100%
rename from code/test/stage1/Util/t.rng.c
rename to code/stage1/test/Util/t.rng.c

diff --git a/code/test/stage1/Util/t.utils.c b/code/stage1/test/Util/t.utils.c
similarity index 89%
rename from code/test/stage1/Util/t.utils.c
rename to code/stage1/test/Util/t.utils.c
index 254ef00..1abed91 100644 (file)
--- a/code/test/stage1/Util/t.utils.c
+++ b/code/stage1/test/Util/t.utils.c
@@ -8,7 +8,7 @@
 //integers
 void t_utils1()
 {
-       FILE* file = fopen("../data/test/integers.txt", "rb");
+       FILE* file = fopen("../tdata/test/integers.txt", "rb");
        int64_t x;
        readInt(file, &x);
        LUT_ASSERT(x == 1234);
@@ -28,7 +28,7 @@ void t_utils1()
 //reals
 void t_utils2()
 {
-       FILE* file = fopen("../data/test/reals.txt", "rb");
+       FILE* file = fopen("../tdata/test/reals.txt", "rb");
        Real x, tol = 1e-10;
        readReal(file, &x);
        LUT_ASSERT(fabs(x - 1234.056) < tol);

diff --git a/code/test/lut.h b/code/stage1/test/lut.h
similarity index 100%
rename from code/test/lut.h
rename to code/stage1/test/lut.h

diff --git a/code/test/stage1/main.c b/code/stage1/test/main.c
similarity index 100%
rename from code/test/stage1/main.c
rename to code/stage1/test/main.c

diff --git a/code/data/test/integers.txt b/code/stage1/test/tdata/integers.txt
similarity index 100%
rename from code/data/test/integers.txt
rename to code/stage1/test/tdata/integers.txt

diff --git a/code/data/test/reals.txt b/code/stage1/test/tdata/reals.txt
similarity index 100%
rename from code/data/test/reals.txt
rename to code/stage1/test/tdata/reals.txt

diff --git a/code/data/test/sample_byCols.bin b/code/stage1/test/tdata/sample_byCols.bin
similarity index 100%
rename from code/data/test/sample_byCols.bin
rename to code/stage1/test/tdata/sample_byCols.bin

diff --git a/code/data/test/sample_byCols.csv b/code/stage1/test/tdata/sample_byCols.csv
similarity index 100%
rename from code/data/test/sample_byCols.csv
rename to code/stage1/test/tdata/sample_byCols.csv

diff --git a/code/data/test/sample_byRows.bin b/code/stage1/test/tdata/sample_byRows.bin
similarity index 100%
rename from code/data/test/sample_byRows.bin
rename to code/stage1/test/tdata/sample_byRows.bin

diff --git a/code/data/test/sample_byRows.csv b/code/stage1/test/tdata/sample_byRows.csv
similarity index 100%
rename from code/data/test/sample_byRows.csv
rename to code/stage1/test/tdata/sample_byRows.csv

diff --git a/code/src/stage2/.gitkeep b/code/stage2/src/.gitkeep
similarity index 100%
rename from code/src/stage2/.gitkeep
rename to code/stage2/src/.gitkeep

diff --git a/code/test/stage2/.gitkeep b/code/stage2/test/.gitkeep
similarity index 100%
rename from code/test/stage2/.gitkeep
rename to code/stage2/test/.gitkeep

diff --git a/communication/.gitignore b/communication/.gitignore
new file mode 100644 (file)
index 0000000..bb8be15
--- /dev/null
+++ b/communication/.gitignore
@@ -0,0 +1,8 @@
+#ignore all files produced by LaTeX compilation
+*.aux
+*.log
+*.nav
+*.snm
+*.toc
+*.out
+*.pdf