removed hard linking of HDF5 (#32)

* switch to compiling with h5pcc
* reworked GitHub actions

.github/workflows/main.yml

@@ -35,7 +35,7 @@ jobs:
     # as part of the job.
     steps:
     - name: Check out repository code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4.1.7
 
     - name: Update repository code
       run: |
@@ -51,31 +51,31 @@ jobs:
         echo "CC=mpicc" >> $GITHUB_ENV
         echo "CPPFLAGS=-I/usr/include/hdf5/mpich" >> $GITHUB_ENV
         echo "LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/mpich" >> $GITHUB_ENV
+        echo "LIBS=-lhdf5" >> $GITHUB_ENV
 
     - name: Install Dependencies (Linux--HDF5-develop)
       if: matrix.hdf5 == 'develop'
       run: |
         # Use the newest stable gcc compiler
         sudo apt-get install automake autoconf libtool libtool-bin
         sudo apt-get install -qq mpich
-        echo "CC=mpicc" >> $GITHUB_ENV
 
         ##################################
         # INSTALL HDF5 FROM SOURCE
         ##################################
         git clone https://github.com/HDFGroup/hdf5.git
         export HOME_DIR=$(echo ~)
         cd hdf5
+        export HDF5_DIR=$PWD/hdf5
+        echo "HDF5_DIR=$HDF5_DIR" >> $GITHUB_ENV
         ./autogen.sh
-        ./configure --enable-build-mode=debug --without-szlib --disable-fortran --disable-hl \
+        CC=mpicc ./configure --enable-build-mode=debug --without-szlib --disable-fortran --disable-hl \
         --disable-tests --disable-tools \
-        --prefix=$HOME_DIR/hdf5 \
+        --prefix=$HDF5_DIR \
         --enable-parallel
         make -j 8 install
         mydir="$PWD"
-        export HDF5_DIR=$mydir/hdf5/hdf5
-        echo "CPPFLAGS=-I$HOME_DIR/hdf5/include" >> $GITHUB_ENV
-        echo "LDFLAGS=-L$HOME_DIR/hdf5/lib" >> $GITHUB_ENV
+        echo "CC=$HDF5_DIR/bin/h5pcc" >> $GITHUB_ENV
 
 ##################################
 # CONFIGURE (Autotools)

configure.ac

@@ -14,4 +14,12 @@ AM_INIT_AUTOMAKE([foreign])
 
 AC_CONFIG_FILES([Makefile src/Makefile])
 
+# Checks for libraries.
+PKG_CHECK_MODULES([uuid], [uuid],
+                  [], [AC_MSG_ERROR([Could not find libuuid])])
+
+# Checks for header files.
+AC_CHECK_HEADER([uuid/uuid.h], [],
+                [AC_MSG_ERROR([Couldn't find uuid/uuid.h])])
+
 AC_OUTPUT

examples/hdf5-iotest.sm.ini

@@ -0,0 +1,21 @@
+[DEFAULT]
+version = 0
+steps = 2 
+arrays = 4
+rows = 32
+columns = 128 
+process-rows = 4
+process-columns = 1
+# [weak, strong]
+scaling = weak
+# align along increment [bytes] boundaries
+alignment-increment = 16777216 
+# minimum object size [bytes] to force alignment (0=all objects)
+alignment-threshold = 0
+# minimum metadata block allocation size [bytes]
+meta-block-size = 2048
+# [posix, core, mpi-io-uni]
+single-process = mpi-io-uni
+[CUSTOM]
+hdf5-file = hdf5-iotest.sm.h5
+csv-file = hdf5-iotest.sm.csv

src/Makefile.am

@@ -5,4 +5,4 @@ dist_pkgdata_DATA = hdf5_iotest.ini combinator.sh
 hdf5_iotest_SOURCES = configuration.c dataset.c hdf5_iotest.c ini.c read_test.c \
 	utils.c write_test.c
 
-hdf5_iotest_LDADD = -lhdf5 -luuid
+hdf5_iotest_LDADD = -luuid