fix cmake compile

[psychocoderHPC]

close #103

• fix missing mpi.h by adding cflags to
  • tests
  • utils
  • examples
• fix that ADIOSLIB_LDADD is linked to read only executables (use ADIOSREADLIB_LDADD instead)
• fix missing pthread library by adding to ADIOS*SLIB_* and ADIOSLIB_LDADD
• add mpi flags to each programm which links against mpi
• add missing pthread library to adios
• fix global_range_select/array_[writer|reader]

Test

• [x] compile with cmake without mpicc (used gcc 4.9.2)

[pnorbert]

This branch does not build with my standard MPI settings on Ubuntu 16.04 LTS + openmpi. The -I option with many paths concatenated with ; throws off the compile command.

[ 3%] Building C object src/CMakeFiles/adios_internal_nompi.dir/core/mpidummy.c.o cd /home/adios/work/ADIOS/build.cmake/src && /usr/bin/mpicc -I/home/adios/work/ADIOS -I/home/adios/work/ADIOS/src/zfp/zfp-0.5.0/inc -I/home/adios/work/ADIOS/build.cmake -I/home/adios/work/ADIOS/src -I/home/adios/work/ADIOS/src/core -I/home/adios/work/ADIOS/src/core/transforms -I/home/adios/work/ADIOS/build.cmake/src -I/home/adios/work/ADIOS/build.cmake/src/public -I/home/adios/work/ADIOS/src/mxml/mxml-2.9 -g -O0 -fPIC -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast -D_INTERNAL -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_GNU_SOURCE -DMPICH_IGNORE_CXX_SEEK -D_NOMPI -I/opt/netcdf-4.4.0/include -I/opt/hdf5-1.8.17/include -DZLIB -I/usr/include -DBZIP2 -I/usr/include -DSZIP -I/opt/szip/include -DISOBAR -I/opt/isobar/include -DALACRITY -I/opt/alacrity/include -DZFP -I/home/adios/work/ADIOS/src/zfp/zfp-0.5.0/inc -DFASTBIT -I/opt/fastbit/include/fastbit -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi -I/opt/chaos/include -I/opt/hdf5-1.8.17-parallel/include -DZLIB -I/usr/include -DBZIP2 -I/usr/include -DSZIP -I/opt/szip/include -DISOBAR -I/opt/isobar/include -DALACRITY -I/opt/alacrity/include -DZFP -I/home/adios/work/ADIOS/src/zfp/zfp-0.5.0/inc -DFASTBIT -I/opt/fastbit/include/fastbit -o CMakeFiles/adios_internal_nompi.dir/core/mpidummy.c.o -c /home/adios/work/ADIOS/src/core/mpidummy.c gcc: fatal error: no input files compilation terminated. /bin/sh: 1: /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include: Permission denied /bin/sh: 1: /usr/lib/openmpi/include: Permission denied /bin/sh: 1: /usr/lib/openmpi/include/openmpi: Permission denied src/CMakeFiles/adios_internal_nompi.dir/build.make:62: recipe for target 'src/CMakeFiles/adios_internal_nompi.dir/core/mpidummy.c.o' failed make[2]: *** [src/CMakeFiles/adios_internal_nompi.dir/core/mpidummy.c.o] Error 126

[pnorbert]

The settings for configuration for the above build are coming from ./cmake_init for adiosVM.

[psychocoderHPC]

it looks like this line is the reason for the crash. I will fix it

[psychocoderHPC]

I updated the branch and removed the ;

I tested only the C build, because I have no mpi for fortran avail.

[psychocoderHPC]

Where can I find the adiosVM image?

[pnorbert]

The cmake build has been fixed for 1.12, so these commits don't need to be merged. Let us know if you still have any issues with cmake build of the master branch.