Commit 0e7d96ea authored by Atkins, Charles Vernon's avatar Atkins, Charles Vernon
Browse files

Update CMake install docs

parent 2b1eb656

docs/user_guide/source/installation/cmake.rst

+242 −63
Original line number Diff line number Diff line
@@ -10,53 +10,68 @@ To build ADIOS2: 


.. code-block:: bash 

    

    $ git clone https://github.com/ornladios/ADIOS2.git 

    $ git clone https://github.com/ornladios/ADIOS2.git adios2-source





2. Create a separate build directory: 



.. code-block:: bash 

    

    $ mkdir build 

    $ mkdir adios2-build





3. Configure the project with CMake: 



.. code-block:: bash



    $ cd build 

    $ cmake -DADIOS2_USE_Fortran=ON ../ADIOS2 

    -- The C compiler identification is GNU 5.4.0

    -- The CXX compiler identification is GNU 5.4.0

    -- Check for working C compiler: /usr/bin/cc

    -- Check for working C compiler: /usr/bin/cc -- works

    $ cd adios2-build 

    $ cmake ../adios2-source

    -- The C compiler identification is GNU 7.3.0

    -- The CXX compiler identification is GNU 7.3.0

    -- Check for working C compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gcc

    -- Check for working C compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gcc -- works

    -- Detecting C compiler ABI info

    -- Detecting C compiler ABI info - done

    -- Detecting C compile features

    -- Detecting C compile features - done

    -- Check for working CXX compiler: /usr/bin/c++

    -- Check for working CXX compiler: /usr/bin/c++ -- works

    -- Check for working CXX compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/g++

    -- Check for working CXX compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/g++ -- works

    -- Detecting CXX compiler ABI info

    -- Detecting CXX compiler ABI info - done

    -- Detecting CXX compile features

    -- Detecting CXX compile features - done

    -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") 

    -- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6") 

    -- Looking for BZ2_bzCompressInit

    -- Looking for BZ2_bzCompressInit - found

    -- Could NOT find ZFP (missing: ZFP_LIBRARY ZFP_INCLUDE_DIR) 

    -- The Fortran compiler identification is GNU 5.4.0

    -- Check for working Fortran compiler: /usr/bin/gfortran

    -- Check for working Fortran compiler: /usr/bin/gfortran  -- works

    -- Could NOT find SZ (missing: SZ_LIBRARY ZLIB_LIBRARY ZSTD_LIBRARY SZ_INCLUDE_DIR) 

    -- Could NOT find MGARD (missing: MGARD_LIBRARY ZLIB_LIBRARY MGARD_INCLUDE_DIR) 

    -- Looking for a Fortran compiler

    -- Looking for a Fortran compiler - /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran

    -- The Fortran compiler identification is GNU 7.3.0

    -- Check for working Fortran compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran

    -- Check for working Fortran compiler: /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran  -- works

    -- Detecting Fortran compiler ABI info

    -- Detecting Fortran compiler ABI info - done

    -- Checking whether /usr/bin/gfortran supports Fortran 90

    -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes

    -- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so (found version "3.0") 

    -- Found MPI_Fortran: /usr/lib/openmpi/lib/libmpi_usempif08.so (found version "3.0") 

    -- Found MPI: TRUE (found version "3.0") found components:  C Fortran 

    -- Found ZeroMQ: /usr/lib/x86_64-linux-gnu/libzmq.so  

    -- Checking whether /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran supports Fortran 90

    -- Checking whether /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran supports Fortran 90 -- yes

    -- Found MPI_C: /opt/ohpc/pub/mpi/openmpi3-gnu7/3.1.0/lib/libmpi.so (found version "3.1") 

    -- Found MPI_Fortran: /opt/ohpc/pub/mpi/openmpi3-gnu7/3.1.0/lib/libmpi_usempif08.so (found version "3.1") 

    -- Found MPI: TRUE (found version "3.1") found components:  C Fortran 

    -- Found ZeroMQ: /usr/lib64/libzmq.so (found suitable version "4.1.4", minimum required is "4.1") 

    -- HDF5: Using hdf5 compiler wrapper to determine C configuration

    -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16") found components:  C 

    -- Found HDF5: /opt/ohpc/pub/libs/gnu7/openmpi3/hdf5/1.10.2/lib/libhdf5.so (found version "1.10.2") found components:  C 

    -- Found PythonInterp: /usr/bin/python3 (found version "3.4.9") 

    -- Found PythonLibs: /usr/lib64/libpython3.4m.so (found version "3.4.9") 

    -- Found PythonModule_numpy: /opt/ohpc/pub/libs/gnu7/numpy/1.14.3/lib64/python3.4/site-packages/numpy  

    -- Found PythonModule_mpi4py: /opt/ohpc/pub/libs/gnu7/openmpi3/mpi4py/3.0.0/lib64/python3.4/site-packages/mpi4py  

    -- Found PythonFull: /usr/bin/python3  found components:  Interp Libs numpy mpi4py 

    -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") 

    -- Checking for module 'libfabric'

    --   No package 'libfabric' found

    -- Could NOT find LIBFABRIC (missing: LIBFABRIC_LIBRARIES) (Required is at least version "1.6")

    -- Looking for shmget

    -- Looking for shmget - found

    -- Looking for pthread.h

    -- Looking for pthread.h - found

    -- Looking for pthread_create
@@ -66,14 +81,8 @@ To build ADIOS2: 
    -- Looking for pthread_create in pthread

    -- Looking for pthread_create in pthread - found

    -- Found Threads: TRUE  

    -- Found PythonInterp: /usr/bin/python3 (found version "3.5.2") 

    -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.5m.so

    -- Found PythonModule_numpy: /usr/lib/python3/dist-packages/numpy  

    -- Found PythonModule_mpi4py: /usr/lib/python3/dist-packages/mpi4py  

    -- Found PythonFull: /usr/bin/python3  found components:  Interp Libs numpy mpi4py 

    -- Could NOT find EVPath (missing:  EVPath_LIBRARY EVPath_INCLUDE_DIR) 

    -- Looking for shmget

    -- Looking for shmget - found



    -- ADIOS2 ThirdParty: Configuring KWSys

    -- Checking whether header cstdio is available

    -- Checking whether header cstdio is available - yes

    -- Checking for Large File Support
@@ -104,7 +113,176 @@ To build ADIOS2: 
    -- Checking whether CXX compiler struct stat has st_mtimespec member - no

    -- Checking whether <ext/stdio_filebuf.h> is available

    -- Checking whether <ext/stdio_filebuf.h> is available - yes

    -- pybind11 v2.2.1



    -- ADIOS2 ThirdParty: Configuring GTest

    -- Check if compiler accepts -pthread

    -- Check if compiler accepts -pthread - yes



    -- ADIOS2 ThirdParty: Configuring pybind11

    -- Found PythonLibs: /usr/lib64/libpython3.4m.so

    -- pybind11 v2.2.2



    -- ADIOS2 ThirdParty: Configuring pugixml



    -- ADIOS2 ThirdParty: Configuring nlohmann_json

    -- Using the single-header code from /home/khq.kitware.com/chuck.atkins/Code/adios2/source/master/thirdparty/nlohmann_json/nlohmann_json/single_include/



    -- ADIOS2 ThirdParty: Configuring atl

    -- Looking for sys/types.h

    -- Looking for sys/types.h - found

    -- Looking for stdint.h

    -- Looking for stdint.h - found

    -- Looking for stddef.h

    -- Looking for stddef.h - found

    -- Check size of double

    -- Check size of double - done

    -- Check size of float

    -- Check size of float - done

    -- Check size of int

    -- Check size of int - done

    -- Check size of short

    -- Check size of short - done

    -- Looking for include file malloc.h

    -- Looking for include file malloc.h - found

    -- Looking for include file unistd.h

    -- Looking for include file unistd.h - found

    -- Looking for include file stdlib.h

    -- Looking for include file stdlib.h - found

    -- Looking for include file string.h

    -- Looking for include file string.h - found

    -- Looking for include file sys/time.h

    -- Looking for include file sys/time.h - found

    -- Looking for include file windows.h

    -- Looking for include file windows.h - not found

    -- Looking for fork

    -- Looking for fork - found

    -- Found atl: /home/chuck/adios2-build/thirdparty/atl/atl/atl-config.cmake (found version "2.2.1") 



    -- ADIOS2 ThirdParty: Configuring dill

    -- Check size of void*

    -- Check size of void* - done

    -- Check size of long

    -- Check size of long - done

    -- Check if the system is big endian

    -- Searching 16 bit integer

    -- Check size of unsigned short

    -- Check size of unsigned short - done

    -- Using unsigned short

    -- Check if the system is big endian - little endian

    -- Checking for module 'libffi'

    --   No package 'libffi' found

    -- Could NOT find LibFFI (missing: LIBFFI_LIBRARIES) 

    -- Disabling emulation

    -- Looking for include file stdarg.h

    -- Looking for include file stdarg.h - found

    -- Looking for include file memory.h

    -- Looking for include file memory.h - found

    -- Found dill: /home/chuck/adios2-build/thirdparty/dill/dill/dill-config.cmake (found version "2.4.0") 



    -- ADIOS2 ThirdParty: Configuring ffs

    -- Check size of off_t

    -- Check size of off_t - done

    -- Check size of long double

    -- Check size of long double - done

    -- Check size of long long

    -- Check size of long long - done

    -- Check size of size_t

    -- Check size of size_t - done

    -- Looking for socket

    -- Looking for socket - found

    -- Found BISON: /usr/bin/bison (found version "3.0.4") 

    -- Found FLEX: /usr/bin/flex (found version "2.5.37") 

    -- Found dill: /home/chuck/adios2-build/thirdparty/dill/dill/dill-config.cmake (found suitable version "2.4.0", minimum required is "2.3.1") 

    -- Found atl: /home/chuck/adios2-build/thirdparty/atl/atl/atl-config.cmake (found suitable version "2.2.1", minimum required is "2.2.1") 

    -- Looking for netdb.h

    -- Looking for netdb.h - found

    -- Looking for sockLib.h

    -- Looking for sockLib.h - not found

    -- Looking for sys/select.h

    -- Looking for sys/select.h - found

    -- Looking for sys/socket.h

    -- Looking for sys/socket.h - found

    -- Looking for sys/times.h

    -- Looking for sys/times.h - found

    -- Looking for sys/uio.h

    -- Looking for sys/uio.h - found

    -- Looking for sys/un.h

    -- Looking for sys/un.h - found

    -- Looking for winsock.h

    -- Looking for winsock.h - not found

    -- Looking for strtof

    -- Looking for strtof - found

    -- Looking for strtod

    -- Looking for strtod - found

    -- Looking for strtold

    -- Looking for strtold - found

    -- Looking for getdomainname

    -- Looking for getdomainname - found

    -- Check size of struct iovec

    -- Check size of struct iovec - done

    -- Performing Test HAS_IOV_BASE_IOVEC

    -- Performing Test HAS_IOV_BASE_IOVEC - Success

    -- Found ffs: /home/chuck/adios2-build/thirdparty/ffs/ffs/ffs-config.cmake (found version "1.6.0") 



    -- ADIOS2 ThirdParty: Configuring enet

    -- Looking for getaddrinfo

    -- Looking for getaddrinfo - found

    -- Looking for getnameinfo

    -- Looking for getnameinfo - found

    -- Looking for gethostbyaddr_r

    -- Looking for gethostbyaddr_r - found

    -- Looking for gethostbyname_r

    -- Looking for gethostbyname_r - found

    -- Looking for poll

    -- Looking for poll - found

    -- Looking for fcntl

    -- Looking for fcntl - found

    -- Looking for inet_pton

    -- Looking for inet_pton - found

    -- Looking for inet_ntop

    -- Looking for inet_ntop - found

    -- Performing Test HAS_MSGHDR_FLAGS

    -- Performing Test HAS_MSGHDR_FLAGS - Success

    -- Performing Test HAS_SOCKLEN_T

    -- Performing Test HAS_SOCKLEN_T - Success

    -- Found enet: /home/chuck/adios2-build/thirdparty/enet/enet/enet-config.cmake (found version "1.3.14") 



    -- ADIOS2 ThirdParty: Configuring EVPath

    -- Performing Test HAVE_MATH

    -- Performing Test HAVE_MATH - Failed

    -- Performing Test HAVE_LIBM_MATH

    -- Performing Test HAVE_LIBM_MATH - Success

    -- Found ffs: /home/chuck/adios2-build/thirdparty/ffs/ffs/ffs-config.cmake (found suitable version "1.6.0", minimum required is "1.5.1") 

    -- Could NOT find nvml (missing: NVML_LIBRARY NVML_INCLUDE_DIR) 

    -- Looking for clock_gettime

    -- Looking for clock_gettime - found

    -- Found enet: /home/chuck/adios2-build/thirdparty/enet/enet/enet-config.cmake (found suitable version "1.3.14", minimum required is "1.3.13") 

    --  - Udt4 library was not found.  This is not a fatal error, just that the Udt4 transport will not be built.

    -- Checking for module 'libfabric'

    --   No package 'libfabric' found

    -- Looking for ibv_create_qp

    -- Looking for ibv_create_qp - not found

    -- Looking for ibv_create_qp in ibverbs

    -- Looking for ibv_create_qp in ibverbs - not found

    -- Could NOT find IBVERBS (missing: IBVERBS_LIBRARY) 

    -- Looking for hostlib.h

    -- Looking for hostlib.h - not found

    -- Looking for sys/sockio.h

    -- Looking for sys/sockio.h - not found

    -- Performing Test HAVE_FDS_BITS

    -- Performing Test HAVE_FDS_BITS - Failed

    -- Looking for writev

    -- Looking for writev - found

    -- Looking for uname

    -- Looking for uname - found

    -- Looking for getloadavg

    -- Looking for getloadavg - found

    -- Looking for gettimeofday

    -- Looking for gettimeofday - found

    -- Looking for getifaddrs

    -- Looking for getifaddrs - found

    -- Found EVPath: /home/chuck/adios2-build/thirdparty/EVPath/EVPath/EVPathConfig.cmake (found version "4.4.0") 



    -- Performing Test HAS_FLTO

    -- Performing Test HAS_FLTO - Success

    -- LTO enabled
@@ -112,49 +290,52 @@ To build ADIOS2: 
    -- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling

    -- Verifying Fortran/CXX Compiler Compatibility

    -- Verifying Fortran/CXX Compiler Compatibility - Success

    -- Found MPI: TRUE (found version "3.0") found components:  C 

    -- Found MPI: TRUE (found version "3.1") found components:  C 



    ADIOS2 build configuration:

      ADIOS Version: 2.2.0

      C++ Compiler : GNU 5.4.0 

        /usr/bin/c++

      ADIOS Version: 2.3.0

      C++ Compiler : GNU 7.3.0 

        /opt/ohpc/pub/compiler/gcc/7.3.0/bin/g++



      Fortran Compiler : GNU 5.4.0 

        /usr/bin/gfortran

      Fortran Compiler : GNU 7.3.0 

        /opt/ohpc/pub/compiler/gcc/7.3.0/bin/gfortran



      Installation prefix: /usr/local

            bin: bin

            lib: lib

        include: include

          cmake: lib/cmake/adios2

         python: lib/python3.5/site-packages

         python: lib/python3.4/site-packages



      Features:

        Library Type: shared

        Build Type:   Debug

        Build Type:   Release

        Testing: ON

        Build Options:

          BZip2    : ON

          ZFP      : OFF

          SZ       : OFF

          MGARD    : OFF

          MPI      : ON

          DataMan  : ON

          SST      : OFF

          SST      : ON

          ZeroMQ   : ON

          HDF5     : ON

          Python   : ON

          Fortran  : ON

          SysVShMem: ON

          Endian_Reverse: OFF



    -- Configuring done

    -- Generating done

    -- Build files have been written to: /home/wgodoy/workspace/build  

    -- Build files have been written to: /home/chuck/adios2-build

 



4. Compile using make -j cores



.. code-block:: bash 

    

    $ make -j 4 

    $ make -j 16 



5. Run tests with make test or ctest
@@ -163,21 +344,21 @@ To build ADIOS2: 
    $ ctest

    Test project /home/wgodoy/workspace/build

            Start   1: ADIOSInterfaceWriteTest.DefineVar_int8_t_1x10

     1/62 Test  #1: ADIOSInterfaceWriteTest.DefineVar_int8_t_1x10 ............................   Passed    0.16 sec

      1/295 Test   #1: ADIOSInterfaceWriteTest.DefineVar_int8_t_1x10 .........................   Passed    0.16 sec

            Start   2: ADIOSInterfaceWriteTest.DefineVar_int16_t_1x10

     2/62 Test  #2: ADIOSInterfaceWriteTest.DefineVar_int16_t_1x10 ...........................   Passed    0.06 sec

      2/295 Test   #2: ADIOSInterfaceWriteTest.DefineVar_int16_t_1x10 ........................   Passed    0.06 sec

            Start   3: ADIOSInterfaceWriteTest.DefineVar_int32_t_1x10

          

          ...

               

          Start 61: ADIOSBZip2Wrapper.WrongParameterValue

    61/62 Test #61: ADIOSBZip2Wrapper.WrongParameterValue ....................................   Passed    0.00 sec

          Start 62: ADIOSBZip2Wrapper.WrongBZip2Name

    62/62 Test #62: ADIOSBZip2Wrapper.WrongBZip2Name .........................................   Passed    0.00 sec

            Start 294: ADIOSBZip2Wrapper.WrongParameterValue

    294/295 Test #294: ADIOSBZip2Wrapper.WrongParameterValue .................................   Passed    0.00 sec

            Start 295: ADIOSBZip2Wrapper.WrongBZip2Name

    295/295 Test #295: ADIOSBZip2Wrapper.WrongBZip2Name ......................................   Passed    0.00 sec

    

    100% tests passed, 0 tests failed out of 62

    100% tests passed, 0 tests failed out of 295

    

    Total Test time (real) =   3.95 sec

    Total Test time (real) =   95.95 sec

    



5. Install
@@ -231,22 +412,20 @@ In addition to the `ADIOS2_USE_Feature` options, the following options are also 
 CMake VAR Options                       Values                                       Description                                                                          |

==================================== =============================================== ===============================

 `BUILD_SHARED_LIBS`                   ``ON``/OFF                                     Build shared libraries.                                                               

 `CMAKE_POSITION_INDEPENDENT_CODE`     ``ON``/OFF                                     Enable fPIC.                                

 `ADIOS2_BUILD_EXAMPLES`               ``ON``/OFF                                     Build examples.                                                                       

 `ADIOS2_BUILD_TESTING`                ``ON``/OFF                                     Build test code.                                                                      

 `CMAKE_INSTALL_PREFIX`                /path/to/install (``/usr/local``)              Installation location.                                                                     

 `CMAKE_BUILD_TYPE`                    ``Debug``/Release/RelWithDebInfo/MinSizeRel    Compiler optimization levels.                                            

==================================== =============================================== ===============================



Example: the following configuration will build, test and install under /opt/adios2/2.2.0 an optimized (Release) version of ADIOS2.

Example: the following configuration will build, test and install under /opt/adios2/2.3.0 an optimized (Release) version of ADIOS2.



.. code-block:: bash



    $ cd build 

    $ cmake -DADIOS2_USE_Fortran=ON -DCMAKE_INSTALL_PREFIX=/opt/adios2/2.2.0 -DCMAKE_BUILD_Type=Release ../ADIOS2

    $ make -j 4

    $ cmake -DADIOS2_USE_Fortran=ON -DCMAKE_INSTALL_PREFIX=/opt/adios2/2.3.0 -DCMAKE_BUILD_Type=Release ../ADIOS2

    $ make -j16 

    $ ctest

    $ make install

 

For a full configurable script example, click `here. <https://github.com/ornladios/ADIOS2/tree/master/scripts/runconf/runconf.sh>`_