FAQs Answered

Can I use the same library for MPI and non-MPI code?

Short answer: Yes, since version 2.6.0.

Long answer: One build of ADIOS can be used by both serial and parallel applications. Use the -s and -m flags in the adios2-config command. By default, or with the -m flag, the command gives the flags for a parallel build, which add -DADIOS2_USE_MPI to the compilation flags and include extra libaries containing the MPI implementations into the linker flags. The -s flag will omit these flags. For example, if ADIOS is installed into /opt/adios2, the flags for a Fortran application will look like these:

$ /opt/adios2/bin/adios2-config --fortran-flags
-DADIOS2_USE_MPI -I/opt/adios2/include/adios2/fortran
$ /opt/adios2/bin/adios2-config --fortran-flags -m
-DADIOS2_USE_MPI -I/opt/adios2/include/adios2/fortran
$ /opt/adios2/bin/adios2-config --fortran-flags -s

$ /opt/adios2/bin/adios2-config --fortran-libs
-Wl,-rpath,/opt/adios2/lib /opt/adios2/lib/libadios2_fortran_mpi.so.2.6.0 /opt/adios2/lib/libadios2_fortran.so.2.6.0 -Wl,-rpath-link,/opt/adios2/lib
$ /opt/adios2/bin/adios2-config --fortran-libs -s
-Wl,-rpath,/opt/adios2/lib /opt/adios2/lib/libadios2_fortran.so.2.6.0 -Wl,-rpath-link,/opt/adios2/lib

If using cmake, there are different targets to build parallel

find_package(MPI REQUIRED)
find_package(ADIOS2 REQUIRED)
add_library(my_library src1.cxx src2.cxx)
target_link_libraries(my_library PRIVATE adios2::cxx11_mpi MPI::MPI_C)
add_library(my_f_library src1.F90 src2.F90)
target_link_libraries(my_f_library PRIVATE adios2::fortran_mpi adios2::fortran MPI::MPI_Fortran)

and serial applications:

find_package(ADIOS2 REQUIRED)
add_library(my_library src1.cxx src2.cxx)
target_link_libraries(my_library PRIVATE adios2::cxx11)
add_library(my_f_library src1.F90 src2.F90)
target_link_libraries(my_f_library PRIVATE adios2::fortran)

Can I use ADIOS 2 C++11 library with C++98 codes?

Use the C bindings. C++11 is a brand new language standard and many new (and old, e.g. std::string) might cause ABI conflicts.

Why are C and Fortran APIs missing functionality?

Because language intrinsics are NOT THE SAME. For example, C++ and Python support key/value pair structures natively, e.g. std::map and dictionaries, respectively. Fortran and C only support arrays natively. Use the right language (tool) for the right task.

C++11: Why are std::string arguments passed sometimes by value and sometimes by reference?

C++11, provides mechanisms to optimize copying small objects, rather than passing by reference. The latter was always the rule for C++98. When a string is passed by value, it’s assumed that the name will be short, <= 15 characters, most of the time. While passing by reference indicates that the string can be of any size. Check the isocpp guidelines on this topic for more information.

C++11: Should I pass adios2:: objects by value or by reference?

adios2::ADIOS: always pass by reference this is the only “large memory” object; all others: pass by reference or value depending on your coding standards and requirements, they are small objects that wrap around a pointer to an internal object inside adios2::ADIOS.

Fortran: Can I pass slices and temporary arrays to adios2_put?

By definition the lifetime of a temporary if the scope of the function is passed to. Therefore, you must use sync mode with adios2_put. Deferred mode will save garbage data since the memory location of a temporary is undefined after adios2_put, not able to reach adios2_end_step, adios2_close or adios2_perform_puts where the memory is actually used.

How do I enable the Python bindings on Titan?

The default ADIOS2 configuration on Titan builds a static library. Python bindings require enabling the dynamic libraries and the Cray dynamic environment variable. See Building on HPC Systems and Enabling the Python bindings. For example:

[atkins3@titan-ext4 code]$ mkdir adios
[atkins3@titan-ext4 code]$ cd adios
[atkins3@titan-ext4 adios]$ git clone https://github.com/ornladios/adios2.git source
[atkins3@titan-ext4 adios]$ module swap PrgEnv-pgi PrgEnv-gnu
[atkins3@titan-ext4 adios]$ module load cmake3/3.11.3
[atkins3@titan-ext4 adios]$ module load python python_numpy python_mpi4py
[atkins3@titan-ext4 adios]$ export CRAYPE_LINK_TYPE=dynamic CC=cc CXX=CC FC=ftn
[atkins3@titan-ext4 adios]$ mkdir build
[atkins3@titan-ext4 build]$ cd build
[atkins3@titan-ext4 build]$ cmake ../source
-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Cray Programming Environment 2.5.13 C
-- Check for working C compiler: /opt/cray/craype/2.5.13/bin/cc
-- Check for working C compiler: /opt/cray/craype/2.5.13/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Cray Programming Environment 2.5.13 CXX
-- Check for working CXX compiler: /opt/cray/craype/2.5.13/bin/CC
-- Check for working CXX compiler: /opt/cray/craype/2.5.13/bin/CC -- works
-- Found PythonInterp: /sw/titan/.swci/0-login/opt/spack/20180315/linux-suse_linux11-x86_64/gcc-4.3.4/python-2.7.9-v6ctjewwdx6k2qs7ublexz7gnx457jo5/bin/python2.7 (found version "2.7.9")
-- Found PythonLibs: /sw/titan/.swci/0-login/opt/spack/20180315/linux-suse_linux11-x86_64/gcc-4.3.4/python-2.7.9-v6ctjewwdx6k2qs7ublexz7gnx457jo5/lib/libpython2.7.so (found version "2.7.9")
-- Found PythonModule_numpy: /sw/xk6/python_numpy/1.7.1/python2.7.9_craylibsci_gnu4.9.0/lib64/python2.7/site-packages/numpy
-- Found PythonModule_mpi4py: /lustre/atlas/sw/xk7/python_mpi4py/2.0.0/cle5.2up04_python2.7.9/lib64/python2.7/site-packages/mpi4py
-- Found PythonFull: /sw/titan/.swci/0-login/opt/spack/20180315/linux-suse_linux11-x86_64/gcc-4.3.4/python-2.7.9-v6ctjewwdx6k2qs7ublexz7gnx457jo5/bin/python2.7  found components:  Interp Libs numpy mpi4py
ADIOS2 build configuration:
  ADIOS Version: 2.4.0
  C++ Compiler : GNU 6.3.0 CrayPrgEnv

  Fortran Compiler : GNU 6.3.0 CrayPrgEnv

  Installation prefix: /usr/local
        bin: bin
        lib: lib
    include: include
      cmake: lib/cmake/adios2
     python: lib/python2.7/site-packages

    Library Type: shared
    Build Type:   Release
    Testing: ON
    Build Options:
      BZip2    : ON
      ZFP      : OFF
      SZ       : OFF
      MGARD    : OFF
      MPI      : ON
      DataMan  : ON
      SST      : ON
      ZeroMQ   : OFF
      HDF5     : OFF
      Python   : ON
      Fortran  : ON
      SysVShMem: ON
      Endian_Reverse: OFF

-- Configuring done
-- Generating done
-- Build files have been written to: /ccs/home/atkins3/code/adios/build

How do I build ADIOS 2 on Fujitsu FX100?

  • Cross-compilation (building on the login node) is not recommended. Submit an interactive job and build on the compute nodes.

  • Make sure CMake >= 3.6 is installed on the compute nodes. If not, you need to build and install it from source since CMake does not provide SPARC V9 binaries.

  • Use gcc instead of the Fujitsu compiler. We tested with gcc 6.3.0

  • CMake fails to automatically find the correct MPI library on FX100. As a workaround, set CC, CXX, and FC to the corresponding MPI compiler wrappers:

    $ CC=mpigcc CXX=mpig++ FC=mpigfortran cmake  ..

SST engine hangs on Fujitsu FX100. Why?

The communication thread of SST might have failed to start. FX100 requires users to set the maximum stack size manually when launching POSIX threads. One way to do this is through ulimit (e.g. ulimit -s 1024). You can also set the stack size when submitting the job. Please contact your system administrator for details.