Cannot find 'adios_config' #1424

cbontoiu · 2023-04-16T11:05:56Z

Hi,
I am trying to install openPMD-api with ADIOS2. My installation of ADIOS2 is here

Now, from a build folder inside the openPMD-api distribution I tried:

sudo cmake 
-DCMAKE_PREFIX_PATH=/usr/local/adios2/bin 
-DopenPMD_USE_MPI=ON 
-DCMAKE_INSTALL_PREFIX=~/lib/openPMD-api 
-DopenPMD_USE_ADIOS2=ON 
-DopenPMD_USE_HDF5=OFF 
-DCMAKE_C_COMPILER=/usr/local/openmpi/bin/mpicc 
-DCMAKE_CXX_COMPILER=/usr/local/openmpi/bin/mpicxx 
-DPython_EXECUTABLE=/usr/bin/python3 
-DopenPMD_USE_PYTHON=ON 
..

where for the first option to cmake I tried:

-DCMAKE_PREFIX_PATH=/usr/local/adios2/bin 
-DCMAKE_PREFIX_PATH=/usr/local/adios2
-DCMAKE_PREFIX_PATH=/usr/local

The installer complains about not finding adios_config but I have adios2-config:

-- Can NOT find 'adios_config' - set ADIOS_ROOT, ADIOS_DIR or INSTALL_PREFIX, or check your PATH
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.13.1")

Please let me know how can I complete the installation in this case.
Thank you

The text was updated successfully, but these errors were encountered:

franzpoeschel · 2023-04-18T12:11:31Z

Hello,
I think that there is no issue. Note that adios_config and adios2_config are two different things, referring to ADIOS1 and ADIOS2 respectively. CMake does not find adios_config and accordingly disables ADIOS1. Looking at the configuration output, ADIOS2 is being found and enabled.

cbontoiu · 2023-04-18T18:16:50Z

@franzpoeschel thank you your reply.

I went on with the installation and obtained an error:

ADIOS2IOHandler.cpp:73:7: error: no matching function for call to ‘adios2::ADIOS::ADIOS(<brace-enclosed initializer list>)’
   73 |     , m_ADIOS{ communicator, ADIOS2_DEBUG_MODE }

Could you help with that, please?
Thank you.

Cristian

sudo make -j 16 install
[  4%] Built target CatchMain
[  4%] Built target CatchRunner
[  5%] Building CXX object CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS2IOHandler.cpp.o
/home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp: In constructor ‘openPMD::ADIOS2IOHandlerImpl::ADIOS2IOHandlerImpl(openPMD::AbstractIOHandler*, MPI_Comm, nlohmann::json, std::string)’:
/home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp:73:7: error: no matching function for call to ‘adios2::ADIOS::ADIOS(<brace-enclosed initializer list>)’
   73 |     , m_ADIOS{ communicator, ADIOS2_DEBUG_MODE }
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/adios2/include/adios2.h:18,
                 from /home/quasar/src/openPMD-api/include/openPMD/IO/ADIOS/ADIOS2Auxiliary.hpp:30,
                 from /home/quasar/src/openPMD-api/include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp:26,
                 from /home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp:22:
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:120:5: note: candidate: ‘adios2::ADIOS::ADIOS(adios2::ADIOS&&)’
  120 |     ADIOS(ADIOS &&) = default;
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:120:5: note:   candidate expects 1 argument, 2 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:106:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, const string&)’
  106 |     ADIOS(const std::string &configFile, const std::string &hostLanguage);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:106:30: note:   no known conversion for argument 1 from ‘MPI_Comm’ {aka ‘ompi_communicator_t*’} to ‘const string&’ {aka ‘const std::__cxx11::basic_string<char>&’}
  106 |     ADIOS(const std::string &configFile, const std::string &hostLanguage);
      |           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:95:5: note: candidate: ‘adios2::ADIOS::ADIOS()’
   95 |     ADIOS();
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:95:5: note:   candidate expects 0 arguments, 2 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:89:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&)’
   89 |     ADIOS(const std::string &configFile);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:89:5: note:   candidate expects 1 argument, 2 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:78:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, MPI_Comm, const string&)’
   78 |     ADIOS(const std::string &configFile, MPI_Comm comm,
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:78:5: note:   candidate expects 3 arguments, 2 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:67:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, MPI_Comm)’
   67 |     ADIOS(const std::string &configFile, MPI_Comm comm);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:67:30: note:   no known conversion for argument 1 from ‘MPI_Comm’ {aka ‘ompi_communicator_t*’} to ‘const string&’ {aka ‘const std::__cxx11::basic_string<char>&’}
   67 |     ADIOS(const std::string &configFile, MPI_Comm comm);
      |           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:56:5: note: candidate: ‘adios2::ADIOS::ADIOS(MPI_Comm)’
   56 |     ADIOS(MPI_Comm comm);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:56:5: note:   candidate expects 1 argument, 2 provided
/home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp: In constructor ‘openPMD::ADIOS2IOHandlerImpl::ADIOS2IOHandlerImpl(openPMD::AbstractIOHandler*, nlohmann::json, std::string)’:
/home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp:86:7: error: no matching function for call to ‘adios2::ADIOS::ADIOS(<brace-enclosed initializer list>)’
   86 |     , m_ADIOS{ ADIOS2_DEBUG_MODE }
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/adios2/include/adios2.h:18,
                 from /home/quasar/src/openPMD-api/include/openPMD/IO/ADIOS/ADIOS2Auxiliary.hpp:30,
                 from /home/quasar/src/openPMD-api/include/openPMD/IO/ADIOS/ADIOS2IOHandler.hpp:26,
                 from /home/quasar/src/openPMD-api/src/IO/ADIOS/ADIOS2IOHandler.cpp:22:
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:120:5: note: candidate: ‘adios2::ADIOS::ADIOS(adios2::ADIOS&&)’
  120 |     ADIOS(ADIOS &&) = default;
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:120:11: note:   no known conversion for argument 1 from ‘const bool’ to ‘adios2::ADIOS&&’
  120 |     ADIOS(ADIOS &&) = default;
      |           ^~~~~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:106:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, const string&)’
  106 |     ADIOS(const std::string &configFile, const std::string &hostLanguage);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:106:5: note:   candidate expects 2 arguments, 1 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:95:5: note: candidate: ‘adios2::ADIOS::ADIOS()’
   95 |     ADIOS();
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:95:5: note:   candidate expects 0 arguments, 1 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:89:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&)’
   89 |     ADIOS(const std::string &configFile);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:89:30: note:   no known conversion for argument 1 from ‘const bool’ to ‘const string&’ {aka ‘const std::__cxx11::basic_string<char>&’}
   89 |     ADIOS(const std::string &configFile);
      |           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:78:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, MPI_Comm, const string&)’
   78 |     ADIOS(const std::string &configFile, MPI_Comm comm,
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:78:5: note:   candidate expects 3 arguments, 1 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:67:5: note: candidate: ‘adios2::ADIOS::ADIOS(const string&, MPI_Comm)’
   67 |     ADIOS(const std::string &configFile, MPI_Comm comm);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:67:5: note:   candidate expects 2 arguments, 1 provided
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:56:5: note: candidate: ‘adios2::ADIOS::ADIOS(MPI_Comm)’
   56 |     ADIOS(MPI_Comm comm);
      |     ^~~~~
/usr/local/adios2/include/adios2/cxx11/ADIOS.h:56:20: note:   no known conversion for argument 1 from ‘const bool’ to ‘MPI_Comm’ {aka ‘ompi_communicator_t*’}
   56 |     ADIOS(MPI_Comm comm);
      |           ~~~~~~~~~^~~~
make[2]: *** [CMakeFiles/openPMD.dir/build.make:544: CMakeFiles/openPMD.dir/src/IO/ADIOS/ADIOS2IOHandler.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:193: CMakeFiles/openPMD.dir/all] Error 2
make: *** [Makefile:141: all] Error 2

franzpoeschel · 2023-04-18T18:38:53Z

It seems that you are trying to compile an old openPMD-api version against a new ADIOS2 version. That constructor has been removed in recent ADIOS2, you should try either openPMD-api in version 0.14.5 (last stable) or 0.15.1 (current stable).

cbontoiu · 2023-04-18T18:48:58Z

@franzpoeschel thanks. Indeed with the new version I don't get that error anymore.

I saw a warning:

/usr/bin/ld: warning: libzstd.so, needed by /usr/local/sz/lib/libSZ.so, not found (try using -rpath or -rpath-link)

I have sz installed at /usr/local/sz but I don't know how to make it available with rpath. Please help me with this, if it is needed to improve the performance of openPMD-api

Thank you.

cbontoiu · 2023-04-18T19:11:37Z

Hi @franzpoeschel

I thought I fixed this issue with LD_LIBRARY_PATH=/usr/local/sz/lib and ldconfig but my installation was not complete because PIConGPU gave me this error:

The link interface of target "openPMD::openPMD" contains: adios2::cxx11_mpi

so I realized that the openPMDapi is not properly installed. Retrying to install openPMDapi, I am prompted about the missing libzstd.so

What would you suggest?

ax3l · 2023-04-20T18:20:05Z

Hi, there is a small detail here:

-DCMAKE_PREFIX_PATH=/usr/local/adios2/bin
-DCMAKE_PREFIX_PATH=/usr/local/adios2
-DCMAKE_PREFIX_PATH=/usr/local

This way, you overwrite the value of CMAKE_PREFIX_PATH multiple times instead of appending it.

You can either use it as an environment variable, separated by :

export CMAKE_PREFIX_PATH=/usr/local:/other/paths

or as a command line argument separated by ;

cmake -S . -B build -DCMAKE_PREFIX_PATH="/usr/local;/other/paths"

If the install prefix of ADIOS2 is /usr/local than that is enough as a hint. For ADIOS2, we do not need query adios2-config to find it with CMake.

ax3l · 2023-04-20T18:22:14Z

For your SZ issue, did you install this manually for ADIOS2 (optional component)? Can you provide the CMake summary section you got when building ADIOS2 and the CMake options you used to build it?

cbontoiu · 2023-04-20T20:38:38Z

I am installing again ADIOS2 and again SZ is found correctly.

Command:

sudo cmake -DPYTHON_EXECUTABLE=/usr/bin/python -DSZ_ROOT=/usr/local/sz -DADIOS2_USE_SZ=ON -DBZip2_ROOT=/usr/local/bzip2 -DADIOS2_USE_BZip2=ON -DUCX_ROOT=/usr/local/ucx -DADIOS2_USE_UCX=ON -DMPI_ROOT=/usr/local/openmpi -DADIOS2_USE_MPI=ON -DBLOSC2_ROOT=/usr/local/c-blosc2 -DADIOS2_USE_Blosc2=ON -DCMAKE_INSTALL_PREFIX=/usr/local/adios2 -DCMAKE_BUILD_Type=Release -DADIOS2_USE_Python=OFF -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_IME=OFF -DADIOS2_USE_HDF5=OFF ..

Summary:

ADIOS2 build configuration:
  ADIOS Version: 2.9.0.79
  C++ Compiler : GNU 11.1.0 
    /usr/bin/c++
  Installation prefix: /usr/local/adios2
        bin: bin
        lib: lib
    include: include
      cmake: lib/cmake/adios2
     python: lib/python3/dist-packages
  Features:
    Library Type: shared
    Build Type:   Release
    Testing: ON
    Examples: ON
    Build Options:
      BP5       : ON
      DataMan   : OFF
      DataSpaces: OFF
      HDF5      : OFF
      HDF5_VOL  : OFF
      MHS       : ON
      SST       : ON
      Fortran   : OFF
      MPI       : ON
      Python    : OFF
      Blosc2    : ON
      BZip2     : ON
      LIBPRESSIO: OFF
      MGARD     : OFF
      PNG       : ON
      SZ        : ON
      ZFP       : OFF
      DAOS      : OFF
      IME       : OFF
      O_DIRECT  : ON
      Sodium    : OFF
      Catalyst  : OFF
      SysVShMem : ON
      UCX       : ON
      ZeroMQ    : OFF
      Profiling : ON
      Endian_Reverse: OFF
      AWSSDK    : OFF
      GPU_Support: OFF
      CUDA      : OFF
      Kokkos    : OFF
      Kokkos_CUDA: OFF
      Kokkos_HIP: OFF
    RDMA Transport for Staging: Available
-- Configuring done (5.2s)
-- Generating done (0.3s)
-- Build files have been written to: /home/quasar/Downloads/ADIOS2/adios2-build

I remember that, when seeing this error shown in the image, I went to that file and changed MPI_REAL8 into MPI_REAL but this doesn't seem important. I will need to apply this change again to complete the installation.

cbontoiu · 2023-04-20T21:01:50Z

I completed ADIOS2 installation and moved to openpmd-api. Quite a few time the warning:

/usr/bin/ld: warning: libzstd.so, needed by /usr/local/sz/lib/libSZ.so, not found (try using -rpath or -rpath-link)

appears, but SZ is found:

(base) quasar@ubuntu:~$ whereis sz
sz: /usr/local/sz

This is how I built it

(base) quasar@ubuntu:~/Downloads/openPMD-api/build$ sudo cmake -DopenPMD_USE_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/quasar/lib/openPMD-api -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_HDF5=OFF -DCMAKE_C_COMPILER=/usr/local/openmpi/bin/mpicc -DCMAKE_CXX_COMPILER=/usr/local/openmpi/bin/mpicxx -DPython_EXECUTABLE=/usr/bin/python3 -DopenPMD_USE_PYTHON=ON ..
-- The C compiler identification is GNU 11.1.0
-- The CXX compiler identification is GNU 11.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/local/openmpi/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/local/openmpi/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found MPI_CXX: /usr/local/openmpi/bin/mpicxx (found version "3.1") 
-- Found MPI: TRUE (found version "3.1") found components: CXX 
-- Using the single-header code from /home/quasar/Downloads/openPMD-api/share/openPMD/thirdParty/json/single_include/
-- nlohmann-json: Using INTERNAL version '3.9.1'
-- toml11: Using INTERNAL version '3.7.1'
-- Found MPI_C: /usr/local/openmpi/bin/mpicc (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Found ADIOS2: /usr/local/adios2/lib/cmake/adios2/adios2-config.cmake (found suitable version "2.9.0.79", minimum required is "2.7.0") found components: C CXX MPI 
-- Found Python: /usr/bin/python3 (found version "3.8.10") found components: Interpreter Development.Module 
-- pybind11 v2.10.1 
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- pybind11: Using INTERNAL version 2.10.1
-- Catch2: Using INTERNAL version '2.13.10'
-- Python LTO/IPO: ON
-- Note: Skipping example and tool runs (missing openPMD-example-datasets)
-- Note: run
    /home/quasar/Downloads/openPMD-api/share/openPMD/download_samples.sh
to add example files to samples/git-sample/ directory!
-- Could NOT find mpi4py (will NOT run MPI-parallel Python examples)

openPMD build configuration:
  library Version: 0.16.0
  openPMD Standard: 1.1.0
  C++ Compiler: GNU 11.1.0 
    /usr/local/openmpi/bin/mpicxx

  Install with RPATHs: ON
  Installation prefix: /home/quasar/lib/openPMD-api
        bin: bin
        lib: lib
    include: include
      cmake: lib/cmake/openPMD
     python: lib/python3.8/site-packages

  Build Type: Release
  Library: shared
  CLI Tools: ON
  Examples: ON
  Testing: ON
  Invasive Tests: OFF
  Internal VERIFY: ON
  Build Options:
    MPI: ON
    HDF5: OFF
    ADIOS2: ON
    PYTHON: ON
    CUDA_EXAMPLES: OFF

-- Configuring done (0.6s)
-- Generating done (0.0s)
-- Build files have been written to: /home/quasar/Downloads/openPMD-api/build

and the output at installation:

(base) quasar@ubuntu:~/Downloads/openPMD-api/build$ sudo make -j 16 install
[  0%] Building CXX object CMakeFiles/CatchMain.dir/test/CatchMain.cpp.o
[  1%] Building CXX object CMakeFiles/CatchRunner.dir/test/CatchRunner.cpp.o
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Install the project...
-- Install configuration: "Release"
-- Installing: /home/quasar/lib/openPMD-api/lib/libopenPMD.so
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-- Installing: /home/quasar/lib/openPMD-api/include/openPMD/Series.hpp
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cbontoiu · 2023-04-21T19:53:48Z

after installing openPMD-api as shown above, I tried to compile the LWFA example which comes with the master version of PIConGPU but I got many errors related to openPMD-api. They are in the log file attached.

build_log.txt

franzpoeschel · 2023-04-24T08:45:32Z

The latest (rather outdated) release of PIConGPU is on C++14, but you installed a very recent version of openPMD-api that is written in C++17. To fix this, you need to:

either install an older version of openPMD-api (0.14.5)
or build a more recent version of PIConGPU (dev branch)

@psychocoderHPC are there any known issues on the current dev branch?

psychocoderHPC · 2023-04-24T11:16:55Z

@psychocoderHPC are there any known issues on the current dev branch?

Only one physics issue with ionization: ComputationalRadiationPhysics/picongpu#4541 which will be merged soon.

ax3l · 2023-04-25T18:36:51Z

@cbontoiu just FYI, you don't need libSZ, you can fully compile and run without it. It's an optional (lossy) compressor. You can use -DADIOS2_USE_SZ=OFF.
A compressor that I would recommend is C-Blosc with ZStd.

For the ADIOS2 example issue, consider building with -DADIOS2_BUILD_EXAMPLES=OFF.
I will push a fix to ADIOS2 for this example as well: ornladios/ADIOS2#3593
For curiosity, which exact OpenMPI version and system architecture is this?

@franzpoeschel's guidance above is good.

@psychocoderHPC to avoid confusion, maybe it's easy to do a near-term C++17 release for PIConGPU users as well from the current dev?

psychocoderHPC · 2023-04-28T08:20:56Z

@psychocoderHPC to avoid confusion, maybe it's easy to do a near-term C++17 release for PIConGPU users as well from the current dev?

Yes, this is already in the queue.

cbontoiu · 2023-05-04T11:26:51Z

@ax3l it is CUDA aware openmpi 4.1.5 built with UCX and Gdrcopy. The system is Ubuntu 20 desktop.
Thank you so much for your help.
I will close this ticket.

cbontoiu added the install label Apr 16, 2023

cbontoiu closed this as completed Apr 18, 2023

cbontoiu mentioned this issue Apr 18, 2023

Documentation update needed ComputationalRadiationPhysics/picongpu#4536

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cbontoiu reopened this Apr 19, 2023

ax3l added the backend: ADIOS2 label Apr 20, 2023

ax3l mentioned this issue Apr 25, 2023

Heat Transfer Example: MPI Datatype ornladios/ADIOS2#3593

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cbontoiu closed this as completed May 4, 2023

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Cannot find 'adios_config' #1424

Cannot find 'adios_config' #1424

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Cannot find 'adios_config' #1424

Cannot find 'adios_config' #1424

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