openPMD / openPMD/openPMD-api

Cannot install

Open
#1,367 5 comments 0 reactions 0 assignees View on GitHub
install question
Dominant language
C++
Stars
161
Forks
59
Avg merge
2d 22h
Merged PRs (30d)
7

Description

Hi,

I am trying to install the latest openPMD-api. I got it with

```git clone -b 0.14.4 https://github.com/openPMD/openPMD-api.git```

and then configured trying to use my ```openmpi``` installation (version 4.1):

```cmake -DopenPMD_USE_MPI=ON -DopenPMD_USE_ADIOS2=ON -DCMAKE_C_COMPILER=/usr/local/openmpi/bin/mpicc -DCMAKE_CXX_COMPILER=/usr/local/openmpi/bin/mpicxx -DCMAKE_INSTALL_PREFIX:PATH=~/lib/openPMD-api```

This went smooth with the following result:

```
- The C compiler identification is GNU 11.3.0
-- The CXX compiler identification is GNU 11.3.0
-- 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/src/openPMD-api/share/openPMD/thirdParty/json/single_include/
-- nlohmann-json: Using INTERNAL version '3.9.1'
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
-- 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")
-- 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 "2.8.3", minimum required is "2.7.0") found components: C CXX MPI
-- Could NOT find Python (missing: Python_INCLUDE_DIRS Development.Module) (found suitable version "3.10.6", minimum required is "3.6.0")
-- supported (C++17 or newer): TRUE
-- Catch2: Using INTERNAL version '2.13.4'
-- Note: Skipping example and tool runs (missing openPMD-example-datasets)
-- Note: run
/home/quasar/src/openPMD-api/share/openPMD/download_samples.sh
to add example files to samples/git-sample/ directory!
openPMD build configuration:
library Version: 0.14.4
openPMD Standard: 1.1.0
C++ Compiler: GNU 11.3.0
/usr/local/openmpi/bin/mpicxx
Installation prefix: /home/quasar/lib/openPMD-api
bin: bin
lib: lib
include: include
cmake: lib/cmake/openPMD
Additionally, install following third party libraries:
MPark.Variant: OFF
Build Type: Release
Library: shared
CLI Tools: ON
Examples: ON
Testing: ON
Invasive Tests: OFF
Internal VERIFY: ON
Build Options:
MPI: ON
HDF5: OFF
ADIOS1: OFF
ADIOS2: ON
PYTHON: OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /home/quasar/src/openPMD-api/build
```
But then installation failed:

```sudo make -j16 install```

```
/home/quasar/src/openPMD-api/share/openPMD/thirdParty/catch2/include/catch2/catch.hpp:10822:58: error: call to non-‘constexpr’ function ‘long int sysconf(int)’
10822 | static constexpr std::size_t sigStackSize = 32768 >= MINSIGSTKSZ ? 32768 : MINSIGSTKSZ;
..
/home/quasar/src/openPMD-api/share/openPMD/thirdParty/catch2/include/catch2/catch.hpp:10881:45: error: size of array ‘altStackMem’ is not an integral constant-expression
10881 | char FatalConditionHandler::altStackMem[sigStackSize] = {};
...
make: *** [Makefile:146: all] Error 2
```

Please help me to proceed with the installation.

Thank you.
Cristian

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.