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amusecode / amuse

Astrophysical Multipurpose Software Environment. This is the main repository for AMUSE
http://www.amusecode.org
Apache License 2.0
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Problem with mpiexec #665

Closed mollgal closed 2 years ago

mollgal commented 4 years ago

Hello, I'm having the same issue as #467 but I couldn't understand how it was resolved there. I've just installed AMUSE on Ubuntu 18.04. I've installed it using pip and manually compiled it and it produces the same error when I try to run any of the examples:

If I try the same example as the aforementioned issue I get the same result: test@test-VirtualBox:~/amuse$ ./amuse.sh ./examples/textbook/sun_venus_earth.py [mpiexec@test-VirtualBox] match_arg (utils/args/args.c:159): unrecognized argument pmi_args [mpiexec@test-VirtualBox] HYDU_parse_array (utils/args/args.c:174): argument matching returned error [mpiexec@test-VirtualBox] parse_args (ui/mpich/utils.c:1597): error parsing input array [mpiexec@test-VirtualBox] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1649): unable to parse user arguments [mpiexec@test-VirtualBox] main (ui/mpich/mpiexec.c:149): error parsing parameters

However, if I try running it like this: mpiexec ~/amuse$ ./amuse.sh ./examples/textbook/sun_venus_earth.py Then it doesn't produce any errors. Nevertheless, I still want to be able to run stuff in the python terminal so I would like to resolve the issue if I can.

Can someone please help me?

I'm running mpich version 3.3a2.

The output from the configure script: `checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking whether the Fortran 90 compiler (gfortran -g -O2 ) works... yes checking if the fortran compiler supports iso c binding... checking for a Python interpreter with version >= 3.5... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.6 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.6/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.6/site-packages checking for /usr/bin/python3... (cached) /usr/bin/python3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for python-config... /usr/bin/python-config checking for cython... no checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes checking if possible to embed python... embedded python yes checking for java... /usr/bin/java checking for javac... no checking for jar... no checking whether Java compiler works... no checking whether Java interpreter works... yes checking Java environment... /usr/lib/jvm/java-11-openjdk-amd64 checking Java version... 11 checking for mpiexec... /usr/bin/mpiexec checking for mpicc... mpicc checking checking MPI C flags... flags found checking for MPI_Init... yes checking for mpi.h... yes checking for mpicxx... mpicxx checking checking MPI C++ flags... flags found checking for mpi.h... yes checking for mpicc... (cached) mpicc checking checking MPI C flags... flags found checking for mpi.h... yes checking for mpif90... mpif90 checking checking MPI Fortran flags... flags found checking for mpif.h... yes checking for OpenMP flag of C compiler... -fopenmp checking for OpenMP flag of Fortran compiler... -fopenmp checking if gfortran accepts -dumpversion option... yes checking gfortran version... 7.5.0 checking for a sed that does not truncate output... /bin/sed checking whether we are using the Microsoft C compiler... no checking CL/cl.h usability... no checking CL/cl.h presence... no checking for CL/cl.h... no checking OpenCL/cl.h usability... no checking OpenCL/cl.h presence... no checking for OpenCL/cl.h... no checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for OpenCL library... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for FFTW... yes checking for GMP... no checking gmp.h usability... yes checking gmp.h presence... yes checking for gmp.h... yes checking for __gmpz_init in -lgmp... yes checking for MPFR... no checking mpfr.h usability... yes checking mpfr.h presence... yes checking for mpfr.h... yes checking for mpfr_init in -lmpfr... yes checking for gawk... gawk checking for h5pcc... no checking for h5cc... /usr/bin/h5cc checking for HDF5 type... serial checking for HDF5 libraries... yes (version 1.10.0-patch1) checking hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... yes checking for main in -lhdf5_hl... yes checking for matching HDF5 Fortran wrapper... /usr/bin/h5fc checking for nc-config... no checking for NetCDF4 libraries... no configure: WARNING:

Unable to locate NetCDF4 compilation helper script 'nc-config'. Please specify --with-netcdf4= as the full path prefix where NetCDF4 has been installed. NetCDF4 support is being disabled (equivalent to --with-netcdf4=no).

checking for gcc option to produce PIC... -fPIC checking for GSL... yes checking for python module numpy... found (1.19.1) checking for python module mpi4py... found (3.0.3) checking for python module h5py... found (2.10.0) checking for python module pytest... found (6.0.1) checking for python module docutils... found (0.16) checking for python module zlib... found (1.0) checking for python module matplotlib... found configure: creating ./config.status config.status: creating config.mk config.status: creating build.py config.status: creating bin/amusifier configure: Configuration done. Configuration written to config.mk `

The community codes not installed were: galaxia and distributed. The final output from the make command: `Community codes not built (because of errors):

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed in 28 days if no further activity occurs. Thank you for your contributions.