error: command mpicc failed with exit status -1

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I am compiling h5py v 2.5.0 on my linux cluster, with hdf5 v 1.8.14, mpi4py
v1.3.1, Cythonv0.22 and python3.3.2. I have compiled h5py many times with
other version of python (example 3.3.6 and 2.7.8). I get an error at build
time. The command I am using and the error are shown below:

export CC=mpicc
python3 setup.py configure --hdf5=/clusterdata/afylot/local/ --mpi
python3 setup.py build

mpicc -shared
build/temp.linux-x86_64-3.3/clusterdata/afylot/download/h5py-2.5.0/h5py/defs.o
-L/clusterdata/afylot/local/lib -L/opt/local/lib -L/usr/local/lib
-R/clusterdata/afylot/local/lib -R/opt/local/lib -R/usr/local/lib -lhdf5
-lhdf5_hl -o build/lib.linux-x86_64-3.3/h5py/defs.cpython-33m.so

gcc: error: unrecognized command line option ‘-R’
gcc: error: unrecognized command line option ‘-R’
gcc: error: unrecognized command line option ‘-R’
error: command 'mpicc' failed with exit status 1

2

Hi,

Your question should be directed to the h5py mailing list
https://groups.google.com/forum/#!forum/h5py

my only suggestion would be to drop "export CC=mpicc" and try again.

···

On Thu, Apr 30, 2015 at 04:00:28PM +0200, simona bellavista wrote:

I am compiling h5py v 2.5.0 on my linux cluster, with hdf5 v 1.8.14, mpi4py
v1.3.1, Cythonv0.22 and python3.3.2. I have compiled h5py many times with
other version of python (example 3.3.6 and 2.7.8). I get an error at build
time. The command I am using and the error are shown below:

export CC=mpicc
python3 setup.py configure --hdf5=/clusterdata/afylot/local/ --mpi
python3 setup.py build

mpicc -shared
build/temp.linux-x86_64-3.3/clusterdata/afylot/download/h5py-2.5.0/h5py/defs.o
-L/clusterdata/afylot/local/lib -L/opt/local/lib -L/usr/local/lib
-R/clusterdata/afylot/local/lib -R/opt/local/lib -R/usr/local/lib -lhdf5
-lhdf5_hl -o build/lib.linux-x86_64-3.3/h5py/defs.cpython-33m.so

gcc: error: unrecognized command line option ‘-R’
gcc: error: unrecognized command line option ‘-R’
gcc: error: unrecognized command line option ‘-R’
error: command 'mpicc' failed with exit status 1