pip install not working

Open DaniBodor opened this issue 2 years ago • 0 comments

Describe the bug I was unable to pip install deeprank. I tried the stable version with python 3.7 and the development version with python 3.8 (so not all 4 permutations, but doubt that that is the issue) in fresh environments.

To Reproduce Steps/commands to reproduce the behaviour:

pip install deeprank (or: pip install -e ./ from within the folder) in a fresh environment

Expected Results package gets installed into environment

Actual Results or Error Info brief error message:

Failed to build mpi4py ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

Additional Context

Complete error:

Building wheel for mpi4py (pyproject.toml) ... error error: subprocess-exited-with-error

× Building wheel for mpi4py (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [148 lines of output] running bdist_wheel running build running build_src running build_py creating build creating build/lib.linux-x86_64-cpython-37 creating build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/main.py -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/run.py -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/bench.py -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/init.py -> build/lib.linux-x86_64-cpython-37/mpi4py creating build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-cpython-37/mpi4py/futures creating build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/util/init.py -> build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/py.typed -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/main.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/init.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-cpython-37/mpi4py copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-cpython-37/mpi4py creating build/lib.linux-x86_64-cpython-37/mpi4py/include creating build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-cpython-37/mpi4py/include/mpi4py copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/main.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/init.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/futures copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/util copying src/mpi4py/util/init.pyi -> build/lib.linux-x86_64-cpython-37/mpi4py/util running build_clib MPI configuration: [mpi] from 'mpi.cfg' checking for library 'lmpe' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -llmpe -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -llmpe: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'mpe' dylib library creating build/temp.linux-x86_64-cpython-37 creating build/temp.linux-x86_64-cpython-37/src creating build/temp.linux-x86_64-cpython-37/src/lib-pmpi gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-cpython-37/src/lib-pmpi/mpe.o creating build/lib.linux-x86_64-cpython-37/mpi4py/lib-pmpi gcc -pthread -shared -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -L/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,-rpath=/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-cpython-37/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-cpython-37/mpi4py/lib-pmpi/libmpe.so checking for library 'vt-mpi' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt-mpi: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt.mpi: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt' dylib library gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt.o gcc -pthread -shared -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -L/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,-rpath=/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-cpython-37/mpi4py/lib-pmpi/libvt.so checking for library 'vt-mpi' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-mpi -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt-mpi: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.mpi' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.mpi -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt.mpi: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-mpi' dylib library gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt-mpi.o gcc -pthread -shared -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -L/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,-rpath=/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-cpython-37/mpi4py/lib-pmpi/libvt-mpi.so checking for library 'vt-hyb' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt-hyb -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt-hyb: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o checking for library 'vt.ompi' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -lvt.ompi -o _configtest /home/dbodor/miniconda3/envs/DRCNN/compiler_compat/ld: cannot find -lvt.ompi: No such file or directory collect2: error: ld returned 1 exit status failure. removing: _configtest.c _configtest.o building 'vt-hyb' dylib library gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt-hyb.o gcc -pthread -shared -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -L/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,-rpath=/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,--no-as-needed build/temp.linux-x86_64-cpython-37/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-cpython-37/mpi4py/lib-pmpi/libvt-hyb.so running build_ext MPI configuration: [mpi] from 'mpi.cfg' checking for dlopen() availability ... checking for header 'dlfcn.h' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/dbodor/miniconda3/envs/DRCNN/include/python3.7m -c _configtest.c -o _configtest.o success! removing: _configtest.c _configtest.o success! checking for library 'dl' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/dbodor/miniconda3/envs/DRCNN/include/python3.7m -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-cpython-37 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest checking for function 'dlopen' ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/dbodor/miniconda3/envs/DRCNN/include/python3.7m -c _configtest.c -o _configtest.o gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ _configtest.o -Lbuild/temp.linux-x86_64-cpython-37 -ldl -o _configtest success! removing: _configtest.c _configtest.o _configtest building 'mpi4py.dl' extension gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/dbodor/miniconda3/envs/DRCNN/include/python3.7m -c src/dynload.c -o build/temp.linux-x86_64-cpython-37/src/dynload.o gcc -pthread -shared -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -L/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,-rpath=/home/dbodor/miniconda3/envs/DRCNN/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-cpython-37/src/dynload.o -Lbuild/temp.linux-x86_64-cpython-37 -ldl -o build/lib.linux-x86_64-cpython-37/mpi4py/dl.cpython-37m-x86_64-linux-gnu.so checking for MPI compile and link ... gcc -pthread -B /home/dbodor/miniconda3/envs/DRCNN/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/dbodor/miniconda3/envs/DRCNN/include/python3.7m -c _configtest.c -o _configtest.o _configtest.c:2:10: fatal error: mpi.h: No such file or directory 2 | #include <mpi.h> | ^~~~~~~ compilation terminated. failure. removing: _configtest.c _configtest.o error: Cannot compile MPI programs. Check your configuration!!! [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for mpi4py Successfully built freesasa Failed to build mpi4py ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

Jan 24 '23 16:01 DaniBodor