pip install not working #253
Description
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