Install issue in Windows Subsystem Linux

Michel Ferre

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Feb 28, 2022, 11:09:08 AM2/28/22

to Dedalus Users

Hi everyone,

I'm currently trying to install Dedalus using the "conda" installation procedure on an ubuntu machine installed in windows 10 using Windows Subsystem for Linux. The error that I got is the following:

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Installing dedalus with pip
Collecting http://github.com/dedalusproject/dedalus/zipball/d3/
Downloading http://github.com/dedalusproject/dedalus/zipball/d3/
- 23.3 MB 6.1 MB/s 0:00:04
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [292 lines of output]
Collecting cython>=0.22
Using cached Cython-0.29.28-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Collecting mpi4py>=2.0.0
Using cached mpi4py-3.1.3.tar.gz (2.5 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting numpy>=1.20.0
Using cached numpy-1.22.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Collecting setuptools
Using cached setuptools-60.9.3-py3-none-any.whl (1.1 MB)
Collecting wheel
Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (pyproject.toml): started
Building wheel for mpi4py (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

× Building wheel for mpi4py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [262 lines of output]
running bdist_wheel
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/__init__.py -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/__main__.py -> build/lib.linux-x86_64-3.8/mpi4py
creating build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/__init__.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/__main__.py -> build/lib.linux-x86_64-3.8/mpi4py/futures
creating build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/util/__init__.py -> build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/py.typed -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/__init__.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/__main__.pyi -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.8/mpi4py
copying src/mpi4py/__init__.pxd -> build/lib.linux-x86_64-3.8/mpi4py
creating build/lib.linux-x86_64-3.8/mpi4py/include
creating build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.8/mpi4py/include/mpi4py
copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/__init__.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/futures/__main__.pyi -> build/lib.linux-x86_64-3.8/mpi4py/futures
copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-3.8/mpi4py/util
copying src/mpi4py/util/__init__.pyi -> build/lib.linux-x86_64-3.8/mpi4py/util
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpicc
MPI C++ compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpicxx
MPI F compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpifort
MPI F90 compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpif90
MPI F77 compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpif77
checking for library 'lmpe' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -llmpe -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llmpe
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'mpe' dylib library
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/src
creating build/temp.linux-x86_64-3.8/src/lib-pmpi
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libmpe.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
warning: build_clib: command '/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc' failed with exit code 1

warning: build_clib: building optional library "mpe" failed

checking for library 'vt-mpi' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt-mpi -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt.mpi -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
warning: build_clib: command '/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc' failed with exit code 1

warning: build_clib: building optional library "vt" failed

checking for library 'vt-mpi' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt-mpi -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt.mpi -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-mpi.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
warning: build_clib: command '/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc' failed with exit code 1

warning: build_clib: building optional library "vt-mpi" failed

checking for library 'vt-hyb' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt-hyb -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -lvt.ompi -o _configtest
/home/michelfd/miniconda3/envs/dedalus3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -Wl,--no-as-needed build/temp.linux-x86_64-3.8/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.8/mpi4py/lib-pmpi/libvt-hyb.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
warning: build_clib: command '/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc' failed with exit code 1

warning: build_clib: building optional library "vt-hyb" failed

running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpicc
MPI C++ compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpicxx
MPI F compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpifort
MPI F90 compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpif90
MPI F77 compiler: /home/michelfd/miniconda3/envs/dedalus3/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
/home/michelfd/miniconda3/envs/dedalus3/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c src/dynload.c -o build/temp.linux-x86_64-3.8/src/dynload.o
gcc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include build/temp.linux-x86_64-3.8/src/dynload.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o build/lib.linux-x86_64-3.8/mpi4py/dl.cpython-38-x86_64-linux-gnu.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
warning: build_ext: command '/home/michelfd/miniconda3/envs/dedalus3/bin/gcc' failed with exit code 1

warning: build_ext: building optional extension "mpi4py.dl" failed

checking for MPI compile and link ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for missing MPI functions/symbols ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_real' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_complex' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_c2f' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_f2c' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for symbol 'MPI_LB' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function 'main':
_configtest.c:5:23: error: static assertion failed: "MPI_LB was removed in MPI-3.0. Use MPI_Type_create_resized instead."
5 | MPI_Datatype s; s = MPI_LB; (void)s;
| ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for symbol 'MPI_UB' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function 'main':
_configtest.c:5:23: error: static assertion failed: "MPI_UB was removed in MPI-3.0. Use MPI_Type_create_resized instead."
5 | MPI_Datatype s; s = MPI_UB; (void)s;
| ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c _configtest.c -o _configtest.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include _configtest.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include -fPIC -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1 -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/michelfd/miniconda3/envs/dedalus3/include/python3.8 -c src/MPI.c -o build/temp.linux-x86_64-3.8/src/MPI.o
/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc -pthread -shared -B /home/michelfd/miniconda3/envs/dedalus3/compiler_compat -L/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath=/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/michelfd/miniconda3/envs/dedalus3/lib -Wl,-rpath-link,/home/michelfd/miniconda3/envs/dedalus3/lib -L/home/michelfd/miniconda3/envs/dedalus3/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/michelfd/miniconda3/envs/dedalus3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/michelfd/miniconda3/envs/dedalus3/include build/temp.linux-x86_64-3.8/src/MPI.o -Lbuild/temp.linux-x86_64-3.8 -ldl -o build/lib.linux-x86_64-3.8/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/michelfd/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
error: command '/home/michelfd/miniconda3/envs/dedalus3/bin/mpicc' failed with exit code 1
[end of output]

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

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

----------------------------------------------------------------------------------------------------------------------------------------------

I can't find what I'm doing wrong; thanks in advance.

Best, Michel.

Louis-Alexandre Couston

unread,

Mar 4, 2022, 6:40:07 AM3/4/22

to Dedalus Users

Hey,

I have a similar problem. Did you solve the issue?

Felipe Fortaleza

unread,

Mar 4, 2022, 11:39:55 AM3/4/22

to Dedalus Users

I'm also having the same issue

Ben Brown

unread,

Mar 6, 2022, 1:24:13 PM3/6/22

to Dedalus Users

I've seen this as well while trying to build AWS images starting about two weeks ago.

This looks a lot like problems we've run into in the past; I'll take a look at see if we can sort it out.

--Ben

Louis-Alexandre Couston

unread,

Mar 7, 2022, 3:53:06 AM3/7/22

to Dedalus Users

Hello all,

Thanks Ben. I look forward to your advice, which hopefully will help resolve the same problem I reported on https://groups.google.com/g/dedalus-users/c/c6uUPLaBcFk !

IT scientists at ENS de Lyon have looked into the problem and concluded that the conda install may not work with Debian systems (but ok with RedHat, Centos...).

Here is a recap for install on our local supercomputer, which uses Debian.

The real problem in mpi4py/wheel comes from the error log:

...

/home/lcouston/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /lib64/libpthread.so.0
/home/lcouston/miniconda3/envs/dedalus3/compiler_compat/ld: cannot find /usr/lib64/libpthread_nonshared.a

...

wherein the install can't find pthread libraries.

pthread libraries are installed on Debian systems but not in the places where dedalus is looking.

Dedalus looks into (fine for RedHat, Centos)

/lib64/libpthread.so.0
/usr/lib64/libpthread_nonshared.a
whereas they are in (standard for Debian):
/lib/x86_64-linux-gnu/libpthread.so.0
/usr/lib/x86_64-linux-gnu/libpthread_nonshared.a

A possible solution would be to export the LD_LIBRARY_PATH as follows (at least for us)

export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH

But I don't know whether this is a robust solution. Anyway, dedalus d3 is going to be installed manually full-stack for our supercomputer but for users like me sometimes using ubuntu locally it'd be great to have conda working.

Let me know what you think !

Cheers,

Louis

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