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Installation issues #146

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stevenmcsteven opened this issue Apr 30, 2021 · 16 comments
Open

Installation issues #146

stevenmcsteven opened this issue Apr 30, 2021 · 16 comments

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@stevenmcsteven
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Hello there,

I'm trying to install UncoverML using Ubuntu 18.04 through AWS.
I have been following the installation instructions, but run into problems with:

pip install -r requirements-pykrige.txt

I don't think this file exists anymore, so I have been trying:

pip install -r requirements.txt

This command points to the correct place (i think) but runs into issues with certain packages:

pykrige 1.3.0, revrand, pyshp, ppretty and mpi4py

Are these packages all still available? Newer versions of pykrige for example install just fine but don't seem to be compatible with uncover ml.

I'm still learning a lot so it's quite possible I've missed something, but any advice you have would be greatly appreciated.

Thank you,
Ben
@RichardScottOZ
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pykrigeCapture
that one seems to be, anyway

@stevenmcsteven
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I'm a Masters student trying to use Uncover ML for a project, and any assistance with getting it up and running would be greatly appreciated.

@RichardScottOZ
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Sure... did you get any further? My version is on windows, so has its own idiosyncracies - but you will likely have to specify versions of packages in the installation process to get it to work.

@stevenmcsteven
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I have all the packages from the requirements file installed with the specified versions now except mpi4py.
I keep getting an error or everything freezes when 'Building wheel for mpi4py (setup.py)'

@RichardScottOZ
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Ok - freezes, or errors specifically? What are you installing it with - as per instructions?

@stevenmcsteven
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It freezes every time now during this step. When I was trying to install it originally I would get 'errored out with exit status 1'
but now seems to freeze.

I've been following the instructions for Ubuntu 18.04 on this page:
https://geoscienceaustralia.github.io/uncover-ml/installation.html#ubuntu-18-04

@RichardScottOZ
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Any hints in your errors to if you might be missing development libraries? Which can be a problem on unix.

@stevenmcsteven
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Just tried again,

I'm getting this error message:

ERROR: Command errored out with exit status 1:
command: /home/ubuntu/maybe/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q8fox8ou/mpi4py_3d88f68627404f75bcb042e8d15da37b/setup.py'"'"'; file='"'"'/tmp/pip-install-q8fox8ou/mpi4py_3d88f68627404f75bcb042e8d15da37b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-7ct690kw/install-record.txt --single-version-externally-managed --compile --install-headers /home/ubuntu/maybe/include/site/python3.6/mpi4py
cwd: /tmp/pip-install-q8fox8ou/mpi4py_3d88f68627404f75bcb042e8d15da37b/
Complete output (197 lines):
running install
running build
running build_src
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/run.py -> build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/init.py -> build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/bench.py -> build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/main.py -> build/lib.linux-x86_64-3.6/mpi4py
creating build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/init.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/main.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-3.6/mpi4py/futures
copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/init.pxd -> build/lib.linux-x86_64-3.6/mpi4py
copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.6/mpi4py
creating build/lib.linux-x86_64-3.6/mpi4py/include
creating build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.6/mpi4py/include/mpi4py
running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/bin/mpicc
MPI C++ compiler: /usr/bin/mpicxx
MPI F compiler: /usr/bin/mpifort
MPI F90 compiler: /usr/bin/mpif90
MPI F77 compiler: /usr/bin/mpif77
checking for library 'lmpe' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -llmpe -o _configtest
/usr/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_64-3.6
creating build/temp.linux-x86_64-3.6/src
creating build/temp.linux-x86_64-3.6/src/lib-pmpi
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c src/lib-pmpi/mpe.c -o build/temp.linux-x86_64-3.6/src/lib-pmpi/mpe.o
creating build/lib.linux-x86_64-3.6/mpi4py/lib-pmpi
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--no-as-needed build/temp.linux-x86_64-3.6/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-3.6/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-mpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.mpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c src/lib-pmpi/vt.c -o build/temp.linux-x86_64-3.6/src/lib-pmpi/vt.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--no-as-needed build/temp.linux-x86_64-3.6/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-3.6/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-mpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.mpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c src/lib-pmpi/vt-mpi.c -o build/temp.linux-x86_64-3.6/src/lib-pmpi/vt-mpi.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--no-as-needed build/temp.linux-x86_64-3.6/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-3.6/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt-hyb -o _configtest
/usr/bin/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -lvt.ompi -o _configtest
/usr/bin/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c src/lib-pmpi/vt-hyb.c -o build/temp.linux-x86_64-3.6/src/lib-pmpi/vt-hyb.o
/usr/bin/mpicc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--no-as-needed build/temp.linux-x86_64-3.6/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-3.6/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler: /usr/bin/mpicc
MPI C++ compiler: /usr/bin/mpicxx
MPI F compiler: /usr/bin/mpifort
MPI F90 compiler: /usr/bin/mpif90
MPI F77 compiler: /usr/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
x86_64-linux-gnu-gcc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
x86_64-linux-gnu-gcc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c src/dynload.c -o build/temp.linux-x86_64-3.6/src/dynload.o
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.6/src/dynload.o -Lbuild/temp.linux-x86_64-3.6 -ldl -o build/lib.linux-x86_64-3.6/mpi4py/dl.cpython-36m-x86_64-linux-gnu.so
checking for MPI compile and link ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for missing MPI functions/symbols ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_real' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_complex' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_c2f' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Status_f2c' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for symbol 'MPI_LB' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for symbol 'MPI_UB' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -Lbuild/temp.linux-x86_64-3.6 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/home/ubuntu/maybe/include -I/usr/include/python3.6m -c src/MPI.c -o build/temp.linux-x86_64-3.6/src/MPI.o
gcc: internal compiler error: Killed (program cc1)
Please submit a full bug report,
with preprocessed source if appropriate.
See file:///usr/share/doc/gcc-7/README.Bugs for instructions.
error: command '/usr/bin/mpicc' failed with exit status 4
----------------------------------------
ERROR: Command errored out with exit status 1: /home/ubuntu/maybe/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q8fox8ou/mpi4py_3d88f68627404f75bcb042e8d15da37b/setup.py'"'"'; file='"'"'/tmp/pip-install-q8fox8ou/mpi4py_3d88f68627404f75bcb042e8d15da37b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-7ct690kw/install-record.txt --single-version-externally-managed --compile --install-headers /home/ubuntu/maybe/include/site/python3.6/mpi4py Check the logs for full command output.

@RichardScottOZ
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So missing this one?

/usr/bin/mpicc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -pthread _configtest.o -llmpe -o _configtest
/usr/bin/ld: cannot find -llmpe
collect2: error: ld returned 1 exit status
failure.

@stevenmcsteven
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I think it finally worked!

For those with the same issues, I resolved it with:

sudo apt install mpich

pip install mpi4py==3.0.2

@RichardScottOZ
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Very good - that makes sense that something mpi missing, would have been my next thing to look for.

@RichardScottOZ
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Could maybe add that to the installation notes @zhang01GA ?

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RichardScottOZ commented Jul 10, 2022 •
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I had cause to install on ubuntu, had issues with the install from the repo with numpy api

Second time I made a conda environment, installed the prereqs, then pip installed the uncover-ml package

Had to rollb back jinja2 to an older version doing it this was - 2.11.2 or something taken from what I had in an earlier environment.

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RichardScottOZ commented Oct 10, 2023 •
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rasterio 1.1.5 works too in another environment jinja is at pallets/jinja@737a4cd

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which leads to markupsafe 1.1.1 by the looks to get working

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and in the install in windows 11 I used conda for rasterio which gets you libgdal then geopandas which gets you gdal correctly

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