CODEWITHSUNDEEP
pythonpython-2.7installationscipyslurm
daniel451
daniel451

Reputation: 10992

SciPy fails to install via pip

I try to install SciPy with pip on a SLURM environment. NumPy and some other python modules are already installed and working fine.

However, when I run:

pip2.7 install --user --use-wheel scipy

or

pip2.7 install --user scipy

I always get a huge wall of text ending with:

error: Command "/sw/compiler/gcc-4.9.3/bin/gfortran -Wall -g -shared -Wall -g -shared -shared build/temp.linux-x86_64-2.7/scipy/integrate/_odepackmodule.o -L/sw/env/gcc-4.9.3_openmpi-1.8.8/pkgsrc/2015Q4/lib -L/sw/env/gcc-4.9.3_openmpi-1.8.8/pkgsrc/2015Q4/lib -Lbuild/temp.linux-x86_64-2.7 -lodepack -lmach -llapack -lblas -lpython2.7 -lgfortran -o build/lib.linux-x86_64-2.7/scipy/integrate/_odepack.so" failed with exit status 1

Command "/sw/env/gcc-4.9.3_openmpi-1.8.8/pkgsrc/2015Q4/bin/python2.7 -c "import setuptools, tokenize;file='/work/tmp/node001.admin.2016-02-09-015538.intx033.31602/pip-build-fORQns/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /work/tmp/node001.admin.2016-02-09-015538.intx033.31602/pip-7oTcK5-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /work/tmp/node001.admin.2016-02-09-015538.intx033.31602/pip-build-fORQns/scipy

Unfortunately I don't know what this is supposed to tell me...any ideas?

Upvotes: 0

Views: 587

Answers (2)

bmbigbang
bmbigbang

Reputation: 1378

instead of using gfortran packages, I recommend installing scipy via a scientific package: Python XY Anaconda (supports virtual env)

Upvotes: 0

ev-br
ev-br

Reputation: 26030

You need to have C, C++ and fortran compilers and BLAS/LAPACK libraries to compile scipy. The easiest option is probably gcc+gfortran+prebuilt atlas, which should just work. For performance, esp with linear algebra, you might want to look into using intel MKL or OpenBLAS.

Upvotes: 1

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