psutil, python, and icc

I used to dislike dependency management because there are so many things that require root or are mysteriously incompatible with each other. However, I recently came to realize that the existence of dependency itself is a delicate and elegant system despite being messy at times.

The recent occasion that reminded me the beauty of dependency was to install psutil on an HPC. It ran CentOS 7, and I had Python 3.7.3 with pip 19.0.3 on it. It should have been a straightforward task: Typing pip install psutil --user, and everthing taken care of.

Except that that was not the case. pip complained:

icc -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=561 -DPSUTIL_LINUX=1 -I/share/apps/python3/3.6.3/intel/include/python3.6m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.6/psutil/_psutil_common.o

unable to execute 'icc': No such file or directory

“Obviously pip is using the wrong compiler, but no big deal.” I thought. After all, I did have a C compiler on HPC, GCC 4.8.5, so I re-run pip install with the environment variable CC set: env CC=/usr/bin/gcc pip install psutil --user.

It turned out I was wrong. The same error message persisted, so I dove into StackOverflow for an explanation of this, and found one thread, in which Philip Kearns kindly pointed out that psutil is not always respecting CC.

With this information, I was finally able to fix things (in a the ugly way though). I have $HOME/.local/bin in my $PATH and it is prior to /usr/bin, so I was able to make a symbolic link ( ln -s /usr/bin/gcc $HOME/.local/bin/icc in $HOME/.local/bin to fool psutil by providing gcc when it asked for icc.

This did solve the issue.

I still don’t know why psutil is ignoring CC, or why it tried to find icc instead of cc or something else, but I did learn that dependency and environment variables for compiling should not be taken for granted. Even one line of code ignoring the convention and hard-coded something that was not mentioned as a dependency could be hard to troubleshoot. I was lucky that psutil just needed some common C compiling functionality instead of something specific for icc, or it could be a thousand times harder to find out what went wrong.

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Yen-Chung Chen
PhD Student

Yen is a graduate student interested in developmental biology, neurobiology and bioinformatics.

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