fenics install fails due to cmake python ply issue #25877
Description
I have come across a new error when installing fenics with spack. This seems like a similar issue to #13397.
I am installing spack with the following command:
spack install fenics~hdf5 ^openmpi+pmi schedulers=slurm
I run into cmake issues at the final step. Specifically it cannot locate py-ply and site.py
1 error found in build log:
147 Ignoring EXACT since no version is requested.
148 This warning is for project developers. Use -Wno-dev to suppress it.
149
150 -- Found PythonLibs: /cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/python-3.8.6-u7px4ssttiqjhc6q2arrww4wqceck7nk/lib/libpython3.8.so (found versio
n "3.8.6")
151 ImportError: No module named site
152 -- Could NOT find PY_ply (missing: PY_PLY_path)
>> 153 CMake Error at CMakeLists.txt:438 (message):
154 Required Python module 'ply' (http://www.dabeaz.com/ply/) could not be
155 found. Install ply or set DOLFIN_ENABLE_PYTHON to false.
156
157
158 -- Configuring incomplete, errors occurred!
159 See also "/home/apal/.spack_root/stage/spack-stage-fenics-2016.1.0-mgupwbojaxav4wuo63yfu6gv7oiy5jdn/spack-build-mgupwbo/CMakeFiles/CMakeOutput.log".
See build log for details:
/home/apal/.spack_root/stage/spack-stage-fenics-2016.1.0-mgupwbojaxav4wuo63yfu6gv7oiy5jdn/spack-build-out.txt
I have verified that py-ply is in PYTHONPATH. I have explicitly spack-loaded python3 and py-ply.
[root@L01 tarballs]# spack find --loaded
==> 18 installed packages
-- linux-centos7-zen / [email protected] --------------------------------
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[root@L01 tarballs]#
[root@L01 tarballs]# python -c "import re, ply, site; print(re.compile('/__init__.py.*').sub('',ply.__file__))"
/cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/py-ply-3.11-fpyplf44xgseqlpml5vxvs4r7bxv4c53/lib/python3.8/site-packages/ply
[root@L01 tarballs]# python -c "import re, ply, site; print(re.compile('/__init__.py.*').sub('',site.__file__))"
/cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/python-3.8.6-u7px4ssttiqjhc6q2arrww4wqceck7nk/lib/python3.8/site.py
[root@L01 tarballs]# sed 's/:/\n/g' <<< "$PYTHONPATH"
/cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/py-ply-3.11-fpyplf44xgseqlpml5vxvs4r7bxv4c53/lib64/python3.8/site-packages
/cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/py-ply-3.11-fpyplf44xgseqlpml5vxvs4r7bxv4c53/lib/python3.8/site-packages
/cm/shared/apps/spack-pkgs/linux-centos7-zen/gcc-8.2.0/python-3.8.6-u7px4ssttiqjhc6q2arrww4wqceck7nk/lib/python3.8
Any ideas how to circumvent this issue? Thank you for your attention. Regards.
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