Sorry there was a typo. I mean "mpicc" command, not "epic" command :) On Fri, Jun 16, 2017 at 1:57 PM, Justin Chang <jychang48@gmail.com> wrote:
Hi all,
I am building firedrake using the system provided "mpicc" command. On the NERSC systems, the mpicc command is "cc", so I:
1) built my own firedrake fork of PETSc using the appropriate options 2) passed in "--mpicc cc" to the firedrake-install command.
Everything works until I get to the PyOP2 stage. Upon inspection of firedrake-install.log, it seems the pip install for pyop2 still defaults to the "epic" command (which does not exist on the NERSC system) and not "cc" which I told the firedrake script to use.
2017-06-16 12:31:27,681 INFO Installing PyOP2/
2017-06-16 12:31:27,681 DEBUG /global/u1/j/jychang/Software/firedrake/bin/pip install --no-binary mpi4py --no-deps -vvv -e PyOP2/
2017-06-16 12:31:31,251 DEBUG Obtaining file:///global/u1/j/jychang/ Software/firedrake/src/PyOP2
Running setup.py (path:/global/u1/j/jychang/ Software/firedrake/src/PyOP2/setup.py) egg_info for package from file:///global/u1/j/jychang/Software/firedrake/src/PyOP2
Running command python setup.py egg_info
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running egg_info
creating PyOP2.egg-info
writing requirements to PyOP2.egg-info/requires.txt
writing PyOP2.egg-info/PKG-INFO
writing top-level names to PyOP2.egg-info/top_level.txt
writing dependency_links to PyOP2.egg-info/dependency_links.txt
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pyop2'
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
Source in ./PyOP2 has version 0.13.0+299.g200780c, which satisfies requirement PyOP2==0.13.0+299.g200780c from file:///global/u1/j/jychang/ Software/firedrake/src/PyOP2
Installing collected packages: PyOP2
Running setup.py develop for PyOP2
Running command /global/u1/j/jychang/Software/firedrake/bin/python -c "import setuptools, tokenize;__file__='/global/u1/ j/jychang/Software/firedrake/src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running develop
running egg_info
writing requirements to PyOP2.egg-info/requires.txt
writing PyOP2.egg-info/PKG-INFO
writing top-level names to PyOP2.egg-info/top_level.txt
writing dependency_links to PyOP2.egg-info/dependency_links.txt
reading manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pyop2'
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
running build_ext
cythoning pyop2/sparsity.pyx to pyop2/sparsity.cpp
building 'pyop2.sparsity' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/pyop2
mpicc -fno-strict-aliasing -fmessage-length=0 -grecord-gcc-switches -fstack-protector -O2 -Wall -D_FORTIFY_SOURCE=2 -funwind-tables -fasynchronous-unwind-tables -g -DNDEBUG -fmessage-length=0 -grecord-gcc-switches -fstack-protector -O2 -Wall -D_FORTIFY_SOURCE=2 -funwind-tables -fasynchronous-unwind-tables -g -DOPENSSL_LOAD_CONF -fPIC -Ipyop2 -I/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/numpy/core/include -I/global/u1/j/jychang/ Software/firedrake/lib/python2.7/site-packages/petsc4py/include -I/global/homes/j/jychang/Software/petsc-fd/include -I/global/homes/j/jychang/Software/petsc-fd/arch-cori-c-opt/include -I/usr/include/python2.7 -c pyop2/sparsity.cpp -o build/temp.linux-x86_64-2.7/pyop2/sparsity.o
unable to execute 'mpicc': No such file or directory
error: command 'mpicc' failed with exit status 1
Cleaning up...
Command "/global/u1/j/jychang/Software/firedrake/bin/python -c "import setuptools, tokenize;__file__='/global/u1/j/jychang/Software/firedrake/ src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /global/u1/j/jychang/Software/ firedrake/src/PyOP2/
Exception information:
Traceback (most recent call last):
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/req/req_set.py", line 784, in install
**kwargs
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/req/req_install.py", line 845, in install
install_options, global_options, prefix=prefix)
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/req/req_install.py", line 1007, in install_editable
show_stdout=False)
File "/global/u1/j/jychang/Software/firedrake/lib/ python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "/global/u1/j/jychang/Software/firedrake/bin/python -c "import setuptools, tokenize;__file__='/global/u1/ j/jychang/Software/firedrake/src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /global/u1/j/jychang/Software/ firedrake/src/PyOP2/
2017-06-16 12:31:31,253 INFO
Install log saved in firedrake-install.log
I feel like there's a way to circumvent (or fix) this issue. What is the best way to do this?
Thanks, Justin