Never mind, fixed my own error. I didn't realize that PyOP2 builder required the env $CC to be set if a non mpicc command were to be used On Fri, Jun 16, 2017 at 1:58 PM, Justin Chang <jychang48@gmail.com> wrote:

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/So ftware/firedrake/src/PyOP2

Running setup.py (path:/global/u1/j/jychang/Sof tware/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/So ftware/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/Softwar e/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/s rc/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