Thanks again. That was very helpful.
It seemed to make it to the petsc install before it gave up. I highlighted in read what appeared to me in red.
Any ideas what went wrong and how I could fix it?
Cheers, Francis
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/local/tmp/pip-GY2H_M-build/setup.py", line 302, in <module>
**metadata)
File "/opt/sharcnet/python/2.7.8/intel/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/opt/sharcnet/python/2.7.8/intel/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/opt/sharcnet/python/2.7.8/intel/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/local/tmp/pip-GY2H_M-build/setup.py", line 218, in run
config(prefix, self.dry_run)
File "/local/tmp/pip-GY2H_M-build/setup.py", line 148, in config
if status != 0: raise RuntimeError(status)
RuntimeError: 256
----------------------------------------
Command "/home/fpoulin/software/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/local/tmp/pip-GY2H_M-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code,
__file__, 'exec'))" install --record /tmp/pip-fXQE7k-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/fpoulin/software/firedrake/include/site/python2.7/petsc" failed with error code 1 in /local/tmp/pip-GY2H_M-build/
Traceback (most recent call last):
File "firedrake-install", line 1234, in <module>
install("petsc/")
File "firedrake-install", line 678, in install
run_pip_install(["--ignore-installed", package])
File "firedrake-install", line 548, in run_pip_install
check_call(pipinstall + pipargs)
File "firedrake-install", line 369, in check_call
subprocess.check_call(arguments, env=env)
File "/opt/sharcnet/python/2.7.8/intel/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/fpoulin/software/firedrake/bin/pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
------------------
Francis Poulin
Associate Professor
Department of Applied Mathematics
University of Waterloo
email: fpoulin@uwaterloo.ca
Web: https://uwaterloo.ca/poulin-research-group/
Telephone: +1 519 888 4567 x32637
From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of David Ham [David.Ham@imperial.ac.uk]
Sent: Friday, March 31, 2017 5:55 AM
To: firedrake
Subject: Re: [firedrake] installing firedrake on a cluster
Hi Francis and thanks Justin for the good advice!
First, you almost certainly want to:
unset PYTHONPATH
instead of telling Firedrake to honour it. This is because it's unlikely that there is something in your PYTHONPATH which you want the virtualenv to see (this is why having PYTHONPATH set triggers this error).
Next, assuming that you managed to install pip using Justin's instructions (or by having the sysadmin do it), you can try running:
pip install --user virtualenv
yourself. If that works, try running the install script again. If it fails, then show us the error message and we might be able to understand what's gone wrong.
Regards,
David
If you simply run the above with system python (e.g., 'python get-pip.py') it will return an error because it is trying to install pip into the root directory which I am assuming you have no access to. What you need to do is install pip
locally. I did this on my local cluster through 'python get-pip.py --user' which will install pip into $HOME/.local. I can't remember what I did next but I think I had to ensure that this .local directory was visible through PATH:
export PATH=$HOME/.local:$HOME/.local/bin:$PATH
and then pip worked.
Justin
--
Dr David Ham
Department of Mathematics
Imperial College London