Hi Floriane, OK. This is a bit more mysterious can you: 1. Check that mpicc works from the command line. 2. Try to install with the --log option and post the resulting log file so we can see exactly what goes wrong. Thanks, David On Tue, 17 May 2016 at 15:43 Floriane Gidel [RPG] <mmfg@leeds.ac.uk> wrote:
Dear David,
I have checked and yet openmpi-devel is installed, and MPI is also installed but as part of another software (specific to MARIN). I know the path to MPI, so is there a way to specify it during the installation of Firedrake? But shouldn't it work anyway since openmpi-devel is installed as well?
Thanks, Floriane ------------------------------ *De :* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de David Ham <David.Ham@imperial.ac.uk> *Envoyé :* mardi 17 mai 2016 13:48:26
*À :* firedrake *Objet :* Re: [firedrake] installation Linux Hi Floriane,
The error message says that you don't have MPI installed. A quick google suggests that the package you need for scientific Linux might be openmpi-devel.
Regards,
David
On Tue, 17 May 2016 at 13:38 Floriane Gidel [RPG] <mmfg@leeds.ac.uk> wrote:
Dear David,
Indeed, pip was not installed correctly. This is now fixed but another error occurs during the installation of Firedrake:
******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
------------------------------------------------------------------------------- Did not find package MPI needed by hdf5. Enable the package using --with-mpi
*******************************************************************************
Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-nn0xv2-build/setup.py", line 302, in <module> **metadata) File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip-nn0xv2-build/setup.py", line 218, in run config(prefix, self.dry_run) File "/tmp/pip-nn0xv2-build/setup.py", line 148, in config if status != 0: raise RuntimeError(status) RuntimeError: 256
---------------------------------------- Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-nn0xv2-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-_EAAFI-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code 1 in /tmp/pip-nn0xv2-build/
Traceback (most recent call last): File "firedrake-install", line 876, in <module> install("petsc/") File "firedrake-install", line 491, in install run_pip_install(["--ignore-installed", package]) File "firedrake-install", line 354, in run_pip_install check_call(pipinstall + pipargs)
File "firedrake-install", line 205, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/fgidel/firedrake/bin/pip', 'install', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero exit status 1
Do you know what's missing?
Best wishes,
Floriane
------------------------------ *De :* firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de David Ham <David.Ham@imperial.ac.uk> *Envoyé :* mercredi 11 mai 2016 11:05:33 *À :* firedrake
*Objet :* Re: [firedrake] installation Linux Hi Floriane,
That error strongly suggests that pip is not installed. Can you please tell us what the result of:
pip install --user virtualenv
is?
In addition, I notice that you are installing Firedrake as root. We recommend in the strongest possible terms that you do not do this. You should install Firedrake yourself as your normal user.
Regards,
David
On Wed, 11 May 2016 at 10:58 Floriane Gidel [RPG] <mmfg@leeds.ac.uk> wrote:
Dear all,
The IT team is still struggling to install Firedrake on the linux machine. This is the error that they get:
root@lin0320 ~ # firedrake-install --no-package-manager -bash: firedrake-install: command not found root@lin0320 ~ # python firedrake-install --no-package-manager apt-get not found or disabled. Proceeding on the rash assumption that your compiled dependencies are in place. If this is not the case, please install the following and try again: * A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * MPI * Blas and Lapack * Git, Mercurial * Python version 2.7 * pip and the Python headers * CMake * libspatialindex and headers * zlib Installing virtualenv. Traceback (most recent call last): File "firedrake-install", line 813, in <module> check_call(["pip", "install", "--user", "virtualenv"]) File "firedrake-install", line 205, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
Do you have any suggestion? Thanks, Floriane ________________________________________ De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Floriane Gidel [RPG] <mmfg@leeds.ac.uk> Envoyé : mardi 10 mai 2016 09:46:54 À : firedrake@imperial.ac.uk Objet : Re: [firedrake] installation Linux
Ok, thanks!
Floriane
________________________________________ De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Envoyé : mardi 10 mai 2016 09:42:37 À : firedrake@imperial.ac.uk Objet : Re: [firedrake] installation Linux
On 10/05/16 09:34, Floriane Gidel [RPG] wrote:
Hi David,
Thanks for your reply. I am now based at MARIN where I work on a machine with Scientific Linux release 7.2 (Nitrogen). Which packages do I need in that case?
The same as on CentOS (SL is basically the same, just with a different badge). I'm not sure what those are called. They probably have very similar names to the packages on ubuntu.
Lawrence
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