Re: [firedrake] installation Linux

26 May 2016

      Hi David,

Thanks for you help, Firedrake is now running!

Best,

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 25 mai 2016 10:25:09
À : firedrake
Objet : Re: [firedrake] installation Linux

Hi Floriane,

That error is a PETSc configure error so you have to provide any options that it wants by setting the PETSC_CONFIGURE_OPTIONS environment variable to contain those options.

Regards,

David

On Wed, 25 May 2016 at 10:14 Floriane Gidel [RPG] <mmfg@leeds.ac.uk<mailto:mmfg@leeds.ac.uk>> wrote:

Dear David,

I could fixed the issue by loading the MPI module in my terminal. However I now get an issue with BLAS (see error below). I tried to use the argument --with-blas-lib=<lib> but it is not recognized ( error: "

firedrake-install: error: unrecognized arguments: --with-blas-lib=/home/fgidel/BLAS-3.6.0/blas_LINUX.a " ).

How can I indicate the library containing BLAS then?

Thanks,
Floriane

 *******************************************************************************
             UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
    -------------------------------------------------------------------------------
    Could not find a functional BLAS. Run with --with-blas-lib=<lib> to indicate the library containing BLAS.
     Or --download-fblaslapack=1 to have one automatically downloaded and installed

    *******************************************************************************

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-3EIjIm-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-3EIjIm-build/setup.py", line 218, in run
        config(prefix, self.dry_run)
      File "/tmp/pip-3EIjIm-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-3EIjIm-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-Zetm3L-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-3EIjIm-build/

Traceback (most recent call last):
  File "firedrake-install", line 884, 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
De : firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> de la part de David Ham <David.Ham@imperial.ac.uk<mailto:David.Ham@imperial.ac.uk>>
Envoyé : mercredi 18 mai 2016 12:59:51

À : firedrake
Objet : Re: [firedrake] installation Linux
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<mailto: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<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> de la part de David Ham <David.Ham@imperial.ac.uk<mailto: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<mailto: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<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> de la part de David Ham <David.Ham@imperial.ac.uk<mailto: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<mailto: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<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> de la part de Floriane Gidel [RPG] <mmfg@leeds.ac.uk<mailto:mmfg@leeds.ac.uk>>
Envoyé : mardi 10 mai 2016 09:46:54
À : firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk>
Objet : Re: [firedrake] installation Linux

Ok, thanks!

Floriane

________________________________________
De : firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> de la part de Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk<mailto:lawrence.mitchell@imperial.ac.uk>>
Envoyé : mardi 10 mai 2016 09:42:37
À : firedrake@imperial.ac.uk<mailto: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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