call for testing: install script

[j s oishi]

Hi All,

After a ridiculously long delay, the install script for dedalus is finally ready for testing. This install script is based heavily on the yt install script. It is designed to make the full stack required for running Dedalus in parallel on a variety of machines. It is *not* designed to provide the absolute fastest performance possible. My goal with this is to help new users get started, especially on small machines like laptops and desktops. For supercomputing centers and larger high-performance clusters, we should probably continue to update the directions on the website.

It works by first detecting the running operating system, then prompting the user to install several prerequisite packages, either by the system's package manager (if on linux), or manually (if on OSX). Once the user has done this, hitting enter will cause the script to download, from dedalus-project.org, the required software stack, including openmpi (if necessary), python, numpy, scipy, FFTW, HDF5 (if necessary), and freetype (if necessary). After installing all of these packages, the scrip then pip installs nose, mpi4py, h5py, cython, matplotlib, sympy, and optionally ipython. The script does not rely on homebrew for OS X. If you're on OS X, this will also include an OpenMPI install. If you're on linux, we assume you've installed OpenMPI via your package manager.

After the install script successfully completes, the user then enters

$ source path/to/dedalus_x86-64/bin/activate

and, just as in virtualenv, you are in an environment that includes a python3 with dedalus ready to go.

I've tested it on two Ubuntu 14.04 systems (including that the required packages are complete if you have a totally fresh installation), and one OS X 10.8.5 system. However, I have not completed the script for any linux distribution other than Ubuntu (Red Hat, Debian, OpenSUSE, etc), though stubs are in there. I should note that all this means is that the script will not correctly tell you what packages to install. If you have them installed, it should *work* just fine.

To test it, please download

https://bitbucket.org/jsoishi/dedalus2-jsoishi/raw/e711c6f393b37bd0028010c55d212fd4492961b3/docs/install.sh

to somewhere you'd like to install Dedalus, and do

$ bash install.sh

The install it makes will be completely self-contained, so you can just delete the directory it makes, and everything will be back the way you were before.

I've isseued a PR, but please consider it work in progress until we get some more testing done. Please let me know of any problems via comments on the PR.

thanks,

j

[Daniel Lecoanet]

Just tried running this on my laptop (OS X 10.7.5).  Got an error on mpi4py:

pip installing mpi4py.

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

        FAILURE REPORT:

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

removing: _configtest.c _configtest.o

failure.

error: Cannot find 'mpi.h' header. Check your configuration!!!

Daniel

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[j s oishi]

Hi Dan,

Please send me the complete dedalus-x86_64/dedalus_install.log file.

thanks,

j

[Daniel Lecoanet]

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-dev/CAAOZTN_M-xtt%2BvMcqvSP2w_FLD1Lw8qW8RqT_9VQdjCZ4ccQRg%40mail.gmail.com.

[j s oishi]

Hi Dan,

What is the output of

$ gcc --version

? I think you might have an old gcc...

j

[j s oishi]

Hi Dan,

OK, I see that you're using llvm-gcc-4.2, which is indeed old enough to cause the problem you're seeing. I'm not sure what the fix is yet, but I will investigate and get back to you ASAP.

j

[Daniel Lecoanet]

Don't know if this is more/useful information:

gcc -v

Using built-in specs.

Target: i686-apple-darwin11

Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~182/src/configure --disable-checking --enable-werror --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.11~182/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1

Thread model: posix

gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

Daniel

[j s oishi]

Hi Dan,

I have an idea. Try this: after line 175, add

CC=clang
CXX=clang++

Then do

$ rm path/to/dedalus-x86_64/src/openmpi-1.6.5/done

and run the install script again. See if that works.

j

[Daniel Lecoanet]

Same error as before.  Just to be sure that I made the correct edit, my install script now includes this:

    OSX_VERSION=`sw_vers -productVersion`

    if [ "${OSX_VERSION##10.8}" != "${OSX_VERSION}" ]

        then

            MPL_SUPP_CFLAGS="${MPL_SUPP_CFLAGS} -mmacosx-version-min=10.7"

            MPL_SUPP_CXXFLAGS="${MPL_SUPP_CXXFLAGS} -mmacosx-version-min=10.7"

        fi

    INST_OPENMPI=1

    INST_ATLAS=0

    INST_HDF5=1

    INST_FTYPE=1

    IS_OSX=1

    CC=clang

    CXX=clang++

    fi

Daniel