Installaltion problem

[sune....@gmail.com]

Hi,

I am trying to install Dedalus on an Ubuntu OS (and I am completely new to that). I followed the installation notes on http://dedalus-project.readthedocs.io/en/latest/machines/mac_os/mac_os.html.

Unfortunately, the last step always fails. When I type in the command " python3 setup.py build_ext --inplace ", I get the following error:

Looking for fftw prefix
Found env var FFTW_PATH = /home/master/dedalus/src/fftw-3.3.4
Looking for mpi prefix
Found matching library in /usr/lib/openmpi/lib
Looking for fftw prefix
Found env var FFTW_PATH = /home/master/dedalus/src/fftw-3.3.4
dedalus/core/transposes.pyx: cannot find cimported module '..libraries.fftw'
running build_ext
building 'dedalus.libraries.fftw.fftw_wrappers' extension
gcc -pthread -B /home/master/.local/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Idedalus/libraries/fftw/ -I/home/master/.local/anaconda3/lib/python3.6/site-packages/numpy/core/include -I/home/master/.local/anaconda3/lib/python3.6/site-packages/mpi4py/include -I/home/master/dedalus/src/fftw-3.3.4/include -I/usr/lib/openmpi/include -I/home/master/.local/anaconda3/include/python3.6m -c dedalus/libraries/fftw/fftw_wrappers.c -o build/temp.linux-x86_64-3.6/dedalus/libraries/fftw/fftw_wrappers.o -Wno-error=declaration-after-statement
In file included from /home/master/.local/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
from /home/master/.local/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/master/.local/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from dedalus/libraries/fftw/fftw_wrappers.c:559:
/home/master/.local/anaconda3/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
dedalus/libraries/fftw/fftw_wrappers.c:565:23: fatal error: fftw3-mpi.h: Datei oder Verzeichnis nicht gefunden
compilation terminated.
error: command 'gcc' failed with exit status 1

I definitely did all the steps installing mpi. The only thing that did not work out fine was the step "brew tap homebrew/science" - it always says

Error: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.

I am not quite sure, but I don't think it has anything to do with it(?)

Does anyone know how to fix the first thing?

Thanks a lot in advance,

Sune

[sune....@gmail.com]

Oh, by the way, "Datei oder Verzeichnis nicht gefunden" means "file or directory not found"

[Jeffrey S. Oishi]

Hi Sune,

Are you installing on a mac or on ubuntu? You're following the instructions for a mac, but you said it's on Ubuntu. If you're using Ubuntu, you should run the install script, which you can download here:

https://bitbucket.org/dedalus-project/dedalus/raw/4b5eb7c3e23f3344f12c3bcc1f0c1dd6c289bd8a/docs/install.sh

It will tell you which packages you need to install using the apt package manager (this is built in to Ubuntu). You will need to install those first.

Please let us know if you continue to have trouble.

thanks,

Jeff

On Tue, Apr 17, 2018 at 5:30 AM <sune....@gmail.com> wrote:

Oh, by the way, "Datei oder Verzeichnis nicht gefunden" means "file or directory not found"

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[sune....@gmail.com]

Hi Jeff,

thanks a lot for your quick answer. I now deleted all the files and ran the installation script for Ubuntu, but I still struggle with the
"python3 setup.py build_ext --inplace" command.

At first, I got the error
" Cannot find env var FFTW_PATH or libraries matching fftw", but I think I fixed this by setting the path like export FFTW_PATH=~/dedalus/src/fftw-3.3.4
.
Now I get the following:

Looking for fftw prefix
Found env var FFTW_PATH = /home/master/dedalus/src/dedalus/docs/api

Looking for mpi prefix
Found matching library in /usr/lib/openmpi/lib
Looking for fftw prefix

Found env var FFTW_PATH = /home/master/dedalus/src/dedalus/docs/api

dedalus/core/transposes.pyx: cannot find cimported module '..libraries.fftw'
running build_ext

Unfortunately, I have no idea, how to handle this. The suggestion in https://groups.google.com/forum/#!topic/dedalus-users/IYjKXyeEAt0 did not work put for me or I executed it the wrong way.
Could you maybe help me out again? Sorry for bothering you with it.

Best,
Sune

[Keaton Burns]

Hi Sune,

Did you make sure to run the command getting the dependencies from the package manager?  Did these all complete successfully?  If so, can you send along the output log file from the installer?

Best,

-Keaton

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[sune....@gmail.com]

Hi Keaton,

I installed all the required packages or at least all the packages that are listed before running the install file. They all completed succesfully or were already installed. I also set the path for the FFTW_PATH and MPI_PATH environment variables. However, when I try to run the setup.py-file, I get the following error:

Found env var FFTW_PATH = /home/master/dedalus/src/fftw-3.3.4

dedalus/core/transposes.pyx: cannot find cimported module '..libraries.fftw'

usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help

error: no commands supplied

I also tried running another python-code, but then I get

plan = fftw.FourierTransform(dtype, gshape, axis, flags=flags)
File "dedalus/libraries/fftw/fftw_wrappers.pyx", line 194, in dedalus.libraries.fftw.fftw_wrappers.FourierTransform.__init__
raise RuntimeError("FFTW could not create plans.")
RuntimeError: FFTW could not create plans.

I found a solution to this in https://groups.google.com/forum/#!topic/dedalus-users/01kC06t7S9g, but unfortunately, this does not work for me.
I will also send along the output log file from the installer.

Thank you for your help and sorry for bothering you with it!

Best,
Sune

[Sune Kühne]

This is the Installation log file 

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