Re: [Pytom-mail] Compilation Problems

[Cannon L. <wc...@ri...>]

Hi Thomas!

Compile.py is saying that it has found/not found the following:

Searching :  mpicc               Found :  True
Searching :  mpic++              Found :  True
Searching :  openmpic++                  Found :  False
Searching :  mpicxx-openmpi-gcc45                Found :  False
Searching :  libmpi.so           Found :  True
Searching :  mpi.h               Found :  True
Searching :  Python.h            Found :  True
Searching :  libpython2.7.so             Found :  True
Searching :  fftw3.h             Found :  True
Searching :  libfftw3.so                 Found :  True
Searching :  type_traits.hpp             Found :  True
Searching :  ndarrayobject.h             Found :  True

Python     - lib_python: /usr/lib64
Python     - include_python: /usr/include/python2.7/
FFTW3      - lib_fftw: /usr/lib64
FFTW3      - include_fftw: /usr/include
OpenMPI    - mpic++: mpic++
OpenMPI    - libmpi: /usr/lib64/openmpi/lib
OpenMPI    - include_mpi: /usr/include/openmpi-x86_64/
Numpy      - include_numpy:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/
Boost     - include_boost: /usr/include/


I disabled the compilation of peripherals in compile.py like you suggested.
It looks like I'm getting a lot of errors referring to redefinition of
various functions in *transform.cpp/hpp*.

In reference to the contents of /usr/lib64/openmpi/bin, I wasn't able to
find either of the files that compile.py is missing. *Yum provides* and *yum
search* also failed to turn up any results for openmpic++ or
mpicxx-openmpi-gcc45.

Thanks for your help,

Cannon

On Thu, Jun 25, 2015 at 12:43 PM, Thomas Hrabe <th...@gm...> wrote:

> Hi Cannon,
>
> good to hear you are installing pytom!
> I have no experience with Fedora, but in should generally work.
>
> 1. In order to locate your mpi++, try using the yum package manager. They
> may be called differently on your system? Whats is in the
> */usr/lib64/openmpi/bin *folder ?
> 2. Open the compile.py file and disable the printout by setting ll
> 197,198,199 all three to true. That will limit the installation to the
> pytom core. Once the pytom core is compiled, you can come back and compile
> the remaining parts.
> 3. Can you please list all found / not found packages the compile.py is
> listing?
>
> Good luck,
> Thomas
>
> On Jun 25, 2015, at 9:26 AM, Cannon Lewis <wc...@ri...> wrote:
>
> Hello,
>
> I am an undergraduate summer researcher in Wah Chiu's lab at Baylor
> College of Medicine. I've been trying to compile PyTom on my local Fedora
> 21 machine, and I've run into some issues. I've installed all of the
> required libraries via Yum and provided the appropriate directories to
> compile.py, but when I execute the command it simply prints out a bunch of
> debugging information and does not generate the binaries. The command I've
> been running is:
>
>
>
>
> *./compile.py --target all --pythonVersion 2.7 --libDir
> /usr/lib64/openmpi/lib /usr/lib64 --includeDir /usr/include/openmpi-x86_64/
> /usr/include/boost/ /usr/include/python2.7/ /usr/include
> /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ --dirPath
> /usr/bin /usr/lib --exeDir /usr/lib64/openmpi/bin /usr/bin /usr/lib*
> The debugging information says that it's unable to find openmpic++ and
> mpicxx-openmpi-gcc45, but I have been unable to find these files on my
> system. I would really appreciate any help with this issue. I have also
> attached the full debugging information.
>
> Thanks,
>
> Cannon
>
> <debug.txt>
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