Re: [Pytom-mail] Compilation Problems

[Thomas H. <th...@gm...>]

Can you please replace your pytomc/libs/libtomc/src/tom/transf/transform.cpp file with the one attached and re-run compile?

It could be that the bug was fixed before but that the fix was after the release.
It could also be linked to Sara’s compile issue.

Please let me know if it worked.

Thomas 



> On Jun 25, 2015, at 10:56 AM, Cannon Lewis <wc...@ri...> wrote:
> 
> 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 <http://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... <mailto: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... <mailto: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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