Error compilation Phenix-Rosetta interface

[Anonymous]

Hello!

I have been trying to set up the Phenix-Rosetta interface (phenix.rosetta.run_phenix_interface) by compiling rosetta (rosetta_bin_linux_2019.14.60699_bundle) with the command: ./scons.py -j4 bin mode=release extras=python. However, I get the following error:

Running versioning script … Release package detected, using rosetta/main/.release.json to acquire version information…

Done. (0.0 seconds)

Number of option files updated: 0

Total 4414 options.

Finished updating ResidueProperty code

— no changes needed

Finished updating VariantType code

— no changes needed

scons: done reading SConscript files.

scons: Building targets …

g++ -o build/src/release/linux/4.15/64/x86/gcc/7/python/protocols/hybridization/CartesianSampler.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc

In file included from src/protocols/hybridization/CartesianSampler.cc:17:0:

src/core/scoring/cryst/PhenixInterface.hh:18:10: fatal error: Python.h: No such file or directory

 #include “Python.h”

          ^~~~~~~~~~

compilation terminated.

g++ -o build/src/release/linux/4.15/64/x86/gcc/7/python/protocols/hybridization/WeightedFragmentSmoothTrialMover.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/WeightedFragmentSmoothTrialMover.cc

g++ -o build/src/release/linux/4.15/64/x86/gcc/7/python/protocols/hybridization/util.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/util.cc

scons: *** [build/src/release/linux/4.15/64/x86/gcc/7/python/protocols/hybridization/CartesianSampler.os] Error 1

g++ -o build/src/release/linux/4.15/64/x86/gcc/7/python/protocols/fold_from_loops/selectors/ProteinResidueSelector.os -c -std=c++0x -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/7 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/fold_from_loops/selectors/ProteinResidueSelector.cc

scons: building terminated because of errors.

 

I would be very thankful if you can help me to solve this problem.

Best regards,

Karen Gonzalez

[Anonymous]

In order to build the Phenix-Rosetta interface, you need to have the development environment for the particular version of Python you are hoping to use.

How to install this depends a bit on which Python and which distribution you’re using, but if you’re using the default Python for your platform, there’s typically something like a `python-dev` package that can be installed via your distribution’s package manager (e.g. `apt` for Ubuntu). The exact name may vary based on your distribution and the version of python you’re interested in using with Phenix-Rosetta.

The other thing you may need to do is to go into the Rosetta/main/source/tools/build/site.settings file, and uncomment the line for the  INCLUDE environment variable. (To help scons find the Python development headers installed by the python development package.)

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