Compiling IMP on Red Hat
Hi,
I'm trying to compile IMP on a Red Hat machine: > $ cat /etc/issue > Red Hat Enterprise Linux Server release 5.3 (Tikanga) > Kernel \r on an \m > > $ uname -a > Linux n9 2.6.18-128.1.6.el5.Bull.3 #1 SMP Thu Nov 5 11:31:54 CET 2009 > x86_64 x86_64 x86_64 GNU/Linux
I first tried with the latest release (r12787), which compiled on a Mac and on Ubuntu, but not on Red Hat. Since there was a notification of IMP build failure of this release, I tried with the latest successful build revision (r11171), but I get a build/src/IMP_base_wrap.os compilation error (I have reported the details below). The only IMP version I was able to compile on Red Hat was the r12645, but had to disable domino.
Can anyone help me out with this issue?
Thanks, Davide
> g++ -o build/src/IMP_base_wrap.os -c -isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -isystem /apps/PYTHON/2.6.5/include/python2.6 -fPIC -DBOOST_ALL_NO_LIB -DIMP_SWIG_WRAPPER -Ibuild/include -Ibuild/src build/src/IMP_base_wrap.cpp > build/include/IMP/base/log.h: In function 'PyObject* _wrap_push_log_context(PyObject*, PyObject*)': > build/include/IMP/base/log.h:84: error: too many arguments to function 'void IMP::base::push_log_context(std::string)' > build/src/IMP_base_wrap.cpp:9533: error: at this point in file > build/src/IMP_base_wrap.cpp: In function 'PyObject* _wrap_new_CreateLogContext__SWIG_1(PyObject*, PyObject*)': > build/src/IMP_base_wrap.cpp:10099: error: no matching function for call to 'IMP::base::CreateLogContext::CreateLogContext(const char*, const void*)' > build/include/IMP/base/log.h:351: note: candidates are: IMP::base::CreateLogContext::CreateLogContext(const IMP::base::CreateLogContext&) > build/include/IMP/base/log.h:351: note: IMP::base::CreateLogContext::CreateLogContext(std::string) > build/include/IMP/base/log.h:351: note: IMP::base::CreateLogContext::CreateLogContext() > build/src/IMP_base_wrap.cpp: In function 'PyObject* _wrap_CreateLogContext_set__SWIG_0(PyObject*, PyObject*)': > build/src/IMP_base_wrap.cpp:10281: error: no matching function for call to 'IMP::base::CreateLogContext::set(const char*, const void*)' > build/include/IMP/base/log.h:351: note: candidates are: void IMP::base::CreateLogContext::set(std::string) > build/src/IMP_base_wrap.cpp: In function 'PyObject* _wrap_Object_set_check_level(PyObject*, PyObject*)': > build/src/IMP_base_wrap.cpp:10943: error: 'class IMP::base::Object' has no member named 'set_check_level' > build/src/IMP_base_wrap.cpp:10945: error: 'class IMP::base::Object' has no member named 'set_check_level' > build/src/IMP_base_wrap.cpp: In function 'PyObject* _wrap_Object_get_check_level(PyObject*, PyObject*)': > build/src/IMP_base_wrap.cpp:11015: error: 'const class IMP::base::Object' has no member named 'get_check_level' > scons: *** [build/src/IMP_base_wrap.os] Error 1 > scons: building terminated because of errors. > > > IMP configuration: > boost ='yes' > boostlibs ='' > boostversion ='104800' > boostlibsuffix ='' > endian ='little' > boost_filesystem ='yes' > boost_filesystemlibs='boost_filesystem' > cgal ='no' > ann ='no' > hdf5 ='no' > boost_thread ='yes' > boost_threadlibs ='boost_thread' > gsl ='no' > fftw3 ='no' > boost_programoptions='no' > opencv21 ='no' > opencv22 ='no' > bullet ='no' > build ='fast' > prefix ='/usr' > local ='True' > pythonpath ='/project/devel/dbau/imp/imp-r11171' > libpath ='/apps/BOOST/1_48_0/lib' > ldlibpath ='/project/devel/dbau/imp/imp-r11171' > swigpath ='/apps/SWIG/2.0.4/bin' > datapath ='/project/devel/dbau/imp/imp-r11171' > cxxcompiler ='g++' > cxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > pythoncxxflags ='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > bincxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > shliblinkflags =' -shared' > arliblinkflags ='' > binlinkflags ='' > pythonlinkflags =' -shared' > rpath ='True' > static ='False' > pythonsosuffix ='.so' > pkgconfig ='True' > path ="/apps/GCC/4.6.2/bin:/apps/PYTHON/2.6.5/bin:/apps/modules//wrappers/fortran:/apps/modules//wrappers/c++:/apps/modules//wrappers/c:/opt/mpi/mpibull2-1.3.9-18.s/bin:/opt/intel/Compiler/11.0/069/bin/intel64:/usr/kerberos/bin:/opt/cuda//bin:/usr/local/bin:/bin:/usr/bin:/home/devel/dbau/bin" > python ="/apps/PYTHON/2.6.5/bin/python" > > > Enabled dependencies: Boost.FileSystem, Boost.Thread, Boost > Disabled dependencies: Bullet, HDF5, OpenCV21, CGAL, ANN, Boost.ProgramOptions, modeller, FFTW3, GSL, OpenCV22 > > Enabled modules: em, kernel, scratch, domino, misc, fivec, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, restrainer, example_system_local, base, atom, compatibility, display > Disabled modules: rmf, RMF, cgal, multifit, bullet, gsl, modeller, em2d > > Enabled applications: em_tools > Disabled applications: rmf_tools, ligand_score, saxs_tools, nup84, multifit, example_system, rnapii, foxs > > Enabled systems: Groel > > Errors building: > build/src/IMP_base_wrap.os
On 2/21/12 8:05 AM, Davide Baù wrote: > I'm trying to compile IMP on a Red Hat machine: >> $ cat /etc/issue Red Hat Enterprise Linux Server release 5.3 >> (Tikanga)
Is there a reason this machine is years out of date? (The latest update for RHEL 5 is 5.7.) It seems entirely possible that a bug in one of the system headers was fixed in the interim.
> I first tried with the latest release (r12787), which compiled on a > Mac and on Ubuntu, but not on Red Hat.
What was the problem you encountered with that revision? According to the nightly build results, it compiled fine last night (no 'red boxes' for Linux).
Ben
participants (2)
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Ben Webb
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Davide Baù