getting Rosetta to work with Phenix

Member Site Forums Rosetta 3 Rosetta 3 – Build/Install getting Rosetta to work with Phenix

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    • #1191

        I am trying to get Rosetta to work with Phenix phenix-1.7.3-928. But first I need to
        get rosetta compiled. It does not compile without an error.I start with:

        [rosetta@paprika ~/Desktop]$ python -V
        Python 2.6.6

        python bin mode=release

        and it runs for a while and then:

        g++ -o build/src/release/linux/2.6/64/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/protocols/nonlocal/
        src/protocols/nonlocal/ In static member function ‘static void protocols::nonlocal::NonlocalAbinitioReader::read(const std::string&, utility::vector1 >*)’:
        src/protocols/nonlocal/ internal compiler error: Segmentation fault
        Please submit a full bug report,
        with preprocessed source if appropriate.
        See <> for instructions.
        Preprocessed source stored into /tmp/ccUmFWht.out file, please attach this to your bugreport.
        scons: *** [build/src/release/linux/2.6/64/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os] Error 1
        scons: building terminated because of errors.

        Does this look like a gcc problem, a python problem, or a Rosetta problem.

        My system is a RHEL6.2 X86_64 system.

        Linux paprika 2.6.32-220.4.2.el6.x86_64 #1 SMP Mon Feb 6 16:39:28 EST 2012 x86_64 x86_64 x86_64 GNU/Linux

        [rosetta@paprika rosetta_source]$ gcc -v
        Using built-in specs.
        Target: x86_64-redhat-linux
        Configured with: ../configure –prefix=/usr –mandir=/usr/share/man –infodir=/usr/share/info –with-bugurl= –enable-bootstrap –enable-shared –enable-threads=posix –enable-checking=release –with-system-zlib –enable-__cxa_atexit –disable-libunwind-exceptions –enable-gnu-unique-object –enable-languages=c,c++,objc,obj-c++,java,fortran,ada –enable-java-awt=gtk –disable-dssi –with-java-home=/usr/lib/jvm/java-1.5.0-gcj- –enable-libgcj-multifile –enable-java-maintainer-mode –with-ecj-jar=/usr/share/java/eclipse-ecj.jar –disable-libjava-multilib –with-ppl –with-cloog –with-tune=generic –with-arch_32=i686 –build=x86_64-redhat-linux
        Thread model: posix
        gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC)

        Do I have the wrong OS?


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