rosetta 3.3 Installation failed by Segmentation fault

[Anonymous]

I downloaded Rosetta3.3_bundles.tgz, but file failed to be uncompressed. I downloaded rosetta3.3_source.tgz and rosetta3.3_database.tgz packages and tried to install it on my Fedora 13, which supported Rosetta 3.1, 3.2 and 3.2.1. Unfortunately, the compilation of Rosetta 3.3 failed by Segmentation fault. My system uses scons-2.0.1-1.fc13.noarch. I used “scons bin mode=release” command line.

The second question concerning the new release is: apart from the new functions, is there any change/improvement on the old programs (for example AbinitioRelax) exist in release 3.2.1?

Thank you for your help.
…
g++ -o build/src/release/linux/2.6/32/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/protocols/nonlocal/NonlocalAbinitioReader.cc
src/protocols/nonlocal/NonlocalAbinitioReader.cc: In static member function ‘static void protocols::nonlocal::NonlocalAbinitioReader::read(const std::string&, utility::vector1 >*)’:
src/protocols/nonlocal/NonlocalAbinitioReader.cc:112: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccwJt5Nx.out file, please attach this to your bugreport.
scons: *** [build/src/release/linux/2.6/32/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os] Error 1
scons: building terminated because of errors.

[Anonymous]

For the broken tar file: please see this thread: http://www.rosettacommons.org/content/busted-tape-archive-ie-tar-error

For the compiler error: (quoting Sergey), this is due to a bug in GCC 4.4 series. Upgrading to 4.5 or downgrading to 4.3 should resolve it.
Please see: http://www.rosettacommons.org/node/2274 and http://gcc.gnu.org/bugzilla/show_bug.cgi?id=47478 for more details.

For changes to abrelax: there are no changes that I am aware of. I think Docking has undergone a major upgrade. (It had one late last year in trunk, anyway). I don’t think docking’s performance improved, only its interface. I know I made some improvements to FloppyTail.

[Anonymous]

I tried to build rosetta3.3 on my RHEL6.1-x86_64 too, and meet the same problem, my original gcc version is GCC-4.4.5, scons couldn’t work on mode=release, then I build GCC-4.5.3 and GCC-4.6.1 with GMP-5.0.2, MPFR-4.13 and MPC-0.9, but still, scons doesn’t work with GCC-4.6, and couldn’t work with mode=release for GCC-4.5.

ERR:
src/protocols/nonlocal/NonlocalAbinitioReader.cc: In static member function ‘static void protocols::nonlocal::NonlocalAbinitioReader::read(const std::string&, utility::vector1 >*)’:
src/protocols/nonlocal/NonlocalAbinitioReader.cc:112: internal compiler error: Segmentation fault
*****
*****
scons: *** [build/src/release/linux/2.6/64/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os] Error 1
scons: building terminated because of errors.

[Anonymous]

Did you try fiddling with -finline-limit as suggested in the links in my earlier post?

[Anonymous]

Yes, I also tried to change finline-limit=1133 in /tools/build/basic.settings, but still doesn’t work.

src/protocols/nonlocal/NonlocalAbinitioReader.cc: In static member function ‘static void protocols::nonlocal::NonlocalAbinitioReader::read(const std::string&, utility::vector1 >*)’:
src/protocols/nonlocal/NonlocalAbinitioReader.cc:112: internal compiler error: Segmentation fault
******
******
scons: *** [build/src/release/linux/2.6/64/x86/gcc/protocols/nonlocal/NonlocalAbinitioReader.os] Error 1
scons: building terminated because of errors.

[Anonymous]

If the stuff that’s been suggested before isn’t working for you, then it’s a different error, and I don’t know how to fix it.

You can try setting the inline limit lower (like 200).

When you say “scons doesn’t work with 4.6”, if you mean it’s not recognized, add it to the list in tools/build/options.settings and it ought to work.

When you say you’ve tried all these compilers – may I ask what you did to verify SCons was using the compiler you meant for it to use? (like, cxx_ver= ??)

[Anonymous]

I added 4.6 to gcc list in options.settings, and 12.0 to icc either. GCC4.6 could compile now but stopped at the same point as before.

lower the inline limit still doesn’t work.

“what you did to verify SCons was using the compiler you meant for it to use? (like, cxx_ver= ??)”

I just set the environment: set path=(/usr/local/gcc4.6/bin $path) in ~/.tcshrc
and add /usr/local/gcc461/lib64:/usr/local/gcc4.6/lib to LD_LIBRARY_PATH in ~/.tcshrc
And:
c++: /usr/local/gcc4.6/bin/c++
icc -v: Version 12.0.4

[Anonymous]

If you run “which g++” and trace that back, does it point to the version of gcc you wish to use? You should also try adding cxx=gcc cxx_ver=4.6 in your command line, I’m not sure if you did or not.

[Anonymous]

“which g++” /usr/local/gcc4.6/bin/g++

After I added cxx=gcc cxx_ver=4.6 to scons command line, and set finline-limit=487 in basic.settings and 4.6 for gcc & 12.0 for icc in options.settings, now scons could build rosetta in mode=release. (finline-limit=1133. 1023, 800 failed)

Thank you very much!

[Author]

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