Problems compiling on cluster

[Anonymous]

Hello,

I’ve gotten a fair way through the installation process for the latest weekly build of Rosetta, but have run into an issue.

I start SCons using:

./scons.py -j3 mode=release bin

and everything seems good until about 30 minutes into compiling this happens:

src/core/import_pose/import_pose.cc:63:30: error: cifparse/CifFile.h: No such file or directory

src/core/import_pose/import_pose.cc:64:36: error: cifparse/CifParserBase.h: No such file or directory

src/core/import_pose/import_pose.cc: In function ‘core::import_pose::FileType core::import_pose::determine_file_type(const std::string&)’:

src/core/import_pose/import_pose.cc:224: error: invalid use of undefined type ‘struct CifFile’

src/core/import_pose/import_pose.hh:37: error: forward declaration of ‘struct CifFile’

src/core/import_pose/import_pose.cc:226: error: invalid use of undefined type ‘struct CifParser’

src/core/import_pose/import_pose.hh:38: error: forward declaration of ‘struct CifParser’

src/core/import_pose/import_pose.cc:228: error: invalid use of undefined type ‘struct CifParser’

src/core/import_pose/import_pose.hh:38: error: forward declaration of ‘struct CifParser’

src/core/import_pose/import_pose.cc: In function ‘void core::import_pose::pose_from_file(core::pose::Pose&, const core::chemical::ResidueTypeSet&, const std::string&, const core::import_pose::ImportPoseOptions&, bool, core::import_pose::FileType)’:

src/core/import_pose/import_pose.cc:292: error: invalid use of undefined type ‘struct CifFile’

src/core/import_pose/import_pose.hh:37: error: forward declaration of ‘struct CifFile’

src/core/import_pose/import_pose.cc:293: error: invalid use of undefined type ‘struct CifParser’

src/core/import_pose/import_pose.hh:38: error: forward declaration of ‘struct CifParser’

src/core/import_pose/import_pose.cc:294: error: invalid use of undefined type ‘struct CifParser’

src/core/import_pose/import_pose.hh:38: error: forward declaration of ‘struct CifParser’

g++ -o build/src/release/linux/2.6/64/x86/gcc/4.1/default/core/import_pose/PDBSilentStruct.os -c -std=c++98 -ffor-scope -pipe -march=core2 -mtune=generic -O3 -ffast-math -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_BOOST -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.1 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/core/import_pose/PDBSilentStruct.cc

scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.1/default/core/import_pose/import_pose.os] Error 1

scons: building terminated because of errors.

Any help would be greatly appreciated!

I have attached a partial .log file containing more information.

[Anonymous]

It looks like the issue is that you’re using a rather older version of GCC, (4.1) and our compile system is doing funny things with it.

Ideally, you could use a different, more recent version of the compiler. You can either do that by putting a more recent version of GCC in your default path (probably your best option), or by specifically listing the compiler in the Rosetta settings. (See main/source/tools/build/site.settings.csb for an example of how to modify your main/source/tools/build/user.settings file – particularly the overrides section.)

Alternatively, if you want to still use the default system gcc, then you can try editing the main/source/tools/build/basic.settings file. At around 227, in the gcc 4.1 block, move the “flags” block from the overrides section to the appends section. — I don’t have a gcc 4.1 to test it with, but best I can tell that should help (probably).

[Anonymous]

cif_parse is a recent addition.  If SCons is complaining that it’s absent, it’s worth checking that source/external/cifparse is there as it should be.

[Author]

Posts