- This topic has 4 replies, 3 voices, and was last updated 10 years, 4 months ago by Anonymous.
July 17, 2013 at 2:46 pm #1659Anonymous
I’m trying to install mpi version of rosetta-3.4 in cluster.
I got the error when i did “scons bin mode=release extras=mpi (with and without cxx=icc) “, mpiCC : Command not found
In the cluster there is mpicc, mpicxx. There is NO mpic++, mpiCC.
What should i do now?
How do i install mpiCC without administrative previleges?
Please help me:)
Note:- I’m from non cs background.
July 17, 2013 at 3:43 pm #9073Anonymous
The first thing to try with pathing problems is to copy tools/build/site.settings.topsail into (or over) tools/build/site.settings. Open this file and you’ll see:
“program_path” : os.environ[“PATH”].split(“:”),
“include_path” : os.environ[“INCLUDE”].split(“:”),
“library_path” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
The first line is what you need, it will make scons more aggressive in finding mpiCC. (If you get an include-related error, delete that include_path line).
If that doesn’t work, leaving this trick in place, try (in your home directory) making a symlink between mpiCC and mpicxx, and making sure your home directory is in your $PATH environment variable. This means your system will treat mpicxx as mpiCC (they’re supposed to be the same thing anyway) and hopefully work.
July 17, 2013 at 5:31 pm #9075Anonymous
What machine are you on?
This looks like the same error I had when first trying to compile on lonestar and stampede on the TACC systems. The issue was that TACC is configured to use Intel compilers with MPI libraries, and the way they are linked together is somewhat different than you would do with gcc. I worked out the settings and put them in the files site.settings.tacc.lonestar and site.settings.tacc.stampede (in main/tools/build/). You might try copying one of these to site.settings and seeing if that fixes the problem.
If that works, please report back with the machine name so others know.
July 18, 2013 at 6:54 pm #9084Anonymous
I solved the Problem.
This is what i did:
=> cd rosetta-3.4/rosetta_source/tools/build/
=> vi basic.settings
=> In the file i searched for “mpiCC” and replaced with “mpicxx” (Found at two places)
=> Then when i gave scons bin mode=release extras=mpi (with and without cxx=icc) it gave some error: mpicxx -V-4.3 …
=> Then i searched for “-V-4.3” and deleted it. (Found at two places)/
=> Then when i gave scons bin mode=release extras=mpi it complied successfully.
=> I tested the binaries with relax and it ran successfully.
Note:- During compiling it gave many warnings like:
mpicxx -o build/src/release/linux/2.6/64/x86/gcc/4.3/mpi/protocols/simple_moves/MinMover.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 -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include src/protocols/simple_moves/MinMover.cc
src/protocols/simple_moves/MinMover.hh: In constructor ‘protocols::simple_moves::MinMover::MinMover(core::kinematics::MoveMapOP, core::scoring::ScoreFunctionCOP, const std::string&, core::Real, bool, bool, bool)’:
src/protocols/simple_moves/MinMover.hh:166: warning: ‘protocols::simple_moves::MinMover::cartesian_’ will be initialized after
src/protocols/simple_moves/MinMover.hh:165: warning: ‘core::Real protocols::simple_moves::MinMover::threshold_’
src/protocols/simple_moves/MinMover.cc:107: warning: when initialized here
mpicxx -o build/src/release/linux/2.6/64/x86/gcc/4.3/mpi/protocols/simple_moves/MissingDensityToJumpMover.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 -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include src/protocols/simple_moves/MissingDensityToJumpMover.cc
In file included from src/protocols/simple_moves/MissingDensityToJumpMover.cc:35:
src/core/kinematics/FoldTree.hh: In member function ‘bool core::kinematics::FoldTree::jump_exists(int, int) const’:
src/core/kinematics/FoldTree.hh:731: warning: comparison between signed and unsigned integer expressions
src/core/kinematics/FoldTree.hh: In member function ‘core::Size core::kinematics::FoldTree::jump_nr(core::Size, core::Size) const’:
src/core/kinematics/FoldTree.hh:1051: warning: comparison between signed and unsigned integer expressions
Also “comparion between signed and unsigned integer…” warning also came.
July 18, 2013 at 8:53 pm #9085Anonymous
glad it worked! that was essentially what the site.settings file replaces too. there are also flags in the site.settings.tacc.* files that turn off a few of the most annoying warnings.
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