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v3.5 mpi version

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v3.5 mpi version


I've compiled rosetta-3.5 with command:

scons bin mode=release extra=mpi

before compiling, I've set up the rosetta_source/tools/build/site.settings properly for my MPI environment as following:

import os

settings = {
"gcc, mpi" : {
"overrides" : {
"cxx" : "mpicxx"

"site" : {
"prepends" : {
"program_path" : [

"appends" : {

# Location of standard and system binaries
# "program_path" : [
# root+"/bin",
# root2+"/bin",
# Path to GCC compiler if not in the os rule
# Path to Intel C++ compiler if not in the os rule
# ],
# Location of standard and system header files if not in the os rule
"include_path" : [
# Location of standard and system libraries if not in the os rule.
"library_path" : [
# root+"/lib64",
## root2+"/lib",
# root2+"/lib64",
# root3+"/lib",
# root3+"/lib64",
# /cm/shared/apps/gcc/4.3.4/lib64:/
"removes" : {
"library_path" : [ "/usr/lib", "/usr/local/lib" ],
"overrides" : {
"mpi" : {
"overrides" : {
"cxx" : "mpicxx"

However, when the building is done, I find that rosetta didn't build the program with prefix "XXX.MPI". I am just wondering was the program for my case still built with MPI support?

thank you very much.


Post Situation: 
Sun, 2013-11-03 01:37

It should be "extras=mpi", not "extra=mpi". I'm surprised the missing "s" doesn't give an error, but apparently it doesn't.

Mon, 2013-11-04 07:27


Sorry for interrupting the discussion like this, but ...

I am also having the similar problem of compiling rosetta v3.5 with mpi. I have used the command : scons bin mode=release extras=mpi and before that I have made changes in the file site.settings.topsail, where I have made changes in teh overrides section by using the following two line : "cxx" = "/usr/bin/mpicxx" , "cc":"/usr/bin/mpicc". During the compilation, I am getting the following error:-

scons: Reading SConscript files ... reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets ...
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/4.4/mpi/apps/public/AbinitioRelax.o -c -std=c++98 -isystem external/boost_1_46_1/ -pipe -ffor-scope -Wall -Wextra -pedantic -Wno-long-long -O3 -ffast-math -funroll-loops -finline-functions -s -Wno-unused-variable -finline-limit=487 -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.4 -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/apps/public/
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.4/mpi/apps/public/AbinitioRelax.o] Error 127
scons: building terminated because of errors.

What could be the mistake here ??


Thu, 2013-11-07 18:22

Just checking - when you made the changes to site.settings.topsail did you then copy/symlink that file to "site.settings" in the same directory? The files with 3+ part filenames in that directory are templates for various clusters. (e.g the topsail cluster at UNC, the pirahna cluster at Vanderbilt, etc.) You need to select one as the official site settings for whatever cluster you use by promoting it to just plain "site.settings".

Fri, 2013-11-08 07:15