i have been trying to install rosetta on ubuntu 13.10 but the following last lines happened after command "scons bin mode=release"
sh: 1: o: not found
o build/src/release/linux/3.11/64/x86/gcc/4.8/default/zinc2_homodimer_setup.default.linuxgccrelease "-Wl,-rpath=/home/mehdizadeh/Documents/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source/build/src/release/linux/3.11/64/x86/gcc/4.8/default" "-Wl,-rpath=/home/mehdizadeh/Documents/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source/build/external/release/linux/3.11/64/x86/gcc/4.8/default" -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/3.11/64/x86/gcc/4.8/default/apps/public/design/zinc2_homodimer_setup.o -Lexternal/lib -Lbuild/src/release/linux/3.11/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/release/linux/3.11/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.7 -lprotocols.6 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols_h.4 -lprotocols_g.4 -lprotocols_f.4 -lprotocols_e.4 -lprotocols_d.4 -lprotocols_c.4 -lprotocols_b.4 -lprotocols_a.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3
sh: 1: o: not found
Install file: "build/src/release/linux/3.11/64/x86/gcc/4.8/default/zinc2_homodimer_setup.default.linuxgccrelease" as "bin/zinc2_homodimer_setup.default.linuxgccrelease"
o build/src/release/linux/3.11/64/x86/gcc/4.8/default/apps/public/design/zinc_heterodimer_design.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 -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/design/zinc_heterodimer_design.cc
sh: 1: o: not found
o build/src/release/linux/3.11/64/x86/gcc/4.8/default/zinc_heterodimer_design.default.linuxgccrelease "-Wl,-rpath=/home/mehdizadeh/Documents/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source/build/src/release/linux/3.11/64/x86/gcc/4.8/default" "-Wl,-rpath=/home/mehdizadeh/Documents/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source/build/external/release/linux/3.11/64/x86/gcc/4.8/default" -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/3.11/64/x86/gcc/4.8/default/apps/public/design/zinc_heterodimer_design.o -Lexternal/lib -Lbuild/src/release/linux/3.11/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/release/linux/3.11/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.7 -lprotocols.6 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols_h.4 -lprotocols_g.4 -lprotocols_f.4 -lprotocols_e.4 -lprotocols_d.4 -lprotocols_c.4 -lprotocols_b.4 -lprotocols_a.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3
sh: 1: o: not found
Install file: "build/src/release/linux/3.11/64/x86/gcc/4.8/default/zinc_heterodimer_design.default.linuxgccrelease" as "bin/zinc_heterodimer_design.default.linuxgccrelease"
scons: done building targets.
mehdizadeh@mehdizadeh-All-Series:~/Documents/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source$
The full lines are attached.
Although, you can see "scons: done building targets", it seems Rosetta doesn't work. rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source/bin is full of files but they are all broken.
It would be great if anyone can help.
| Attachment | Size |
|---|---|
 rosetta error.docx | 5.22 KB |
The "o: not found" message usually indicates that the Rosetta scons build script had difficulties finding your compiler. Do you have a compiler installed (For Ubuntu it should be the build-essential package. You'll also need the zlib1g-dev package too.) If they are installed, you'll need to tell scons where to find them. See https://www.rosettacommons.org/content/problems-installing-rosetta-cento... for how one person fixed the problem.
There's a number of example files in the source/tools/build/ directory, with names like site.settings.topsail. Each of these represents the customs settings needed for building on a particular cluster the RosettaCommons developers have used. These can either be copies to just the regular site.settings file, or you can use them as a guide on how to alter your site.settings file or your user.settings file for your particular case.
Thank you for your comment, I installed the packages and it seems the installation was done perfectly. How can I know that Rosetta work well now?
There's various tests that could be run (and we do ship several with the Rosetta releases), but they're mainly geared for developer's purposes.
For practical purposes & from a user's perspective, I'd just recommend running your intended protocol with a simple test case. (For example, what was done in the paper that you're basing your experiments on.) If you get reasonable-looking results, Rosetta should be working well.
The problem is that none of the executable files in bin directory (after scons bin command) doesn't run.Also python test/run.py leads tofollowing lines:
mehdizadeh@mehdizadeh-All-Series:/opt/rosetta 2013 wk52/rosetta_2013wk52_bundle/main/source$ python test/run.py
Identifying platform...
Platform found: debug/linux/3.11/64/x86/gcc/4.8/default
/bin/sh: 1: cd: can't cd to build/test/debug/linux/3.11/64/x86/gcc/4.8/default
Traceback (most recent call last):
File "test/run.py", line 505, in
if __name__ == "__main__": main(sys.argv)
File "test/run.py", line 498, in main
T.runUnitTests()
File "test/run.py", line 293, in runUnitTests
else: self.runOneSuite(lib, suite)
File "test/run.py", line 206, in runOneSuite
f = open(log_file, 'w'); f.write(output); f.close()
IOError: [Errno 2] No such file or directory: 'build/test/debug/linux/3.11/64/x86/gcc/4.8/default/protocols.test.found.log'
Traceback (most recent call last):
File "test/run.py", line 505, in
if __name__ == "__main__": main(sys.argv)
File "test/run.py", line 498, in main
T.runUnitTests()
File "test/run.py", line 290, in runUnitTests
pid = self.mfork()
File "test/run.py", line 59, in mfork
for p in self.jobs: os.waitpid(p, 0)
OSError: [Errno 10] No child processes
I don't know what is going wrong.
So, you built Rosetta using scons bin mode=release -jx? Nothing is in build directory at all? As for the tests, you need to build these separately, usually using debug mode (the debug binaries is what run.py is not finding): scons bin mode=debug -jx && scons bin mode=debug cat=test && python test/run.py -d ../database -jx
To expand upon what Jared is saying, the test/run.py script is running the "unit tests", which aren't normally built by scons. You need to run a seperate scons command to build them.
This is a completely separate issue from "none of the executable files in bin directory [run]". This latter issue is more concerning, as those should work after a successful scons command.
What happens (what gets printed) when you attempt to use the executables in the bin directory directly, as if you're doing a production run?
What happens if you re-run the scons command you used to build them? (It should run much quicker the second time.)
Sorry for delay. I tried the version 3.5 and everything is OK now :). Thank you.