rosetta 3.5 2013wk52 install problem on ubuntu 13.10

[Anonymous]

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.

[Anonymous]

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-centos-fixed#comment-1999 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.

[Anonymous]

Sorry for delay. I tried the version 3.5 and everything is OK now . Thank you.

[Anonymous]

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?

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

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.)

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