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Build Error, ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5, truncation

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Build Error, ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5, truncation

I'm using ubuntu 10.10, scons 2.0, python 2.6.6 and gcc 4.4.5
I built a release version of Rosetta, here are the last few lines of the building process
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/rna_extract.linuxgccrelease" as "bin/rna_extract.linuxgccrelease"
o build/src/release/linux/2.6/32/x86/gcc/apps/public/rosetta_scripts/rosetta_scripts.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/rosetta_scripts/
sh: o: not found
o build/src/release/linux/2.6/32/x86/gcc/rosetta_scripts.linuxgccrelease -Wl,-rpath=/home/administrator/rosetta3.1_Bundles/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/rosetta_scripts/rosetta_scripts.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/rosetta_scripts.linuxgccrelease" as "bin/rosetta_scripts.linuxgccrelease"
o build/src/release/linux/2.6/32/x86/gcc/apps/public/score.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/
sh: o: not found
o build/src/release/linux/2.6/32/x86/gcc/score.linuxgccrelease -Wl,-rpath=/home/administrator/rosetta3.1_Bundles/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/score.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/score.linuxgccrelease" as "bin/score.linuxgccrelease"
o build/src/release/linux/2.6/32/x86/gcc/apps/public/score_jd2.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/
sh: o: not found
o build/src/release/linux/2.6/32/x86/gcc/score_jd2.linuxgccrelease -Wl,-rpath=/home/administrator/rosetta3.1_Bundles/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/score_jd2.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
sh: o: not found
Install file: "build/src/release/linux/2.6/32/x86/gcc/score_jd2.linuxgccrelease" as "bin/score_jd2.linuxgccrelease"
scons: done building targets.
Is this normal? or I'm havean error?
I want to run the AbinitoRelax...So I typed this command in the terminal "AbinitioRelax.linuxgccrelease .silent > folding.log " I got this message
AbinitioRelax.linuxgccrelease: command not found
What should I do?

Thank you for your help,

Post Situation: 
Mon, 2011-01-31 08:02

Your build commands are getting garbled somehow.

Note the error message is "sh: o: not found", meaning it's looking for a program o that doesn't exist.

o doens't exist because the start of each compile line SHOULD read something like:
"g++ -o build/src"... In other words, the "g++ -" portion is getting cut off somehow.

I have seen this issue in three other places, but unfortunately it was always a different solution. It seems to be caused by irregularities in where the python and compiler installations end up.

First, try using the embedded SCons ( in the rosetta_source folder). If that WAS the one you tried, try installing scons separately and using that. If you have other python/gcc versions available, try those. If neither of those work, we can start playing around trying to get SCons to find your compiler...

Mon, 2011-01-31 08:37

Thank you for the quick reply.
so I tried using the embedded scons it gave me the same error I think
ology_broker/TemplateJumpClaimer.os build/src/debug/linux/2.6/32/x86/gcc/protocols/topology_broker/TopologyBroker.os build/src/debug/linux/2.6/32/x86/gcc/protocols/topology_broker/TopologyClaimer.os build/src/debug/linux/2.6/32/x86/gcc/protocols/topology_broker/TopologyClaimerFactory.os build/src/debug/linux/2.6/32/x86/gcc/protocols/topology_broker/util.os -Llib -Lexternal/lib -Lbuild/src/debug/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lcore -lnumeric -lutility -lObjexxFCL -lz
sh: o: not found
gcc -o build/src/debug/linux/2.6/32/x86/gcc/ -shared -Llib -Lexternal/lib -Lbuild/src/debug/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
/usr/bin/ld: cannot find -lprotocols
/usr/bin/ld: cannot find -lcore
/usr/bin/ld: cannot find -lnumeric
/usr/bin/ld: cannot find -lutility
/usr/bin/ld: cannot find -lObjexxFCL
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/debug/linux/2.6/32/x86/gcc/] Error 1
scons: building terminated because of errors.

Mon, 2011-01-31 09:27

OK, let's try figuring out the paths.

There's a scons command that lets you check its internal environment variabies, scons log=environment. You can read about its use in this other thread:

Try that, and see what it says for the compiler flags (CXX and CC are the most relevant).

Tue, 2011-02-01 13:00

Thanks for the help :)
The CXX=g++ and CC=gcc
I built it again I dont have the g++ portion cutting off but still the process was terminated with errors..
-march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/ObjexxFCL/
g++ -o build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Time_Date.os -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/ObjexxFCL/
g++ -o build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/internal/ObserverGraph.os -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/ObjexxFCL/internal/
g++ -o build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/internal/ObserverMediator.os -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/ObjexxFCL/internal/
g++ -o build/src/release/linux/2.6/32/x86/gcc/ -shared build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/char.functions.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Cstring.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Dimension.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/DimensionExpression.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/DimensionExpressionRef.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/DynamicIndexRange.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/formatted.i.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/formatted.o.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Fstring.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/IndexRange.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Observer.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/ObserverMulti.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Star.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/string.functions.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/Time_Date.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/internal/ObserverGraph.os build/src/release/linux/2.6/32/x86/gcc/ObjexxFCL/internal/ObserverMediator.os -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib
g++ -o build/src/release/linux/2.6/32/x86/gcc/ -shared build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os build/src/release/linux/2.6/32/x86/gcc/utility/heap.os build/src/release/linux/2.6/32/x86/gcc/utility/exit.os build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os build/src/release/linux/2.6/32/x86/gcc/utility/Tag/Tag.os build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lObjexxFCL -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/32/x86/gcc/] Error 1
scons: building terminated because of errors.

What's the lz?

Fri, 2011-02-04 11:02

lz means you don't have zlib installed.

Install the package zlib1g-dev (with synaptic, or whatever) and see if that fixes it.

I assume you changed something in the interim such that your g++ pathing is correct...

Fri, 2011-02-04 12:51

yup, I installed g++ and zlib1g-dev
Then I noticed "sh: svnversion: not found sh: svn: not found" this message in the scons log=environment, so I installed svnversion also
and rebuilt it. In the building process I noticed some warnings such as "warning: Ignoring corrupt sconsign entry"
however it halted without errors
-L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: "build/src/release/linux/2.6/32/x86/gcc/score.linuxgccrelease" as "bin/score.linuxgccrelease"
g++ -o build/src/release/linux/2.6/32/x86/gcc/apps/public/score_jd2.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/
g++ -o build/src/release/linux/2.6/32/x86/gcc/score_jd2.linuxgccrelease -Wl,-rpath=/home/meghrig/lib/rosetta3.1_Bundles/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/score_jd2.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: "build/src/release/linux/2.6/32/x86/gcc/score_jd2.linuxgccrelease" as "bin/score_jd2.linuxgccrelease"
scons: done building targets.
Is it correct?
How can run the AbinitioRelax?
Thank you

Sat, 2011-02-05 04:39

Usually, when you get to the "scons: done building targets.", this is it, you completed the compile with success
Your link to the abinitio executable sould be:
Than, it's a matter of preparing your files, setting your flags file, and run:
rosetta_source/bin/AbinitioRelax.linuxgccrelease @filename.flags

Sun, 2011-02-06 09:06

"Then I noticed "sh: svnversion: not found sh: svn: not found" this message in the scons log=environment, so I installed svnversion also"

These errors are irrelevant in the academic/industrial release. There is a system which watermarks the code with its SVN revision number so you can know what version of the code an executable was compiled from. That particular error means that you didn't have subversion and it couldn't include that watermark (which you don't need anyway).

Mon, 2011-02-07 08:41

Thanks alot smlewis and smg3d :)
I ran abinitio on 2 proteins with no errors however on 1rop protein I have the following error
protocols.jumping: compute strand/loop fractions for 63 residues...
protocols.abinitio.AbrelaxApplication: run ClassicAbinitio.....
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
Stage 1
Folding with score0 for max of 2000
protocols.abinitio.FragmentMover: BEGIN: 55 SIZE: 9 TOTAL_RES: 56
protocols.abinitio.FragmentMover: Are the fragments compatible with the fasta or the input PDB used to extract the folding sequence ?
protocols.abinitio.FragmentMover: It appears that the fragments go up to residue 63 while the pose only has 56 residues!

ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );
ERROR:: Exit from: src/protocols/abinitio/ line: 122

I checked teh fragmentMover It says that I should switch off non continuous fragment insertions... I tried some of the options stated in -help didn't work!

Do you have any idea how can I turn that off?

Thanks again,

Mon, 2011-02-07 11:40

Is your protein one contiguous strand or does it have a chainbreak in the middle?

Mon, 2011-02-07 13:12

It is made up of 1 chain A, no chain breaks in the middle.

Tue, 2011-02-08 07:10

I would guess that there's a bug in either your fragments file or the input FASTA. What style of fragments file is it (from Robetta? Some other format?). We need to check that it contains the correct number of positions (presumably 56.)

Tue, 2011-02-08 10:56

Thank you for your help, I wouldn't have gone this far with Rosetta without your help..
I got them from Robetta..and I checked and made the fragments several times..
I'm looking for a description or an interpretation of the columns in the fragment files, it's not found in the user manual...I searched on the web also, where can I find an answer??

Fri, 2011-02-11 13:40

I have no idea how they work either. The easy thing would be to re-generate them with Robetta and see if you get a file of the same size, or smaller.

Looking at a random fragment file from someone else's run on Robetta, it looks like the fragment files have "position" lines - just do a search on "position" in a text editor and see what the largest one is?

Sun, 2011-02-13 12:25

Hi there,

I am having some trouble building/installing the rosetta 3.2 and the problem can be summarized as follows:

My OS is Ubuntu 10.10, on inspiron 6400, dual core 1.8, 2GB RAM

I installed Ubuntu 10.10

then i installed the pyshell from the software manager

I also installed gcc ver4.1 (sudo apt-get install gcc-4.1)

I installed scons (sudo apt-get install scons)

I installed g++ (sudo apt-get install g++)

I also installed svn (sudo apt-get install svn)

Then i tried building rosetta-3.2 (sudo scons bin mode release)

I got:
bomalk@ubuntu://media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source$ scons bin mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConscript", line 40, in
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/release/linux/2.6/32/x86/gcc/apps/public/AbinitioRelax.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/

this ended in the error:
usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/32/x86/gcc/] Error 1
scons: building terminated because of errors.

I tried to look it up and then installed other versions of gcc ver=4.1

Then tried sudo scons bin mode=release cxx=gcc cxx_ver=4.1

i got the same error, so i went to the basic.settings and added
"cc" : "gcc-4.1",
"cxx" : "g++-4.1"
which made my file look like this

# be C99? Are there portability issues?
"cc" : [ "std=c99" ],
"cxx" : [ "std=c++98" ],
"compile" : [ "pipe", "ffor-scope" ],
"cc" : "gcc-4.1",
"cxx" : "g++-4.1",
# By default, warn as much as possible.
"warn" : [ "W", "Wall", "pedantic",

the i ran scons again
scons bin mode=release cxx=gcc cxx_ver=4.1
but then i got another error,

abomalk@ubuntu:/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source$ scons bin mode=release cxx=gcc cxx_ver=4.1
scons: Reading SConscript files ...
Traceback (most recent call last):
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/SConstruct", line 139, in main
build = SConscript("tools/build/")
File "/usr/lib/scons/SCons/Script/", line 614, in __call__
return method(*args, **kw)
File "/usr/lib/scons/SCons/Script/", line 551, in SConscript
return _SConscript(self.fs, *files, **subst_kw)
File "/usr/lib/scons/SCons/Script/", line 260, in _SConscript
exec _file_ in call_stack[-1].globals
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 411, in
build = setup()
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 403, in setup
build.settings = setup_build_settings(build.options)
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 227, in setup_build_settings
settings += [ BuildSettingsCombined(id, supported[id]) ]
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 326, in __init__
setattr(self, name, BuildSettings(value))
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 195, in __init__
self.flags = BuildFlags(**self.flags)
File "/media/F0987CD1987C9834/_Hamada/Docking/Rosetta/rosetta-3.2/rosetta_source/tools/build/", line 175, in __init__
assert type(value) is list, "Parameters of BuildFlags must be lists"
AssertionError: Parameters of BuildFlags must be lists
scons: done reading SConscript files.
scons: Building targets ...
scons: `bin' is up to date.
scons: done building targets.

What should i do next?

Wed, 2011-03-02 02:35

"usr/bin/ld: cannot find -lz"

sudo apt-get install zlib-dev

or whatever the name of the zlib development library is, it might be zlib-dev1g or similar. You may need to undo some of the things you tried after that.

Wed, 2011-03-02 07:22

Thanks a million for your help,

Indeed i undid the cxx commands in the setup file and then after running "scons bin mode=release" things went fine

Could you please tell me how I can check to see if my build was a success?

Thu, 2011-03-03 03:30

There's no formal check, but an easy way is to run the integration tests:

cd rosetta_source/test/integration
python -j(num_procs) -d path/to/rosetta_database

It will take quite a while, as it runs short trajectories of many Rosetta executeables. If none explicitly fail (it will print a failure message), you can look into ref/(testname) to see the results of any given test; if they look like not-garbage then you're probably okay.

Thu, 2011-03-03 11:14

I have been away for some time because of all the events that have been taking place in Egypt,

I would like to ask what else to do after getting this error message?

Running abinitio on localhost ...
Running HOW_TO_MAKE_TESTS on localhost ...
Finished HOW_TO_MAKE_TESTS in 0 seconds
Running backrub on localhost ...
*** Test backrub did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.762222]
Finished backrub in 0 seconds
Running centroid_disulfide_scores on localhost ...
*** Test abinitio did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.768115]
Finished abinitio in 0 seconds
Running classic_relax_1a19 on localhost ...
*** Test centroid_disulfide_scores did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.787778]
Finished centroid_disulfide_scores in 0 seconds
Running cluster on localhost ...
*** Test classic_relax_1a19 did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.797582]
Finished classic_relax_1a19 in 0 seconds
Running combine_silent on localhost ...
*** Test cluster did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.811486]
Finished cluster in 0 seconds
*** Test combine_silent did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.812883]
Finished combine_silent in 0 seconds
Running docking_full_protocol on localhost ...
Running docking_local_refine on localhost ...
*** Test docking_full_protocol did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.825549]
Finished docking_full_protocol in 0 seconds
Running docking_local_refine_min on localhost ...
*** Test docking_local_refine did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.838648]
Finished docking_local_refine in 0 seconds
*** Test docking_local_refine_min did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.840098]
Finished docking_local_refine_min in 0 seconds
Running docking_low_res on localhost ...
Running docking_prepack on localhost ...
*** Test docking_low_res did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.853537]
Finished docking_low_res in 0 seconds
Running enzdes on localhost ...
*** Test enzdes did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.868990]
Finished enzdes in 0 seconds
Running extract_atomtree_diffs on localhost ...
*** Test extract_atomtree_diffs did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.882559]
*** Test docking_prepack did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.882699]
Finished docking_prepack in 0 seconds
Finished extract_atomtree_diffs in 0 seconds
Running extract_pdbs on localhost ...
Running fast_relax on localhost ...
*** Test fast_relax did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.897737]
Finished fast_relax in 0 seconds
Running fixbb on localhost ...
*** Test extract_pdbs did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.906840]
Finished extract_pdbs in 0 seconds
Running flexpepdock on localhost ...
*** Test fixbb did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.925183]
Finished fixbb in 0 seconds
Running FloppyTail on localhost ...
*** Test flexpepdock did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.933073]
Finished flexpepdock in 0 seconds
Running fold_and_dock on localhost ...
*** Test FloppyTail did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.945255]
Finished FloppyTail in 0 seconds
Running kinematic_looprelax on localhost ...
*** Test fold_and_dock did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.953362]
Finished fold_and_dock in 0 seconds
Running ligand_dock_7cpa on localhost ...
*** Test kinematic_looprelax did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.962085]
Finished kinematic_looprelax in 0 seconds
Running ligand_dock_script on localhost ...
*** Test ligand_dock_7cpa did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.973526]
Finished ligand_dock_7cpa in 0 seconds
Running loop_modeling on localhost ...
*** Test ligand_dock_script did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.983064]
Finished ligand_dock_script in 0 seconds
Running match on localhost ...
*** Test loop_modeling did not run! Check your --mode flag and paths. [2011-03-28 15:44:18.991719]
Finished loop_modeling in 0 seconds
Running membrane_abinitio on localhost ...
*** Test match did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.009170]
Finished match in 0 seconds
Running membrane_relax on localhost ...
*** Test membrane_abinitio did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.015607]
Finished membrane_abinitio in 0 seconds
Running molfile_to_params on localhost ...
*** Test molfile_to_params did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.030900]
*** Test membrane_relax did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.034456]
Finished membrane_relax in 0 seconds
Finished molfile_to_params in 0 seconds
Running mr_protocols on localhost ...
Running rosetta_scripts_setup on localhost ...
*** Test rosetta_scripts_setup did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.054830]
*** Test mr_protocols did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.054972]
Finished rosetta_scripts_setup in 0 seconds
Finished mr_protocols in 0 seconds
Running score_aln on localhost ...
Running score12_docking on localhost ...
*** Test score_aln did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.069573]
Finished score_aln in 0 seconds
Running score_jd2 on localhost ...
*** Test score12_docking did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.082229]
Finished score12_docking in 0 seconds
Running score_only_silence on localhost ...
*** Test score_only_silence did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.094471]
Finished score_only_silence in 0 seconds
Running sequence_tolerance on localhost ...
*** Test score_jd2 did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.097106]
Finished score_jd2 in 0 seconds
Running silent2frag on localhost ...
*** Test sequence_tolerance did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.107646]
Finished sequence_tolerance in 0 seconds
Running symmetric_docking on localhost ...
*** Test silent2frag did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.114052]
Finished silent2frag in 0 seconds
Running test_idealize on localhost ...
*** Test symmetric_docking did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.129560]
Finished symmetric_docking in 0 seconds
Running threading on localhost ...
*** Test test_idealize did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.138284]
Finished test_idealize in 0 seconds
*** Test threading did not run! Check your --mode flag and paths. [2011-03-28 15:44:19.145897]
Finished threading in 0 seconds

FAIL abinitio
Files ref/abinitio/.test_did_not_run.log and new/abinitio/.test_did_not_run.log differ

FAIL backrub
Files ref/backrub/.test_did_not_run.log and new/backrub/.test_did_not_run.log differ

FAIL centroid_disulfide_scores
Files ref/centroid_disulfide_scores/.test_did_not_run.log and new/centroid_disulfide_scores/.test_did_not_run.log differ

FAIL classic_relax_1a19
Files ref/classic_relax_1a19/.test_did_not_run.log and new/classic_relax_1a19/.test_did_not_run.log differ

FAIL cluster
Files ref/cluster/.test_did_not_run.log and new/cluster/.test_did_not_run.log differ

FAIL combine_silent
Files ref/combine_silent/.test_did_not_run.log and new/combine_silent/.test_did_not_run.log differ

FAIL docking_full_protocol
Files ref/docking_full_protocol/.test_did_not_run.log and new/docking_full_protocol/.test_did_not_run.log differ

FAIL docking_local_refine
Files ref/docking_local_refine/.test_did_not_run.log and new/docking_local_refine/.test_did_not_run.log differ

FAIL docking_local_refine_min
Files ref/docking_local_refine_min/.test_did_not_run.log and new/docking_local_refine_min/.test_did_not_run.log differ

FAIL docking_low_res
Files ref/docking_low_res/.test_did_not_run.log and new/docking_low_res/.test_did_not_run.log differ

FAIL docking_prepack
Files ref/docking_prepack/.test_did_not_run.log and new/docking_prepack/.test_did_not_run.log differ

FAIL enzdes
Files ref/enzdes/.test_did_not_run.log and new/enzdes/.test_did_not_run.log differ

FAIL extract_atomtree_diffs
Files ref/extract_atomtree_diffs/.test_did_not_run.log and new/extract_atomtree_diffs/.test_did_not_run.log differ

FAIL extract_pdbs
Files ref/extract_pdbs/.test_did_not_run.log and new/extract_pdbs/.test_did_not_run.log differ

FAIL fast_relax
Files ref/fast_relax/.test_did_not_run.log and new/fast_relax/.test_did_not_run.log differ

FAIL fixbb
Files ref/fixbb/.test_did_not_run.log and new/fixbb/.test_did_not_run.log differ

FAIL flexpepdock
Files ref/flexpepdock/.test_did_not_run.log and new/flexpepdock/.test_did_not_run.log differ

FAIL FloppyTail
Files ref/FloppyTail/.test_did_not_run.log and new/FloppyTail/.test_did_not_run.log differ

FAIL fold_and_dock
Files ref/fold_and_dock/.test_did_not_run.log and new/fold_and_dock/.test_did_not_run.log differ

FAIL kinematic_looprelax
Files ref/kinematic_looprelax/.test_did_not_run.log and new/kinematic_looprelax/.test_did_not_run.log differ

FAIL ligand_dock_7cpa
Files ref/ligand_dock_7cpa/.test_did_not_run.log and new/ligand_dock_7cpa/.test_did_not_run.log differ

FAIL ligand_dock_script
Files ref/ligand_dock_script/.test_did_not_run.log and new/ligand_dock_script/.test_did_not_run.log differ

FAIL loop_modeling
Files ref/loop_modeling/.test_did_not_run.log and new/loop_modeling/.test_did_not_run.log differ

FAIL match
Files ref/match/.test_did_not_run.log and new/match/.test_did_not_run.log differ

FAIL membrane_abinitio
Files ref/membrane_abinitio/.test_did_not_run.log and new/membrane_abinitio/.test_did_not_run.log differ

FAIL membrane_relax
Files ref/membrane_relax/.test_did_not_run.log and new/membrane_relax/.test_did_not_run.log differ

FAIL molfile_to_params
Files ref/molfile_to_params/.test_did_not_run.log and new/molfile_to_params/.test_did_not_run.log differ

FAIL mr_protocols
Files ref/mr_protocols/.test_did_not_run.log and new/mr_protocols/.test_did_not_run.log differ

FAIL rosetta_scripts_setup
Files ref/rosetta_scripts_setup/.test_did_not_run.log and new/rosetta_scripts_setup/.test_did_not_run.log differ

FAIL score12_docking
Files ref/score12_docking/.test_did_not_run.log and new/score12_docking/.test_did_not_run.log differ

FAIL score_aln
Files ref/score_aln/.test_did_not_run.log and new/score_aln/.test_did_not_run.log differ

FAIL score_jd2
Files ref/score_jd2/.test_did_not_run.log and new/score_jd2/.test_did_not_run.log differ

FAIL score_only_silence
Files ref/score_only_silence/.test_did_not_run.log and new/score_only_silence/.test_did_not_run.log differ

FAIL sequence_tolerance
Files ref/sequence_tolerance/.test_did_not_run.log and new/sequence_tolerance/.test_did_not_run.log differ

FAIL silent2frag
Files ref/silent2frag/.test_did_not_run.log and new/silent2frag/.test_did_not_run.log differ

FAIL symmetric_docking
Files ref/symmetric_docking/.test_did_not_run.log and new/symmetric_docking/.test_did_not_run.log differ

FAIL test_idealize
Files ref/test_idealize/.test_did_not_run.log and new/test_idealize/.test_did_not_run.log differ

FAIL threading
Files ref/threading/.test_did_not_run.log and new/threading/.test_did_not_run.log differ

38 test(s) failed. Use 'diff' to compare results.

what did i do wrong?

Mon, 2011-03-28 06:47

I would suggest looking in the sub-directories of ref/. There are most likely log files there that might contain error messages which should be helpful in figuring out why the tests didn't run. Unfortunately, figuring out why integration tests didn't run is somewhat of a pain.


Mon, 2011-03-28 08:35

Since ALL of the tests crashed, it means one of three things:

A) The executeables are not present where the script is looking for them. That would be rosetta_source/bin/*.(OS)(compiler)(release/debug). Did you compile release mode?

B) The integration test script cannot properly determine your build settings and is looking for gcc executeables when you built with icc, or a similar problem. You can try these flags (cut from the script itself). If you don't have release/gcc/no extras, use these flags to fix it.

parser.add_option("-c", "--compiler",
help="In selecting binaries, which compiler was used? (default: gcc)",
help="In selecting binaries, which mode was used? (default: release)",
help="in selecting binaries, which options were specified? (default: default)",

C) Something is catastrophically wrong with your build, like trying to run a 64-bit build on a 32-bit system. You can check this by:
cd rosetta_source/bin
fixbb.(whatever extension)
If it errors with a complaint about missing score stuff from the database, you're good.
If it errors with something weird, like "illegal instruction", then it's built wrong somehow.

Mon, 2011-03-28 08:45

Hello, Sorry to interrupt...
where can I find a detailed documentation about how Fragment files are being generated?? I checked the user guides and the Roberta server..
Thank you,


Mon, 2011-03-28 10:14

a) Feel free to start new threads for new questions.

B) I have no idea, the fragment code is black magic to me. The fragment-generating code to which you refer was written for Rosetta 1 (i.e., a long long time ago). I believe Dominik Gront in the Baker lab will be publishing on new fragment functionality in Rosetta 3 sometime soon.

Mon, 2011-03-28 17:27

Hello, a newbie here.
I'm trying to install Rosetta3.2 in a new 64 bit system running Ubuntu11. It complained when I use gcc/g++ 4.5 so I tried installing 4.3 and then 4.2, removing the links to 4.5 and linking to gcc/g++ 4.3 and then 4.2. Compilation went on for about half an hour ending with this error:
/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.2.3/libstdc++.a(functexcept.o): relocation R_X86_64_32 against `std::bad_typeid::~bad_typeid()' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-linux-gnu/4.2.3/libstdc++.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/64/x86/gcc/] Error 1
scons: building terminated because of errors.

Any idea what the problem could be? Thanks, Hugo.

Thu, 2011-05-05 12:42

Sounds more like gcc/g++ are installed subtly wrong, as opposed to a Rosetta problem. Alternatively, you're using a newer Ubuntu than Rosetta has been tested on, so maybe there's some untested incompatibility.

When more than one GCC exists, often you need to add a flag to scons that tells it which to use, like so: "cxx_ver=4.2". That is not terribly likely to be your problem, since your linker path is clearly looking at 4.2.3, but it's worth trying, because it affects what compiler flags scons tries to pass to GCC. So try that first.

The error suggests adding -fPIC to your g++ command lines; we can try that next if the first thing doesn't work...

Fri, 2011-05-06 13:29

Tried with the flag "cxx_ver=4.2", same error. So, how do I add -fPIC to the command lines? Also, it takes about 1 hour of compilation to reach the error, is there a way to test just that part? Thanks, again.

Mon, 2011-05-09 07:27

For reference, my GCC is gcc version 4.3.2 (Ubuntu 4.3.2-1ubuntu12).

I looked into what this "fPIC" does, and it looks like it's a static/dynamic linking thing. This implies that it can't get the C++ standard library it wants for linking; maybe you have the ones for static builds and it wants the ones for dynamic builds.

You may be able to add "extras=static" to your compile command line for the static build, which may fix this.

To try adding -fPIC, go to tools/build/basic.settings, and find the entry for your GCC. You can copy a different version if you need to.

"gcc, 4.1" : {
"appends" : {
"version" : [ "4", "1" ],
"flags" : {
"compile" : [ "-param inline-unit-growth=1000",
"-param large-function-growth=50000" ],

In the flags / compile section, try adding fPIC along with those param flags.

It took an hour because it recompiled from scratch when you added the cxx_ver flag, thinking the compiler had changed. If the compiler actually did change, this is appropriate; if it didn't change, then scons is being screwy. It will probably take an hour again after either of these changes, unfortunately: it's a linker error not a compile error so it can't be seen until after Rosetta is done compiling.

Mon, 2011-05-09 07:38

I'm also trying to get Rosetta 3.2.1 going under Ubuntu 11 and getting no where.

The main problem I had was the inevitable
KeyError: "Unknown version number 4.5 for compiler 'gcc'"

However, specifying with flags
scons bin mode=release cxx=gcc cxx_ver=4.4

Doesnt get you any further, just errors in

Of course you cant run
scons bin mode=release cxx=gcc cxx_ver=4.2
because gcc version 4.2 and before are considered obsolete by Ubuntu 11

The best result so far was actually specifying version 3.4. Which after an hour of processing fell over at:
src/core/conformation/symmetry/ error: expected type-specifier
src/core/conformation/symmetry/ error: conversion from 'int*' to non-scalar type 'core::pose::PDBInfoOP' requested
src/core/conformation/symmetry/ error: expected ',' or ';'
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.4/core/conformation/symmetry/util.os] Error 1
scons: building terminated because of errors.

Which is odd. Cos it looks like it's falling over with gcc 4.4 even when I've specified explicitly to use 3.4.

Having played a bit with the build settings, I think it's fair to say it aint going to get any better until SCons is updated to take gcc 4.5

Tue, 2011-05-10 08:15

To get it to take 4.5, I think all you have to do is duplicate the lines in my preceding post:

"gcc, 4.1" : {
"appends" : {
"version" : [ "4", "1" ],
"flags" : {
"compile" : [ "-param inline-unit-growth=1000",
"-param large-function-growth=50000" ],

and replace the 4.whatever with 4.5. You may wish to lower the inline limit, which is occasionally problematic.

You may also need to add "4.5" to the list in options.settings in the same folder.

Tue, 2011-05-10 08:19

So in the build folder I've now changed the options.settings file so that the first lines read:

options = {
"cxx" : {
"gcc" : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "*" ],

And basic.settings at line 203 I inserted:

"gcc, 4.5" : {
"appends" : {
"version" : [ "4", "5" ],
"flags" : {
"compile" : [ "-param inline-unit-growth=1000",
"-param large-function-growth=50000" ],

From your other post I then ran:
sudo apt-get install zlib1g-dev
sudo apt-get update

I thought I'd try it like this, and it seems to be compiling and churning away to itself. Not saying that this is a fix, until it's finished but it seems to have helped. If it doesn't then I'll try with the -fPIC flags and see what happens.

Thanks for the help

Tue, 2011-05-10 08:35

So after letting the compiling run over night, I've come in this morning to
src/core/conformation/symmetry/ error: expected type-specifier
src/core/conformation/symmetry/ error: conversion from 'int*' to non-scalar type 'core::pose::PDBInfoOP' requested
src/core/conformation/symmetry/ error: expected ',' or ';'
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.5/core/conformation/symmetry/util.os] Error 1
scons: building terminated because of errors.

Looks like I'm gonna have to play with -fPIC flags today

Wed, 2011-05-11 01:31


Install file: "build/src/release/linux/2.6/64/x86/gcc/4.5/super_aln.linuxgccrelease" as "bin/super_aln.linuxgccrelease"
scons: done building targets.

The trick was to trawl through the forum, in one of the Fedora discussions on an identical error message it was recommended that if you edit ([Rosetta_path]/src/core/conformation/symmetry/

At around line 360, edit such that the elseif argument reads like

#ifdef WIN32
pose::PDBInfoOP pdb_info_src (new pose::PDBInfo( pose.pdb_info() ));
/// pose::PDBInfoOP pdb_info_src = new pose::PDBInfo::PDBInfo( pose.pdb_info() );
pose::PDBInfoOP pdb_info_src = new pose::PDBInfo( pose.pdb_info() );

All we've done is comment out the original line and add a slightly different one. Apparently this is as a result of the gcc v4.5 being fussier over it's names than previous versions

I've added a full guide of what I've done to get Rosetta working to my blog

Wed, 2011-05-11 03:47