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problems installing Rosetta on CentOS (fixed)

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problems installing Rosetta on CentOS (fixed)

WhenI type:
[root@localhost rosetta_source]# python external/scons-local/
This happens:
scons: Reading SConscript files ...
sh: svnversion: command not found
sh: svn: command not found
scons: done reading SConscript files.
scons: Building targets ...
o build/src/debug/linux/2.6/64/x86/gcc/numeric/constants.os -c -std=c++98 -pipe
-ffor-scope -W -Wall -pedantic -Wno-long-long -O0 -g -ggdb -ffloat-store -fPIC -
Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isr
c/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src
sh: o: command not found

& it keeps spitting out screens & screens 'til it tells me it crashed. I'm
trying to do this on a 64-bit Dell linux station running Centos 5, which thinks gcc 4.1.2 is THE gcc.
Could this be the problem? Are there environment variables that should or should not be set?


Post Situation: 
Mon, 2010-12-27 22:31

Something somewhere is getting garbled such that your computer is trying to run a program called "o" in place of running gcc. I seem to remember you had a python installation problem - did you ever get that resolved?

If you compare it to the normal output you can see that the starting string that scons is issuing as a command is getting cut off somehow:

scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
g++-4.3 -o build/src/debug/linux/2.6/64/x86/gcc/numeric/model_quality/rms.os -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -O0 -g -ggdb -ffloat-store -fPIC -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/numeric/model_quality/

Notice you're missing the g++-4.3 - before the letter o. (On your system, you should probably just have g++; the system I'm on at the moment has an override in place to use 4.3.

If the problem is a scons/python mismatch, you can try installing a version of scons compatible with your python version. The embedded scons-local is not modified in any way; the scons instruction files native to Rosetta3 should work with most versions of scons.

You can try adding overrides to force use of gcc 4.1.2 into the file tools/build/user.settings:

"overrides" : {
"cc" : "gcc-4.3",
"cxx" : "g++-4.3",

Replace the existing overrides section with that. You'll need to substitute the 3's for either 1's or 1.2's. I'm not optimistic that this will work; this is to force a particular compiler version, whereas you seem to have garbled scons output.

As a dirty trick, you could try aliasing o to something like "gcc -o !:1*" (in tcsh).

Tue, 2010-12-28 10:51

Well... I had to install a g++ to go with the gcc. I'd have thought Centos would have included gcc & g++ when it installed, but no.... SO, having those, I edited the overrides section of user.settings as indicated above & got a **whole lot further**. Thanks a lot! But it didn't finish, so the next problem is:

g++ -o build/src/debug/linux/2.6/64/x86/gcc/ -shared build/src/debug/linux/2.6/64/x86/gcc/utility/basic_sys_util.os build/src/debug/linux/2.6/64/x86/gcc/utility/string_util.os build/src/debug/linux/2.6/64/x86/gcc/utility/heap.os build/src/debug/linux/2.6/64/x86/gcc/utility/exit.os build/src/debug/linux/2.6/64/x86/gcc/utility/LexicographicalIterator.os build/src/debug/linux/2.6/64/x86/gcc/utility/file/file_sys_util.os build/src/debug/linux/2.6/64/x86/gcc/utility/file/FileName.os build/src/debug/linux/2.6/64/x86/gcc/utility/file/gzip_util.os build/src/debug/linux/2.6/64/x86/gcc/utility/file/PathName.os build/src/debug/linux/2.6/64/x86/gcc/utility/boinc/boinc_util.os build/src/debug/linux/2.6/64/x86/gcc/utility/Tag/Tag.os build/src/debug/linux/2.6/64/x86/gcc/utility/options/keys/OptionKeys.os build/src/debug/linux/2.6/64/x86/gcc/utility/io/icstream.os build/src/debug/linux/2.6/64/x86/gcc/utility/io/izstream.os build/src/debug/linux/2.6/64/x86/gcc/utility/io/ocstream.os build/src/debug/linux/2.6/64/x86/gcc/utility/io/ozstream.os build/src/debug/linux/2.6/64/x86/gcc/utility/excn/Exceptions.os build/src/debug/linux/2.6/64/x86/gcc/utility/pointer/ReferenceCount.os build/src/debug/linux/2.6/64/x86/gcc/utility/pointer/ReferenceCountMI_.os build/src/debug/linux/2.6/64/x86/gcc/utility/options/OptionCollection.os build/src/debug/linux/2.6/64/x86/gcc/utility/options/mpi_stderr.os -Llib -Lexternal/lib -Lbuild/src/debug/linux/2.6/64/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/debug/linux/2.6/64/x86/gcc/] Error 1
scons: building terminated because of errors.

What should I do now? Thanks again!

Tue, 2010-12-28 17:43

You need to install the developer's version (code version, not runtime version) of zlib as well. In the ubuntu package manager, it's called zlib1g-dev. In the error "/usr/bin/ld: cannot find -lz", the first part means it's a linker error (ld is the linker), -l means which library is missing, and z identifies the library as zlib.

This is the code called by Rosetta to allow it to support gzipped input/output.

Thu, 2010-12-30 08:54

To get rosetta to install on a Centos 5 linux workstation, [I used the basic, default installation procedure to install Centos], PYTHONHOME & PYTHONPATH need to be unset, gcc, g++ & zlib-devel need to be installed [using rpm], and the overrides section of tools/build/user.settings in rosetta has to be altered to:
overrides" : {
"cc" : "gcc",
"cxx" : "g++",

Thanks for all your help with this!

Mon, 2011-01-03 13:28

Glad you got it fixed. I'm going to edit the topic title to make it obvious to the next user how to do this on CentOS.

Tue, 2011-01-04 06:58

I install gcc-4.5 and gcc-c++-4.5 on fedora 14i686.
In general both the command gcc and g++ seems to work fine, as I checked

[root@localhost rosetta_source]# g++
g++: no input files
[root@localhost rosetta_source]# gcc
gcc: no input files

I tried to run "scons bin mode=release" command and got the error:
g++ -o build/src/debug/linux/2.6/32/x86/gcc/protocols/toolbox/pose_metric_calculators/InterfaceSasaDefinitionCalculator.os -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -malign-double -march=pentium4 -O0 -g -ggdb -ffloat-store -fPIC -Isrc -Iexternal/include -Isrc/platform/linux/32/gcc -Isrc/platform/linux/32 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/protocols/toolbox/pose_metric_calculators/

and it keep flashing again and again.It seems now

Then I also install zlib1g-dev which is zlib-dev in Fedora, but still same error.

I try adding overrides into the file tools/build/user.settings:

"overrides" : {
"cc" : "gcc-4.5",
"cxx" : "g++-4.5",

and also (off-course 1 at a time)
overrides" : {
"cc" : "gcc",
"cxx" : "g++",

and now getting the error:
sh: g++-4.5: command not found
scons: *** [build/src/debug/linux/2.6/32/x86/gcc/apps/public/AbinitioRelax.o] Error 127
scons: building terminated because of errors.

I dont understand why its saying g++-4.5 command not found.

Then I check the version of g++

[root@localhost rosetta_source]# g++ -v
Using built-in specs.
Target: i686-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl= --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,lto --enable-plugin --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj- --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch=i686 --build=i686-redhat-linux
Thread model: posix
gcc version 4.5.1 20100924 (Red Hat 4.5.1-4) (GCC)

Here it showing the gcc version not the gcc-c++ or g++. So, now I don know what to do.
Hope to get some suggestion..!!

Thu, 2012-03-01 18:13

"g++ ..." and the like aren't error messages. They're status messages telling you that g++ is compiling a particular file. You'll see a *lot* of them while you are compiling. Go out and get a coffee.

"sh: g++-4.5: command not found" - This is from your first edit of user.settings right? It simply means that your g++ isn't installed under the alias "g++-4.5". Do a "g++-4.5" at the command line, and you'll likely get the same error message. (It's not the message you're getting with your second, plain gcc/g++, user.settings edit, right?)

It's not surprising that "g++ -v" gives a "gcc version" line. The g++ program is just an alias for the gcc program, which is introspective enough to vary its behavior slightly based on the name you call it as.

Try editing user.settings to be the plain gcc/g++, and then let scons run until it stops on its own. If you're lucky it'll be successful, if not, it should give an error message that's more indicative of the core problem.

Fri, 2012-03-02 10:54