problem compiling rosetta3.1 in windows vista 32 bit using cygwin 1.7.5-1

Hello smlewis..
Thank you for your suggestion earlier. I changed the entry for cygwin-nt-5.1 at line 120 of the file setup_platform.py into 6.0. Then, i executed the command and I’ve got this error message. Could you please tell me what’s wrong and what should I do to fix it?
Thank you very much for your help.
Marsia

marsia@lembayung-vaio ~/rosetta_source
$ /home/marsia/rosetta_source/external/scons-local/scons.py bin mode=release
scons: Reading SConscript files …
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platform/posix.py:38: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
import popen2
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Tool/msvs.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead
import md5
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/Filter.os -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/filters/Filter.cc
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/PackerNeighborGraphFilter.os -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/filters/PackerNeighborGraphFilter.cc
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/RGFilter.os -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/filters/RGFilter.cc
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/ScoreCutoffFilter.os -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/filters/ScoreCutoffFilter.cc
1 [main] python 3232 C:cygwinbinpython.exe: *** fatal error – unable to remap \?C:cygwinlibpython2.6lib-dynloadtime.dll to same address as parent: 0x2B0000 != 0x370000
2 [main] python 4656 fork: child 3232 – died waiting for dll loading, errno 11
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/ScoreCutoffFilter.os] Exception
Traceback (most recent call last):
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Taskmaster.py”, line 222, in execute
self.targets[0].build()
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Node/__init__.py”, line 372, in build
apply(self.get_executor(), (self,), kw)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Executor.py”, line 145, in __call__
return self.do_execute(target, kw)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Executor.py”, line 131, in do_execute
status = apply(act, (self.targets, self.get_sources(), env), kw)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Action.py”, line 698, in __call__
show, execute, chdir)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Action.py”, line 758, in __call__
return apply(c.__call__, args, kw)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Action.py”, line 468, in __call__
stat = self.execute(target, source, env)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Action.py”, line 622, in execute
result = spawn(shell, escape, cmd_line[0], cmd_line, ENV)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platform/posix.py”, line 105, in spawnvpe_spawn
return exec_spawnvpe([sh, ‘-c’, string.join(args)], env)
File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platform/posix.py”, line 69, in exec_spawnvpe
stat = os.spawnvpe(os.P_WAIT, l[0], l, env)
File “/usr/lib/python2.6/os.py”, line 599, in spawnvpe
return _spawnvef(mode, file, args, env, execvpe)
File “/usr/lib/python2.6/os.py”, line 535, in _spawnvef
pid = fork()
OSError: [Errno 11] Resource temporarily unavailable
scons: building terminated because of errors.

Hello,
I fixed the fatal error – unable to remap by doing these steps:
1) close cygwin
2) Open Windows command prompt (start search -> type ‘cmd’)
3) Go to cygwin bin directory by typing cd c:cygwinbin.
4) Type ash
5) Type ‘/usr/bin/rebaseall’
6) Then I restarted the computer.

I tried to compile rosetta again. It seems working (compilation took almost an hour) until it reached another error. Below is some of the output (cut some parts of it). Could you please tell me what’s wrong and what do I have to do to fix it? Many thanks.

Marsia

---

marsia@lembayung-vaio ~/rosetta_source
$ /home/marsia/rosetta_source/external/scons-local/scons.py bin mode=release
scons: Reading SConscript files …
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platfo rm/posix.py:38: DeprecationWarning: The popen2 module is deprecated. Use the su bprocess module.
import popen2
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Tool/m svs.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead
import md5
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/ScoreCutoffFilt er.os -c -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -mar ch=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=200 00 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/cygw in/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/filters/ScoreCutoffFilter.cc
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/SheetFilter.os -c -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -march=pen tium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/cygwin/32/ gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/us r/local/include -I/usr/include src/protocols/filters/SheetFilter.cc
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/protocols/filters/AtomicContactFi lter.os -c -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long -malign-double -m arch=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=2 0000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/cy gwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38 _0 -I/usr/local/include -I/usr/include src/protocols/filters/AtomicContactFilter .cc
build/src/release/cygwin/1.7/32/x86/gcc/utility/file/gzip_util.os:gzip_util.cc:( .text$_ZN7utility2io8ozstream5flushEv[utility::io::ozstream::flush()]+0x82): und efined reference to `_deflate’
build/src/release/cygwin/1.7/32/x86/gcc/utility/file/gzip_util.os:gzip_util.cc:( .text$_ZN7utility2io8ozstream5closeEv[utility::io::ozstream::close()]+0x5c): und efined reference to `_crc32′
build/src/release/cygwin/1.7/32/x86/gcc/utility/file/gzip_util.os:gzip_util.cc:( .text$_ZN7utility2io8ozstream5closeEv[utility::io::ozstream::close()]+0x82): und efined reference to `_deflate’
collect2: ld returned 1 exit status
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/utility.dll] Error 1
scons: building terminated because of errors.

Thanks smlewis for your explanation. Reading the messages archive in this forum, I found that other people encounter problem with zlib as well. Do you think renaming external/lib/z.lib to something else will work to solve this problem?
Marsia

Hello smlewis,
I have tried several things to make the rosetta3.1 compilation work in my computer. So far not successfull (:cry:)
When I typed whereis zlib in the bash shells, here is the output.
marsia@lembayung-vaio ~/rosetta_source
$ whereis zlib
zlib: /usr/include/zlib.h /usr/share/man/man3/zlib.3.gz

Does it mean that I have zlib installed already or not?

Then, assuming that I have zlib, I renamed rosetta_source/external/lib/z.lib into external/lib/z_donotuse.lib (copying what other people did in this forum). Then I typed command

marsia@lembayung-vaio ~/rosetta_source
$ /home/marsia/rosetta_source/external/scons-local/scons.py bin mode=release
scons: Reading SConscript files …
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platform/posix.py:38: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
import popen2
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Tool/msvs.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead
import md5
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …

Then it stopped when the error came up, which is:

g++ -o build/src/release/cygwin/1.7/32/x86/gcc/apps/public/cluster.o -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/cluster.cc
src/apps/public/cluster.cc: In function ‘int main(int, char**)’:
src/apps/public/cluster.cc:117: error: ‘time’ was not declared in this scope
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/apps/public/cluster.o] Error 1
scons: building terminated because of errors.

I also did typed this command to see what’s the difference:

marsia@lembayung-vaio ~/rosetta_source
$ python external/scons-local/scons.py bin mode=release extras=static
scons: Reading SConscript files …
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Platform/posix.py:38: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
import popen2
/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Tool/msvs.py:37: DeprecationWarning: the md5 module is deprecated; use hashlib instead
import md5
svn: ‘.’ is not a working copy
scons: done reading SConscript files.
scons: Building targets …

and it stopped when this same error came up:

g++ -o build/src/release/cygwin/1.7/32/x86/gcc/static/apps/public/cluster.o -c -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/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/apps/public/cluster.cc
src/apps/public/cluster.cc: In function ‘int main(int, char**)’:
src/apps/public/cluster.cc:117: error: ‘time’ was not declared in this scope
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/static/apps/public/cluster.o] Error 1
scons: building terminated because of errors.

What do I have to do to fix this?
Do I have zlib installed already or nort?
At the beginning of the compilation output, there is a line saying:

import md5
svn: ‘.’ is not a working copy

what does it mean?

Thanks for taking time answering my questions.

Marsia

Hello smlewis,

I put a # sign in front of ‘cluster’ in file rosetta_source/src/apps.src.settings, saved the file, then typed command to compile. The scons compilation run without any error message, and here is what I’ve got in the bin:

AbinitioRelax.cygwingccrelease
FloppyTail.cygwingccrelease
backrub.cygwingccrelease
benchmark.cygwingccrelease
ca_to_allatom.cygwingccrelease
combine_silent.cygwingccrelease
ddg_benchmark.cygwingccrelease
design_contrast_and_statistic.cygwingccrelease
docking_protocol.cygwingccrelease
enzyme_design.cygwingccrelease
extract_atomtree_diffs.cygwingccrelease
extract_pdbs.cygwingccrelease
fixbb.cygwingccrelease
idealize.cygwingccrelease
ligand_dock.cygwingccrelease
ligand_rpkmin.cygwingccrelease
loopmodel.cygwingccrelease
loops_from_density.cygwingccrelease
membrane_abinitio2.cygwingccrelease
packstat.cygwingccrelease
relax.cygwingccrelease
rna_database.cygwingccrelease
rna_denovo.cygwingccrelease
rna_design.cygwingccrelease
rna_extract.cygwingccrelease
rosetta_scripts.cygwingccrelease
score.cygwingccrelease
score_jd2.cygwingccrelease

I will still need to use the cluster application. Could you please tell me what and how to do to debug?

Many thanks,

Marsia

Hello smlewis,
Being a novice in this area, I need more hints about what to do. So I was wondering if you can be be more spesific and detail about what I should try. Which file and in which folder I should try to modify?
My current understanding is that I should remove the # sign that I put infront of the “cluster” in file rosetta_sourcesrcapps.src.setting.
Then I should modify this file: rosetta_sourcesrcappspubliccluster.cc by putting # in front of all lines that contain word ‘time’, which are:
line 117: int time_start = time(NULL);
line 142: int time_readin = time(NULL);
line 144: int time_initialc = time(NULL);
line 156: int time_total = time(NULL);
line 179: std::cout

Hello again…
the previous message was truncated. Here is the rest of the message:

line 180:

The message keeps getting truncated… I don’t understand why.
Anyway, please let me know if modifying those files (see my previous message) is the right thing to do.
Also, how to check that I installed everything correctly?
Is there a tutorial about how to use rosetta. I plan to dock peptide (9 mers) into the HLA molecule.
Marsia

Hello smlewis,
I removed the # from apps.src.settings, then in file cluster.cc I typed
#include , then pythhon scons.py bin mode=release, and Rosetta3.1 is successfully compiled (:smile:). Thank you for your guidances.

Is there an easy to follow tutorial for protein-protein docking?

I found the http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_dock.html is not easy to follow.

While the http://graylab.jhu.edu/~mdaily/tutorial/basics_main.html seems not related to what I already have in my computer.

Also I did not find the template for paths.txt file anywhere.

Any suggestion where to start learning rosetta?

Thanks,

Marsia