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

[Anonymous]

Hello..I’m new to cygwin, python, and scons, and I have been trying to compile the rosetta3.1 and I’ve got the following error:

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 Traceback (most recent call last):

File “/home/marsia/rosetta_source/SConstruct”, line 137, in main

build = SConscript(“tools/build/setup.py”)

File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Script/SConscript.py”, line 596, in call

return apply(method, args, kw)

File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Script/SConscript.py”, line 533, in SConscript

return apply(_SConscript, self.fs, + files, subst_kw)

File “/home/marsia/rosetta_source/external/scons-local/scons-local-0.98.5/SCons/Script/SConscript.py”, line 256, in _SConscript

exec _file_ in call_stack-1.globals

File “/home/marsia/rosetta_source/tools/build/setup.py”, line 410, in

build = setup()

File “/home/marsia/rosetta_source/tools/build/setup.py”, line 401, in setup

build.options_requested, build.options = setup_build_options()

File “/home/marsia/rosetta_source/tools/build/setup.py”, line 112, in setup_build_options

actual.os = setup_platforms.select_os(supported, requested.os)

File “/home/marsia/rosetta_source/tools/build/setup_platforms.py”, line 125, in select_os

raise KeyError?, “Operating system ‘%s’ is unsupported.” % (actual) KeyError: “Operating system ‘cygwin_nt-6.0′ is unsupported.” scons: done reading SConscript files. scons: Building targets … scons: `bin’ is up to date. scons: done building targets.

Please someone tell me what should I do to fix this? Although it said that ‘bin is up to date’ and ‘done building targets’, I checked that the bin folder in the rosetta_source is still empty.

Thank you for your help.

Marsia

[Anonymous]

If you look at the file (rosetta)/tools/build/setup_platforms.py, you’ll see and entry for cygwin_nt-5.1 at line 120. Try copy/pasting it and making it an entry for 6.0 instead (still mapping to cygwin).

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

This one is because you do not have zlib installed (or installed properly, or something). I don’t know how to install it on windows; I’ll try contacting someone who might know.

[Anonymous]

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

[Anonymous]

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

[Anonymous]

The svn warnings are irrelevant. We use subversion (svn) to keep development organized; the release version keeps vestiges of svn and is just upset that it no longer has all the svn stuff present.

This is a different error than before, which I suppose is a good thing. I don’t know enough about windows to tell you if you have zlib installed or not.

The error you’re getting is specific to cluster.cc. If you want to use the clustering app, we’ll have to debug why it in particular is failing to build. If not, just put a # sign in front of cluster in the file apps.src.settings and scons will skip it.

[Anonymous]

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

[Anonymous]

Here are some things to try:

A) Include the header. I am 90% certain this will work but since it doesn’t fail for me, I can’t tell.

Comment out all the lines including function calls to time(), and the block of output at the end where time variables are printed. These are just bookkeeping to let you know how long the clustering took to run; their loss won’t affect the results (just the output where it says how long it took). I am 100% certain this will work if you comment enough stuff out; it doesn’t look like you’ll lose any real functionality doing it.

C) Fiddle with the installation of your compiler until the problem goes away (um, not recommended)

[Anonymous]

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

[Anonymous]

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

line 180:

[Anonymous]

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

[Anonymous]

A) Yes, remove the # from apps.src.settings.

By “include the header”, I mean, look at the stack of lines at the top of cluster.cc that look like #include (that’s pound-symbol include left-pointing angle bracket something.hh right-pointing angle bracket). Include a new header to try to fix these compilation errors – the one you want is ctime, I believe. So, add:

#include

to the file. (This is a special C++ file so it is NOT ctime.hh.

C) If that fails, and ONLY if that fails, try deleting all the lines that have the time function in them. You can also comment them out instead of deleting those lines. You’ll need to use // (two forward slashes) instead of a # sign to comment out in cluster.cc. (cluster.cc is in c++; apps.src.settings is in python, the languages have different syntaxes.) You will also find a bunch of output at the end (lines with

[Anonymous]

that pound-include was supposed to be ctime.

[Anonymous]

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

[Anonymous]

Glad to hear you got it compiled!

The first link you mention is about all I know. We’re working on improving the documentation for 3.2, but it’s tough because grad students are poorly incentivized to write documentation. My usual contact in that lab has graduated; you can always try contacting Jeff Gray directly; he’ll farm it out to one of his students.

There is a small demo at test/integration/tests/docking.

The second link you mention is for Rosetta++ (Rosetta 2). paths.txt is dead in Rosetta3. The functional equivalent is the -database flag.

[Anonymous]

Hi,
I’m trying to install in windows using cygwin. I think I am using the same procedure as Marisa (rosetta_source/external/scons-local/scons.py bin mode=release) but I am getting the following error: “No Sconstruct file found”

I checked the rosetta_source folder and the Scontruct file is there.
Does anyone understand where this error is coming from?

[Anonymous]

Try adding -D to your scons command (scons -D) or adding a pound sign (#) in front of bin if you are compiling binaries (scons.py -D #bin). That tells scons to look harder for Sconstruct.

[Author]

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