rosetta.source.release-371 on Ubuntu 18.04.6 LTS

[elvicee]

Greetings dear all,
I would like to use rosetta for protein-ligand docking.
It's my first time to install rosetta. When I run the command ( $ ./scons.py -j6 mode=release bin) in a terminal, I recieve follow issues:

src/protocols/recces/sampler/MC_OneTorsion.cc: In member function 'virtual void protocols::recces::sampler::MC_OneTorsion::update()':
src/protocols/recces/sampler/MC_OneTorsion.cc:109:46: error: call of overloaded 'abs(core::Real)' is ambiguous
if ( std::abs( update_angle - stored_angle_ ) < 1.0e-5 ) {
^
In file included from /usr/include/c++/6/ext/string_conversions.h:41:0,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/c++/6/cstdlib:172:3: note: candidate: long int std::abs(long int)
abs(long __i) { return __builtin_labs(__i); }
^~~
In file included from /usr/include/c++/6/cstdlib:75:0,
from /usr/include/c++/6/ext/string_conversions.h:41,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/stdlib.h:837:12: note: candidate: int abs(int)
extern int abs (int __x) __THROW attribute ((const)) __wur;
^~~
In file included from /usr/include/c++/6/ext/string_conversions.h:41:0,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/c++/6/cstdlib:180:3: note: candidate: long long int std::abs(long long int)
abs(long long __x) { return __builtin_llabs (_x); }
^~~
src/protocols/recces/sampler/MC_OneTorsion.cc:112:53: error: call of overloaded 'abs(core::Real)' is ambiguous
} else if ( std::abs( update_angle - active_angle ) < 1.0e-5 ) {
^
In file included from /usr/include/c++/6/ext/string_conversions.h:41:0,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/c++/6/cstdlib:172:3: note: candidate: long int std::abs(long int)
abs(long __i) { return __builtin_labs(__i); }
^~~
In file included from /usr/include/c++/6/cstdlib:75:0,
from /usr/include/c++/6/ext/string_conversions.h:41,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/stdlib.h:837:12: note: candidate: int abs(int)
extern int abs (int __x) __THROW attribute ((const)) __wur;
^~~
In file included from /usr/include/c++/6/ext/string_conversions.h:41:0,
from /usr/include/c++/6/bits/basic_string.h:5429,
from /usr/include/c++/6/string:52,
from /usr/include/c++/6/stdexcept:39,
from /usr/include/c++/6/array:39,
from /usr/include/c++/6/tuple:39,
from /usr/include/c++/6/functional:55,
from /usr/include/c++/6/memory:79,
from src/utility/pointer/std/owning_ptr.hh:20,
from src/utility/pointer/owning_ptr.hh:15,
from src/protocols/recces/sampler/MC_OneTorsion.fwd.hh:18,
from src/protocols/recces/sampler/MC_OneTorsion.hh:19,
from src/protocols/recces/sampler/MC_OneTorsion.cc:15:
/usr/include/c++/6/cstdlib:180:3: note: candidate: long long int std::abs(long long int)
abs(long long __x) { return __builtin_llabs (__x); }
^~~
scons: *** [build/src/release/linux/5.4/64/x86/gcc/6.5/default/protocols/recces/sampler/MC_OneTorsion.os] Error 1
scons: building terminated because of errors.

[roccomoretti]

I think this is the same issue that is fixed in PR #277 -- that's been merged to the most recent main branch of Rosetta, but if you want to use release-371, then you can manually make the fixes in the PR. (Which is basically just adding #include <cmath> to the top of two files.

[elvicee]

It work fine.
Thank you very much!

[elvicee]

Greetings Dear all,
I want to know if BCL and PyRosetta are included in rosetta.source.release-371. If so how to run them?

[roccomoretti]

The BCL integration is indeed included in Rosetta 3.14. You would need to compile separately with extras=bcl, though, as the integration isn't included in the default compile. -- Note that that's specifically the Rosetta/BCL integration, accessed primarily through RosettaScripts XML. If you're interested in BCL-specific features (like using the conformer generator on its own), it would be best to install the BCL directly.

The ability to build PyRosetta is included in the released sources, but that's somewhat tricky to set up and not recommended unless you're deliberately making changes to the C++ code you want to use on the Python level. If you just want to use the released version of Rosetta in Python as-is, I'd highly recommend just installing PyRosetta directly through pip or conda.

[elvicee]

Greetings, Dear
After installation of BCL v4.3.1 on ubuntu 18.04, I decide to practice BCL workshop 2022 tutorials. Some tutorials worked fine but molecule:ConformerGenerator don't work properly. How can I fix this error :
BCL Error: -1 | function: ~Mutex | file: bcl_sched_mutex.cpp | line: 91
===> cannot delete a mutex that is still locked

BCL_conf-error-log.txt

[roccomoretti]

If you're running BCL by itself, it's probably best to ask over at the BCL Github page (while we can help with the BCL/Rosetta integration, there's more BCL-specific expertise over there.)

Though I will note that in your full log there's an earlier error message: ===> Could not open cod.substructure.txt.gz for reading -- This error message is already covered by BCLCommons/bcl#14 -- if the info in that thread doesn't solve your issue, feel free to open a new Issue or Discussion over on BCLCommons/bcl