RosettaCommons - PyRosetta - Build/Install

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http://www.pyrosetta.org/

FAQ

admin — Mon, 30 Aug 2010 11:19:13 +0000

Where is the main website for PyRosetta?

Who is behind PyRosetta?

PyRosetta was created by the laboratory of Jeff Gray at Johns Hopkins University and is based on Rosetta, a software package built and maintained by consortium of academic researchers from around the world.

Where can I get PyRosetta?

https://www.rosettacommons.org/software/license-and-download
Licenses are free for users at academic and nonprofit research institutions.

If I have a Rosetta license, do I need a separate PyRosetta license?

Yes, Rosetta and PyRosetta are licensed separately.

Where is the PyRosetta documentation?

http://www.pyrosetta.org/documentation

Are there additional PyRosetta FAQs?

http://www.pyrosetta.org/faq

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Compilation

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Solved

Segmentation fault (core dumped) error when importing pyrosetta with Tensorflow

proteinstudio — Mon, 17 Jun 2024 15:00:22 +0000

Hi my workflow involves importing pyrosetta and tensorflow together in a single python script. And whenever I import both modules and run the program, I'm keep getting segmentation fault (core dumped) error. Here is my code:

import tensorflow as tf
from pyrosetta import *

If I put them other way around

from pyrosetta import *
import tensorflow as tf

I get Floating point exception (core dumped)

Here is my system information:

OS type: Fedora Linux 38 (64 bit)

Python: 3.11.4

Pyrosetta: pyrosetta-2023.45+release.a6d9ba8-cp311-cp311-linux_x86_64.whl

Below is the output I get from gdb debugger:

Thread 1 "python" received signal SIGFPE, Arithmetic exception.
0x00007fff7b1a4831 in std::__detail::_Map_base<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*> >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true>, true>::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
(gdb) backtrace
\#0 0x00007fff7b1a4831 in std::__detail::_Map_base<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*>, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, void*> >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true>, true>::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#1 0x00007fff7b1a467f in pybind11::detail::local_internals::local_internals() () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#2 0x00007fff7b1a6207 in pybind11::detail::loader_life_support::get_stack_tls_key() () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#3 0x00007fff7b1a237c in pybind11::cpp_function::dispatcher(_object*, _object*, _object*) () from /home/ju/.cache/pypoetry/virtualenvs/hercules-An2atp8I-py3.11/lib/python3.11/site-packages/tensorflow/python/platform/_pywrap_tf2.so
#4 0x000000000055505b in ?? ()
#5 0x000000000052f0ec in _PyObject_MakeTpCall ()
#6 0x000000000053d28e in _PyEval_EvalFrameDefault ()
#7 0x0000000000613134 in ?? ()
#8 0x0000000000612797 in PyEval_EvalCode ()
#9 0x000000000062c513 in ?? ()
#10 0x000000000054adab in ?? ()
#11 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#12 0x0000000000565f23 in _PyFunction_Vectorcall ()
#13 0x0000000000553b10 in ?? ()
#14 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#15 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#16 0x0000000000598d96 in ?? ()
#17 0x000000000054adab in ?? ()
#18 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#19 0x0000000000565f23 in _PyFunction_Vectorcall ()
#20 0x0000000000553b10 in ?? ()
#21 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#22 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#23 0x0000000000598d96 in ?? ()
#24 0x000000000054adab in ?? ()
#25 0x00000000005458d7 in _PyEval_EvalFrameDefault ()
#26 0x0000000000565f23 in _PyFunction_Vectorcall ()
#27 0x0000000000553b10 in ?? ()
#28 0x0000000000583dc1 in PyObject_CallMethodObjArgs ()
#29 0x0000000000583860 in PyImport_ImportModuleLevelObject ()
#30 0x00000000005428f7 in _PyEval_EvalFrameDefault ()
#31 0x0000000000613134 in ?? ()
#32 0x0000000000612797 in PyEval_EvalCode ()
#33 0x00000000006335ab in ?? ()
#34 0x000000000062f7f4 in ?? ()
#35 0x0000000000643e95 in ?? ()
#36 0x0000000000643504 in _PyRun_SimpleFileObject ()
#37 0x0000000000643317 in _PyRun_AnyFileObject ()
#38 0x000000000063dea9 in Py_RunMain ()
#39 0x0000000000603b0d in Py_BytesMain ()
#40 0x00007ffff7c29d90 in __libc_start_call_main (main=main@entry=0x603a60, argc=argc@entry=2, argv=argv@entry=0x7fffffffdde8) at ../sysdeps/nptl/libc_start_call_main.h:58
#41 0x00007ffff7c29e40 in __libc_start_main_impl (main=0x603a60, argc=2, argv=0x7fffffffdde8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffddd8) at ../csu/libc-start.c:392
#42 0x0000000000603995 in _start ()

Any Idea why this is happening in general with Tensorflow? Are those two modules trying to get access to the memory at the same time or something?

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Serialization for Python 3.5

Getmo — Fri, 31 May 2024 19:36:43 +0000

I am working with a GitHub repo (Link) that creates a pipeline for the Rocklin et al. 2017, Science metrics. The provided environment yml file specifies python 3.5 while the code imports pyrosetta.distributed libraries. I've looked through the archive release versions of PyRosetta but did not see a serialization/distributed build for Python 3.5. I've tried running the code with the available 3.5 build but get the following error code:

"CRITICAL:root:Exception while running score_designs.score_pdb_file: __cereal_getstate__ requires pyrosetta '--serialization' build."

Is there an internal or old version of PyRosetta that supports serialization for Python 3.5?

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Unable to get non-commercial license to get username/password

David123 — Fri, 17 May 2024 22:39:02 +0000

Hi team,

As noted in the steps to get non commercial license, there is a license form people can fill up to register for username/password to use Pyrosetta. Seems the form is unable to find.

Thanks for assistance.

david

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Installing pyrosetta for proteinmpnn use

lwhitm1 — Mon, 06 Nov 2023 12:38:02 +0000

What is the best way to install PyRosetta for use with Protein MPNN? I am installing it for myself on an hpc cluster (redhat linux 8) and haven't found much documentation outside of that for the general PyRosetta install.

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Design

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Install pyrosetta on Ubuntu

Xiao Zhu — Mon, 06 Feb 2023 15:02:04 +0000

I recently download the rosetta 2022.46 source code and rosetta 2022.46 ubuntu binanry. Then I'm confused how to install them. I try to unpack the binary file into my home directory, but then it seems nothing has been installed. for examle, "no module called pyrosetta" or "no module called pyrosetta.toolbox" or "init is not defined".

And I also complie the source code using scons , but it seems just create a bin folder contained release in some specific folder, but not installed in the system.

Who can help me to solve this problem?

I have Ubuntu 20.04 on windows

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Compilation

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Installing PyRosetta on Jupyterlab notebook (i.e. not colab)

johnnytam100 — Thu, 15 Dec 2022 08:23:35 +0000

Hi Rosetta team.

I want to install PyRosetta on Jupyterlab notebook (i.e. not colab).

More specifically, the Jupyterlab notebook was spun up from a virtual machine (VM) on the Google Cloud Platform (GCP).

I tried to use ordinary installation commands from colab notebooks, that were

!pip install pyrosettacolabsetup

import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()

but didn't work, giving

ModuleNotFoundError: No module named 'google.colab'

Besides, from the terminal I tried to install from wheel but had no luck, that I was getting:

(base) jupyter@tam-notebook:~/script$ pip install pyrosetta-2022.49+release.201d7639f91-cp310-cp310-linux_x86_64.whl 
ERROR: pyrosetta-2022.49+release.201d7639f91-cp310-cp310-linux_x86_64.whl is not a supported wheel on this platform.

Any idea how to install PyRosetta on Jupyterlab notebook (i.e. not colab)?

Thank you.

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How to resolve the error about pyrosetta.distributed

TENY BAEK — Tue, 13 Dec 2022 08:45:10 +0000

Hello. I'm getting a lot of help from looking at the questions and answers here.

I'm learning it by running it one by one through pyrosetta notebook.

distributed_overview.ipynb

It says pyrosetta is not recognized when running in the conda environment with the above file, is there any way?

Also, the pyrosetta.distributed environment is not working well, so do you have a URL or guide to refer to?

Thank you in advance for your reply.

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Install Error in Google Colab

TENY BAEK — Mon, 17 Oct 2022 04:09:35 +0000

PyRosetta is being tested one by one in Google Collaboration. "01.02-PyRosetta-Google-Drive-Usage-Example.ipynb"

When I checked the file above while running it on Google Collabor, I got an error as below.

The previous 01.01 went well without errors, but the error comes out as below.
(version is PyRosetta4.MinSizeRel.python37.linux.release-332.tar. )

Please look down and give me your opinion.

- OS type : Windows
- OS version : 10
- OS arch (32 or 64bit) : 64bit

- Python version : 3.7
- Python arch (32 or 64bit) if different from OS

# Notebook setup

import sys

if 'google.colab' in sys.modules:

!pip install pyrosettacolabsetup

import pyrosettacolabsetup

pyrosettacolabsetup.setup()

print ("Notebook is set for PyRosetta use in Colab. Have fun!")

Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Collecting pyrosettacolabsetup
  Downloading pyrosettacolabsetup-1.0.6-py3-none-any.whl (4.7 kB)
Installing collected packages: pyrosettacolabsetup
Successfully installed pyrosettacolabsetup-1.0.6

---------------------------------------------------------------------------

AttributeError                            Traceback (most recent call last)

<ipython-input-2-dcbe4bc00f39> in <module>
      4     get_ipython().system('pip install pyrosettacolabsetup')
      5     import pyrosettacolabsetup
----> 6     pyrosettacolabsetup.setup()
      7     print ("Notebook is set for PyRosetta use in Colab.  Have fun!")

AttributeError: module 'pyrosettacolabsetup' has no attribute 'setup'

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