RosettaCommons - Rosetta 3 - Build/Install

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Error concerning PhenixInterface upon running rosetta.run_tests

vcalderone — Sat, 15 Jun 2024 15:02:30 +0000

I have successully compiled rosetta 2019.47.61047_bundle using 'rosetta.build_phenix_interface' command on a fedora 40 pc with gcc-12.3.0.

When I run 'rosetta.run_tests' I get the following error that apparently concerns PhenixInterface.

The same error occurs even with the most recent rosetta version on the website.

Any hint?

##############################################################################################################
#
# Rosetta crash log.
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2019.47+release.3d995b1
[COMMIT_DATE]: 2019-11-23T16:25:53.340829
[APPLICATION]: /usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease
[MODE]: Release
[EXTRAS]: python
[OS]: GNU/Linux
[COMPILER]: GCC version "12.3.0"
[STDLIB]: libstdc++ version 20230508
[START_OPTIONS]
-in:file:s=1yjp_rosetta_in.pdb -out:nstruct=1 -out:suffix=_1 -run:preserve_header -parser:protocol=/usr/local/rosetta_src_2019.47.61047_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -parser:script_vars=symmdef=1yjp_rosetta.symm bfactstrat=individual map_type=Auto -cryst:mtzfile=1yjp_rosetta_data.mtz -cryst:crystal_refine

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.6.so(backtrace_string(int)+0x37) [0x148676316b87]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x7b) [0x148670e98cdb]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::string const&)+0xa2) [0x148670f4c9a2]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::exit(char const*, int, std::string const&, int)+0x34) [0x148670f4c564]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.3.so(core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)+0x2003) [0x1486743bf1b3]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.4.so(protocols::cryst::FitBfactorsMover::apply(core::pose::Pose&)+0xa1) [0x14867980e381]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xd39) [0x148676f02c89]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x18b) [0x148676f0486b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x49) [0x148676eec099]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4025ed]
/lib64/libc.so.6(+0x2a088) [0x14867063d088]
/lib64/libc.so.6(__libc_start_main+0x8b) [0x14867063d14b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4028a5]

[END_BACKTRACE]

[FILE]: src/core/scoring/cryst/PhenixInterface.cc
[LINE]: 257
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: importing phenix.refine failed

[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log.
#

[END_OPTIONS]

[END_BACKTRACE]

[FILE]: src/protocols/jd2/JobDistributor.cc
[LINE]: 329
[START_MESSAGE]
1 jobs failed; check output for error messages

[END_MESSAGE]
[END_CRASH_REPORT]

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Issues building for Phenix interface

jmheumann — Tue, 16 Apr 2024 22:54:54 +0000

Hi,

I'm having trouble building 3.14 from the release 371 source on RHEL8 using gcc 8.5.0 following the instructions at https://phenix-online.org/documentation/reference/rosetta_install.html. I realize this is a newer compiler / glibc, but that doesn't seem to be the issue. Instead I seem to be seeing missing / incompatible header issues. Specifically, I get:

g++ -o build/src/release/linux/4.18/64/x86/gcc/8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc
src/core/scoring/cryst/PhenixInterface.cc: In constructor 'core::scoring::cryst::PhenixInterface::PhenixInterface()':
src/core/scoring/cryst/PhenixInterface.cc:66:20: error: 'basic::options' has not been declared
mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:66:44: error: 'basic::options' has not been declared

followed by many more errors all indicative of missing namespaces-names or incomplete / incorrect declarations, and ultimately terminating in a sizeof failure due to application to an incomplete type. (I've attached the complete error log). I tried explicitly including src/basic/basic.hh from PhenixInterface.cc, but that doesn't seem to help. Suggestions would be greatly appreciated.

Thanks!

-jh-

Attachment	Size
error.log	63.79 KB

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Where are exact source files for rosetta graphics 6.04 beta?

Charlei Fenton — Fri, 12 Apr 2024 15:12:53 +0000

I'm hoping someone here can point me to the actual source tree that was used to build rosetta_graphics_6.04_x86_64-apple-darwin.

I am the long time volunteer Mac programmer for BOINC and am working on fixing the problems with the BOINC screensaver when running under MacOS 14 Sonoma. I want to build the Rosetta graphics app rosetta_graphics_6.04_x86_64-apple-darwin from the source files but link it with my modified BOINC libraries to confirm that my code fixes the screensaver for project graphics.

I have been working with the source trees for both Rosetta 3.14 (March 7, 2024) and Rosetta 2023.35 (September 6, 2023), as well as the GitHub repository, but the run time behavior is different from that of rosetta_graphics_6.04_x86_64-apple-darwin. So I need the exact source tree which was actually used to build the rosetta graphics 6.04 beta.

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Issues building rosetta in Mac

mamunoz1 — Mon, 08 Apr 2024 16:30:40 +0000

Hello, I downloaded the last github version of Rosetta, and trying to build it in my Mac. I'm facing the next errors that stop the building:

"Running versioning script ...

Encounter error while executing: git rev-parse "HEAD:source/src/python/PyRosetta/binder"

fatal: not a git repository (or any of the parent directories): .git"

My laptop details are:

Model Name: MacBook Air

Model Identifier: MacBookAir10,1

Model Number: MGN73LL/A

Chip: Apple M1

Total Number of Cores: 8 (4 performance and 4 efficiency)

Memory: 8 GB

System Firmware Version: 10151.101.3

OS Loader Version: 10151.101.3

Thanks for your help.

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Downloading Rosetta: "Forbidden. You don't have permission...."

kmyers2 — Fri, 05 Apr 2024 21:24:11 +0000

hi! i'm trying to download Rosetta as an academic user. Whenever I attempt to download Rosetta (Software > License & Download > Academic Download > Download Rosetta 3.14 or any of the releases), I get an error saying "Forbidden. You don't have permission to access /downloads/academic/3.14 on this server." I tried reaching out to the CoMotion people at UW, and they said they cannot help and to ask here. How do I get access to download Rosetta? I keep looking for a license agreement i need to fill out or something but can't find anything. Thank you!

Attachment	Size
Screenshot 2024-04-05 at 2.23.55 PM.png	16.51 KB

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Issues with compilation on MacOS

olivia.macleod — Fri, 05 Apr 2024 14:52:31 +0000

Hi, I am having difficult with downloading and compiling the academic version of Rosetta from github (but perhaps that is the wrong way to do it by cloning it onto my Desktop - MacOS 14.4). I tried to compile using scons and it seemed to work following the full instructions, but I noticed I do not have a rosetta/main/ folder. I found a rosetta/source/bin folder and compiled into that source folder. Is that correct? I can now see a number .macosclangrelease files. Thank you.

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Errors in RosettaAntibody distributed static linux binary

marzen — Thu, 08 Feb 2024 20:12:33 +0000

Hello,

I am attempting to install a modern version of the RosettaAntibody protocol, and I’m encountering errors with the Linux binary of the protocol provided for commercial download (antibody.static.linuxgccrelease). For reference, I am using the latest available weekly release: 2023.45 from November 2023.

While other protocols from this binary distribution are working correctly in our hands, the RosettaAntibody is failing with the below compiler version error:

ERROR: ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody grafting.

ERROR:: Exit from: src/protocols/antibody/grafting/regex_based_cdr_detection.cc line: 50

The Rosetta crash log further indicates that the GCC version is not modern enough to support C++11 regex (< 5.2, relevant lines below). This would be consistent with previous forum posts on similar issues with the RosettaAntibody protocol. The full crash log is attached.

[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-44)"

[STDLIB]: libstdc++ version 20150623

As this Rosetta distribution consists of static binaries, however, my reading of this error is that the distributed binary was compiled with too low a version to support the C++11 regex required by the protocol. I’ve also tried defaulting different GCC versions on my end, and the compiler/stdlib variables in the crash log do not change after rerunning the protocol.

Is my interpretation correct, or is the script somehow pulling in a local GCC version? If the former case, is there a different recent release we can download instead? Or can the protocol be compiled with an updated version of GCC in an upcoming distribution?

For further context, the script we are using to run the RosettaAntibody protocol is a basic grafting protocol with a known good sequence. This script/sequence pair runs the protocol successfully on our currently installed version of Rosetta (3.8).

Thanks in advance for any help that can be provided.

Attachment	Size
ROSETTA_CRASH.log	1.24 KB

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rosetta install failure

paulbo — Wed, 13 Dec 2023 13:20:55 +0000

hello, I seem to meet the same problem on ubuntu22.04 install rosetta_new_daily_release https://www.rosettacommons.org/node/10991. I used the command sudo apt install python-is-python2,but wrong in connect python2 candidate. So i used sudo apt install python-is-python3. And type the comand "./scons.py -j 12 mode=release bin extras=mpi" ,but wrong :

It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):

mca_base_var_init failed --> Returned value -1 instead of OPAL_SUCCESS -------------------------------------------------------------------------- scons: *** [build/src/release/linux/6.2/64/x86/gcc/11/mpi/protocols/antibody_legacy/LHSnugFitLegacy.os] Error 255 scons: building terminated because of errors. `

so what could i do for next step? thanks your greeting answer if you coud help. My mpiexec --version is mpiexec (Open MPI) 5.0.0.

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Installing rosetta.source.release-362 with MPI

mb0261 — Fri, 08 Dec 2023 13:56:34 +0000

Greetings,

I'm trying to compile rosetta on my $SCRTACH directory in a HPC using a conda environment (Python 3.7) to use Scons. But all I get is the following error message:

scons: *** [build/src/release/linux/3.10/64/x86/gcc/12.2/mpi/AbinitioRelax.mpi.linuxgccrelease] TypeError `File /shared/software/cuda/11.7/lib64/libcufft.so.10 found where directory expected.' trying to evaluate `${_concat(LIBDIRPREFIX, LIBPATH, LIBDIRSUFFIX, __env__, RDirs, TARGET, SOURCE)}'

scons: building terminated because of errors.

This is the following modules I have available:

module load lang/gcc/12.2.0

module load parallel/cuda/12.3

module load parallel/openmpi/4.1.5_gcc122

./scons.py -j8 mode=release extras=mpi bin

Can someone help me solve this issue?

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