The problem has been solved
Previously I made a params file creation and modification Python 3 module, as mentioned here: https://www.rosettacommons.org/node/10811
I'm doing a very simple relax to optimize and score 100.000 pdb files.
Rosetta was compiled with MPI+MYSQL support.
If I call the relax application on a single PDB file, it works.
Since I have a 64 core machine + 196 GB RAM (with MPI installed), I would like to relax 63 structures in parallel.
This is the command i'm executing with MPI:
mpiexec -np 63 /rosetta2020/main/source/bin/relax.mpimysql.linuxgccrelease @relax.flags.database
Hi, I had some problems downloading Pyrosetta (macOS 10.15.3 Catalina, python2.7.16, Pyrosetta-Release-2.7 from download page on website). After unzipping and running the setup command, I tried to import the pyrosetta library (import pyrosetta; pyrosetta.init() ) but got the error message
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pyrosetta/__init__.py", line 15, in <module>
import pyrosetta.rosetta as rosetta
Hello all,
I noticed rosetta creates 23 tables in MySQL when using it as output backend in the RELAX application.
For my specific research I only need to hold the per-residue energies and the total energies... I don't need the atoms, topology or PDB data to be saved after each cycle, as it consumes a lot of memory.
I tried running relax compiled with MPI and MYSQL.
MySQL was configured properly. A test run without MPI successfully created tables and wrote data to MySQL.
The protocol file @relax.flags was created with the following options:
-list pdblist.txt
-relax:script relax.script
-relax:bb_move false
-score:output_residue_energies
-score:weights res2015
Dear users and developers,
I was running RosettaDesign and an error was reported as "[FILE]: src/utility/options/OptionCollection.cc
[LINE]: 536
[START_MESSAGE]
Option file open failed for: '/**/general_FD.flags'".
This flag file worked on other server previously. Is this an error with compiling Rosetta or with the flag file? Could anyone please give some suggestions about how to fix this? Thank you so much.
Best,
Hi all,
I'm trying to run all unit test by using test/run.py from /source and get the following:
More than one test to run - enabling mute.
Identifying platform...
Hi, good day everyone,
I was trying to compile Rosetta 3 and after running smoothly for two hours it stopped, and I got the following error message:
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
scons: *** [build/src/release/linux/5.3/64/x86/gcc/7/default/core/io/pose_from_sfr/chirality_resolution.os] Error 4
Hello,i use scons to complie.
Recently,I write some class in .cc and .hh files , when i #include<~path/name.hh>,i find that it did not compile .cc files. I have read sconstruct file but do not know how to add my own file to compile with.
Please give me some help
