Hello everyone! I'm trying to run a command in paper_interface_design_pilot_1000_commands.list generated in step 12 “Running a pilot job”
the commands are as follows:
cd /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/paper_interface_design_pilot_1000/00000
/home/cooben/rosettatest/rosetta_src_2021.07.61567_bundle/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/cooben/rosettatest/cao_2021_protocol/paper_interface_design.xml -beta_nov16 -in:file:silent /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/pilot_splits/xat.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/cooben/rosettatest/cao_2021_protocol @/home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/design.flags > log.log 2>&1
An error occurred after execution:
Segmentation Fault
My design flags：
-script_vars patchdock_res=97,98,99,100,101,102,103,104
-script_vars runpsipred_single=/home/cooben/rosettatest/psipred/runpsipred_single
-dalphaball /home/cooben/rosettatest/rosetta_src_2021.16.61629_bundle/main/source/external/DAlpahBall/DAlphaBall.gcc
-indexed_structure_store:fragment_store /home/cooben/rosettatest/ss_grouped_vall_all.h5
-dunbrack_prob_buried 0.8
-dunbrack_prob_nonburied 0.8
-dunbrack_prob_buried_semi 0.8
-dunbrack_prob_nonburied_semi 0.8
I'm using Rosetta version rosetta-3.13 with GCC 6.3.0 as the compiling environment (while separately building rosetta-3.9 with GCC 6.1.0). Has anyone encountered this error before? How should I resolve it?
Thank you for your suggestions！
| Attachment | Size |
|---|---|
 log.log | 59.87 KB |
| ROSETTA_CRASH.log | 5.43 KB |
Later I discovered the issue. I mistakenly compiled Rosetta-3.9 using the rosetta_src_2019.12.60667_bundle.tgz package instead of the correct version. During the installation of RIFDOCK, an error occurred in the RotamerGenerator.cc file regarding the get_acceptor_rays_lkball function, indicating an array out-of-bounds error. I made modifications to the array definition within the get_acceptor_rays_lkball function and proceeded with the compilation.
Subsequently, I reinstalled the correct version of Rosetta-3.9 (rosetta_src_2018.09.60072_bundle.tgz) along with RIFDOCK. After these adjustments, the error no longer occurred when running a pilot job.