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RosettaCommons
Compiler problem with tcrmodel.static.linuxgccrelease
Hi,
I downloaded the binaries rosetta.binary.linux.release-371, but I have an error using tcrmodel.static.linuxgccrelease
It does not seem a problem with my local compiler, but with the compiler used to build the binaries, can you help me in solving this issue?
$ strace -f -e execve \
> /opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease \
> --database /opt/tools/deg/Rosetta/rosetta.binary.linux.release-362/main/database \
> -alpha VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAGTTVTVRA \
> -beta VTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTSMYLCAWGTLATEQYFGPGTRLTVT \
> -remodel_tcr_cdr3_loops True 2>&1 | tee strace_tcrmodel.log
execve("/opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease", ["/opt/tools/deg/Rosetta/rosetta.b"..., "--database", "/opt/tools/deg/Rosetta/rosetta.b"...,
"-alpha", "VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAG"..., "-beta", "VTQSSRYLVKRTGEKVFLECVQDMDHENMFWY"..., "-remodel_tcr_cdr3_loops", "True"], 0x7ffc9a339918 /* 91 vars */) = 0
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email [email protected] for more details. **********
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.linux.release-371 r371 2024.09+release.06b3cf8 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-03-01T01:30:53.796737
core.init: command: /opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease --database /opt/tools/deg/Rosetta/rosetta.binary.linux.release-362/main/database -alpha VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAGTTVTVRA -beta VTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTSMYLCAWGTLATEQYFGPGTRLTVT -remodel_tcr_cdr3_loops True
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2002964941 seed_offset=0 real_seed=-2002964941
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2002964941 RG_type=mt19937
protocols.tcr.util: Reading numbering scheme: PierceLab:AHO_Scheme
ERROR: ERROR: Your compiler does not have full support for C++11 regex.
ERROR:: Exit from: src/protocols/tcr/util.cc line: 224
[ ERROR ]: Caught exception:
File: src/protocols/tcr/util.cc:224
[ ERROR ] UtilityExitException
ERROR: ERROR: Your compiler does not have full support for C++11 regex.
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
+++ exited with 1 +++
$ grep -iE 'gcc|g\+\+|ld|as' strace_tcrmodel.log
execve("/opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease", ["/opt/tools/deg/Rosetta/rosetta.b"..., "--database", "/opt/tools/deg/Rosetta/rosetta.b"...,
"-alpha", "VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAG"..., "-beta", "VTQSSRYLVKRTGEKVFLECVQDMDHENMFWY"..., "-remodel_tcr_cdr3_loops", "True"], 0x7ffc9a339918 /* 91 vars */) = 0
* Use of Rosetta for commercial purposes may require purchase of a license. *
core.init: Rosetta version: rosetta.binary.linux.release-371 r371 2024.09+release.06b3cf8 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-03-01T01:30:53.796737
core.init: command: /opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease --database /opt/tools/deg/Rosetta/rosetta.binary.linux.release-362/main/database -alpha VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAGTTVTVRA -beta VTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTSMYLCAWGTLATEQYFGPGTRLTVT -remodel_tcr_cdr3_loops True
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-2002964941 seed_offset=0 real_seed=-2002964941
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-2002964941 RG_type=mt19937
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
(Rosetta) [imerelli@slurmlogin Rosetta]$ ls
ROSETTA_CRASH.log rosetta.binary.linux.release-362 rosetta.binary.linux.release-371 rosetta_bin_linux_3.14_bundle.tar.bz2
ncaa_rotamer_libraries rosetta.binary.linux.release-362.tar.bz2 rosetta.ncaa.rotamer.libraries.tar.gz strace_tcrmodel.log
(Rosetta) [imerelli@slurmlogin Rosetta]$ cat ROSETTA_CRASH.log
ncaa_rotamer_libraries/ rosetta.binary.linux.release-362.tar.bz2 rosetta_bin_linux_3.14_bundle.tar.bz2 rosetta.ncaa.rotamer.libraries.tar.gz
rosetta.binary.linux.release-362/ rosetta.binary.linux.release-371/ ROSETTA_CRASH.log strace_tcrmodel.log
cat ROSETTA_CRASH.log
[END_BACKTRACE]
[FILE]: src/protocols/tcr/util.cc
[LINE]: 224
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: ERROR: Your compiler does not have full support for C++11 regex.
[END_MESSAGE]
[END_CRASH_REPORT]
##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2024.09+release.06b3cf8
[COMMIT_DATE]: 2024-03-01T01:30:53.796737
[APPLICATION]: /opt/tools/deg/Rosetta/rosetta.binary.linux.release-371/main/source/bin/tcrmodel.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-44)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
-alpha=VTQLGSHVSVSEGALVLLRCNYSDYKLSFGAGTTVTVRA -beta=VTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTSMYLCAWGTLATEQYFGPGTRLTVT -in:path:database=/opt/tools/deg/Rosetta/rosetta.binary.linux.release-362/main/database/ -tcrmodel:remodel_tcr_cdr3_loops
[END_OPTIONS]
[START_BACKTRACE]: RAW_LIBC
[0x6bfa9f0]
[0x6b53223]
[0x6c001d6]
[0xc634ab]
[0xc56720]
[0xc57145]
[0x41c141]
[0x73cb214]
[0x73cb491]
[0x655196]
[END_BACKTRACE]
[FILE]: src/protocols/tcr/util.cc
[LINE]: 224
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: ERROR: Your compiler does not have full support for C++11 regex.
[END_MESSAGE]
[END_CRASH_REPORT]
This message does indeed have to do with which compiler was used to compile the Rosetta binaries (not which compiler you currently have installed.)
For maximum compatibility with older systems, the precompiled "linux" binaries we provide (at least for older releases) are compiled with GCC version 4.8, which is before GCC fully implemented C++11 regex support. This works for most things, but unfortunately not for tcrmodel.
To be able to use the regex support, you'd either need to download a version of the binaries compiled with a more recent compiler (the Ubuntu ones should have regex support, I believe), or you would need to recompile Rosetta using your own, GCC 5.2-or-later compiler. (You should be able to recompile in the current download -- we provide the full source along with the prebuilt binaries.)
