Segfault when applying patch 4.1.1-230110

Install, Configure and Update
1

Hello,

I get the following segfault when running cryosparcm patch --install with latest patch (previous patches forked fine)

Patching master...                                                                                                                                                                                                                                                                                                       
Done.                                                                                                                                                                                                                                                                                                                    
Skipped worker patch.                                                                                                                                                                                                                                                                                                    
[1]    548885 segmentation fault (core dumped)  ./cryosparcm patch --install

And gdb output looks as follows:

Starting program: /usr/bin/bash ./cryosparcm patch --force --install
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[...]
process 549408 is executing new program: /home/bsobol/software/software/cryoSPARC/4.1.1-230110/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/python3.8
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Patching master...
Done.
Skipped worker patch.

Program received signal SIGSEGV, Segmentation fault.
0x000055555566473c in visit_decref (parent=<optimized out>, op=0x7ffff2f5ebe0 <__pyx_type_9cryosparc_4core_Data>) at /usr/local/src/conda/python-3.8.15/Modules/gcmodule.c:380
380     /usr/local/src/conda/python-3.8.15/Modules/gcmodule.c: No such file or directory.

I get the same result on two different environments (machines).

2

For this patch, the segmentation fault may be safe to ignore. Once workers have also been patched, please can you confirm proper function with the benchmark workflow.

2 Likes
3

Just to note: this happens again with 4.4.1-240110 (exactly a year after :smile:)

4

@bsobol Patch 240110 for v4.4.1 includes a fix for a segmentation fault (for future patch operations).

1 Like