release version of spatial stringmol crashes

[franticspider]

release/stringmol 33 ~/git/stringmol/config/spatial_stringmol_v2.0.3.r4.conf

segfaults after initialisation, but

debug/stringmol 33 ~/git/stringmol/config/spatial_stringmol_v2.0.3.r4.conf

works fine. Makefile problem?

[nhpackard]

On Mac 10.14.6.
make runs fine, but segfault with release/stringmol 33 config/spatial_stringmol_v2.0.3.r4.conf

Upon trying debug version:

• debug version in repo is compiled for linux:

N-Pro:stringmol n$ debug/stringmol 33 config/spatial_stringmol_v2.0.3.r4.conf
-bash: debug/stringmol: cannot execute binary file
N-Pro:stringmol n$ 
N-Pro:stringmol n$ file debug/stringmol 
debug/stringmol: ELF 64-bit LSB pie executable x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/l, for GNU/Linux 3.2.0, BuildID[sha1]=d0439fd2d526822247e8692b9373a8ef53ae53b9, with debug_info, not stripped

• in src, make debug fails:

N-Pro:src n$ make debug
g++ -O0 -Wall -Wunused -std=c++11 -DDEBUG -g -o ../debug/stringmol -lm ../debug/stringmol.o \
			../debug/hsort.o ../debug/mathutil.o ../debug/memoryutil.o ../debug/microbial_ga.o ../debug/params.o ../debug/randutil.o ../debug/mt19937-2.o  ../debug/lodepng.o ../debug/agents_base.o ../debug/alignment.o ../debug/instructions.o ../debug/rules.o ../debug/setupSM.o ../debug/SMspp.o ../debug/stringmanip.o ../debug/stringPM.o ../debug/tests.o \
			
clang: error: no such file or directory: '../debug/stringmol.o'
clang: error: no such file or directory: '../debug/hsort.o'
clang: error: no such file or directory: '../debug/mathutil.o'
clang: error: no such file or directory: '../debug/memoryutil.o'
...

also tried `make clean` followed by `make debug`:  no joy.

I will try debugging compile on mac when I get some time...

[franticspider]

Hi Norman, I've had a look at this and I think the debug/stringmol file is a hanger-on from an earlier working compile. I'm in the middle of a significant refactoring and the segfault is an error I need to track down.

Can I suggest you download release version 0.2.3.5 - this compiles and runs (on my system!)

To compile a new debug version, you need to manually remove the *.o files from the debug directory - for reference in resolving the build debug issue, the following commands currently successfully build:

cd src
rm ../debug/*.o
rm ../release/*.o
make clean
make debug

[franticspider]

Finally getting around to looking at this

The segfault is happening because the species list is not populated -- partly because the config file described above isn't describing the species properly.

There's a call to "print_conf" within smspatial, and the segfault happens when the program first tries to access the species list.

Earlier versions of stringmol didn't "print_conf" at this point, so one (dumb) thing to try is to comment out that line. I'm guessing that as soon as a molecule is replicated, the splist will be poulated and print_conf will work. A better approach would be to

1. check whether the species list is NULL before accessing it

and

2. put the species in the config file.

[franticspider]

Proposed fix: if the config file doesn't have species listed, after loading all the molecules we can go through the cohort and generate the species list from that