Problem of “Aborted (core dumped) ”

[diaobk]

I use the auto_martini-refactor.zip on ubuntu 14.04.
All dependencies are installed.
I use beautifulsoup4, so I add "from bs4" before import BeautifulSoup in auto_martini.py

But when I use
./auto_martini.py --smi "N1=C(N)NN=C1N" --mol GUA --verbose --fpred
Output:
INFO:main:------------------------------------------------------
INFO:main:; Heavy atoms:
INFO:main:; ['N', 'C', 'N', 'N', 'N', 'C', 'N']
INFO:main:; ring atoms: [[0, 1, 3, 4, 5]]
INFO:main:; [0] -27.6130945208
INFO:main:; [1] -38.0635593097
INFO:main:; [2] 16.4001120276
INFO:main:; [3] -28.4635382315
INFO:main:; [4] -28.0024324069
INFO:main:; [5] -37.8796622141
INFO:main:; [6] 16.6193853655
INFO:main:; CG bead: 1
INFO:main:; with energy: -38.0635593097
INFO:main:; [0, 2] -21.9287319767
INFO:main:; [0, 3] -64.2263393324
INFO:main:; [0, 4] -63.7983238197
INFO:main:; [0, 6] -21.7076565399
INFO:main:; [1, 4] -68.2625846096
INFO:main:; [1, 5] -75.4338808284
INFO:main:; [1, 6] -33.8916513407
INFO:main:; [2, 3] -22.7761151134
INFO:main:; [2, 4] -24.1365999277
INFO:main:; [2, 5] -33.9317685447
INFO:main:; [2, 6] 16.3628159478
INFO:main:; [3, 5] -68.7005219875
INFO:main:; [3, 6] -24.3387784779
INFO:main:; [4, 6] -22.0925627479
INFO:main:; CG bead: 1
INFO:main:; CG bead: 5
INFO:main:; with energy: -75.4338808284
INFO:main:; [0, 2, 3] -51.8374656978
INFO:main:; [0, 2, 4] -53.2310408241
INFO:main:; [0, 2, 6] -12.8605754412
INFO:main:; [0, 3, 6] -53.3983269634
INFO:main:; [0, 4, 6] -51.1852015454
INFO:main:; [1, 4, 6] -57.382992347
INFO:main:; [2, 3, 5] -58.0481172276
INFO:main:; [2, 3, 6] -15.488636805
INFO:main:; [2, 4, 6] -15.064011714
INFO:main:; Max. number of attempts: 13
INFO:main:; Atom partitioning: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1}
Aborted (core dumped)

When I use another smi("CC(=O)OC1=CC=CC=C1C(O)=O")
A new warning appeared before "Aborted (core dumped)" 👍
WARNING:main:Error with BeautifulSoup constructor
python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed.

How can I get this work?

[tbereau]

Looks like a problem with boost. See if updating boost helps resolve the issue.

[diaobk]

I‘ve updated boost to 1.60.
It seems nothing changed.

find / -name libboost_random.so*
/usr/lib/x86_64-linux-gnu/libboost_random.so.1.54.0
/usr/lib/x86_64-linux-gnu/libboost_random.so
/usr/local/lib/libboost_random.so.1.60.0
/usr/local/lib/libboost_random.so

Was there anything wrong in my updating?

tar -zxvf boost_1_60_0.tar.gz
./bootstrap.sh
sudo ./b2 install

[tbereau]

I've heard of problems with Beautiful Soup 4. Could you try downgrading to Beautiful Soup 3? If you have conda or some other python package manager, it's easy to do.

[diaobk]

Many thanks.
Using Beautiful Soup 3, top file seems to be generated successfully.
But the output is still strange.
################ "N1=C(N)NN=C1N"
[moleculetype]
; molname nrexcl
GUA 2

[atoms]
; id type resnr residue atom cgnr charge smiles
1 SP2 1 GUA S01 1 0 ; [N]c1n[c]nn1
2 SP2 1 GUA S02 2 0 ; [N]c1n[c]nn1

[constraints]
; i j funct length
1 2 1 0.21

Aborted (core dumped)
################# "CC(=O)OC1=CC=CC=C1C(O)=O"
......
[dihedrals]
; i j k l funct angle force.c.
1 2 3 4 2 163.8 10.0
1 2 4 3 2 -115.2 10.0
2 3 4 5 2 0.6 10.0
2 5 4 3 2 -0.6 10.0
3 2 4 5 2 -179.4 10.0
3 2 5 4 2 0.6 10.0
3 4 2 5 2 179.4 10.0
4 3 2 5 2 -0.6 10.0

python: /usr/include/boost/thread/pthread/mutex.hpp:108: boost::mutex::~mutex(): Assertion `!posix::pthread_mutex_destroy(&m)' failed.
Aborted (core dumped)
########################

Anything I neglected？

[tbereau]

It's hard to tell--I've never had this bug. Do you get it with other chemical structures as well?

The error message might be related to it, but doesn't have to. I've seen boost generate error messages when it's closing the code, though it doesn't affect the results. You actually seem to be getting all the output. The core dump seems to be boost incorrectly freeing memory. You could try updating boost.