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)" :+1: 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.