Problem of “Aborted (core dumped) ” about auto_martini HOT 5 OPEN

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

from auto_martini.

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

from auto_martini.

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.

from auto_martini.

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？

from auto_martini.

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.

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