[gmx-users] xdrfile library problem on Ubuntu 18.04 LTS

Геннадий Макаров ftorazyne at mail.ru
Wed Jul 18 14:07:20 CEST 2018

Dear GROMACS users and developers,

I have problem with xdrfile library during reading *.xtc from python scripts. A month ago operating system of collectively used computer was upgraded from Ubuntu 12.04 LTS to Ubuntu 18.04 LTS. Since this, xdrfile library do not work even it was re-compiled. 

Debugging with GDB reveals segmentation fault on lines 267 and 279 of xdrfile.c: 
Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x00007fffb805ff49 in xdrfile_read_int (ptr=0x7fffffffcf1c, ndata=1, xfp=0x55f7e240) at xdrfile.c:267
267 while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))
Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x00007fffb805ff9d in xdrfile_write_int (ptr=0x7fffffffd0a8, ndata=1, xfp=0x55e5abf0) at xdrfile.c:279
279 while(i<ndata && xdr_int((XDR *)(xfp->xdr),ptr+i))


This phenomenon is present for any *.xtc file and for libxdrfile.so compiled by GCC 4.4, 4.6, 4.8 and 7.3. Help me please, because of this error I can not use my inhouse Python programs for analysis of trajectories.

Gennady Makarov

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