[gmx-users] Re: crash in double precision GROMACS

[Claudio Arlandini]

Here is the debugger (gdb) output.
I compiled with CFLAGS "-g" ,HP compilers and MPI libraries
with configure --enable-mpi --disable-float --without-x
BTW: in my makelog file it results gmxfio.c is compiled and without errors.

------------------------

Division over nodes in atoms:
   7600  7600  7600  7600  7600  7600  7625  7626  7626  7626  7626  7626 
7626  7626  7626  7623
writing run input file...

Back Off! I just backed up 1md.tpr to ./#1md.tpr.2#

Program received signal SIGBUS, Bus error.
0x7fe18 in do_xdr (item=0x40044474 "", nitem=1, eio=0, desc=0x40016c98 
"ir->epsilon_surface", srcfile=0x40016cb0 "tpxio.c",
     line=186) at gmxfio.c:520
520     gmxfio.c: No such file or directory.


(gdb) bt
#0  0x7fe18 in do_xdr (item=0x40044474 "", nitem=1, eio=0, desc=0x40016c98 
"ir->epsilon_surface",
     srcfile=0x40016cb0 "tpxio.c", line=186) at gmxfio.c:520
#1  0x59544 in do_inputrec (ir=0x40044408, bRead=0) at tpxio.c:186
#2  0x61ae4 in do_tpx (fp=0, bRead=0, step=0x70bd2cc8, t=0x70bd2cc0, 
lambda=0x70bd2cb8, ir=0x40044408, box=0x70bd1aa0,
     natoms=0x70bd2cac, x=0x434dfeb0, v=0x437a9eb8, f=0x0, top=0x40052230) 
at tpxio.c:820
#3  0x62080 in write_tpx (fn=0x40049930 "1md.tpr", step=0, t=0, lambda=0, 
ir=0x40044408, box=0x70bd1aa0, natoms=121856,
     x=0x434dfeb0, v=0x437a9eb8, f=0x0, top=0x40052230) at tpxio.c:882
#4  0x30158 in main (argc=1, argv=0x70bd0aa4) at grompp.c:1008


Thanks, Claudio



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Dr.  Claudio Arlandini,  PhD                \ C onsorzio
    System Administration                     \ I nteruniversitario
                                               \ L ombardo per la
    e-mail arlandini at cilea.it                  \ E laborazione
    ph. +39 02 26995.246 (fax +39 02 2135520)  \ A utomatica

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\/~~~~~~~~~~~~~~~~~~~~~~~~~~~~~