[gmx-users] g_rms on large (1.5 GB) trr file

dr.horsfield at physics.org dr.horsfield at physics.org
Fri Aug 30 14:08:12 CEST 2002


I have been using g_rms to monitor the progress of a job that has been
running for some weeks, and have never had any trouble until now. I now
get the error:

  trn version: GMX_trn_file
  Reading frame    1460 time 2920.000   There were 4 inconsistent shifts. 
  Check your topology
  Segmentation fault (core dumped)

I assume the problem is related to the size of the trr file (1.5GB), 
though I am not sure why this should be the case.

I recompiled g_rms with the -g option, and looked at the core file with 
gdb, and got:

(gdb) bt
#0  0x403f023d in xdr_string (xdrs=0x81740f8, cpp=0xbfff2d24,
    maxsize=3873791243) at xdr.c:716
#1  0x08086eef in do_xdr (item=0xbfff2e50, nitem=1, eio=7,
    desc=0x815ff9f "buf", srcfile=0x815ff91 "trnio.c", line=83) at gmxfio.c:609
#2  0x0808eedc in do_trnheader (fp=0, bRead=1, sh=0xbfff2fa0, bOK=0xbfff2f9c)
    at trnio.c:83
#3  0x0809003e in fread_trnheader (fp=0, trn=0xbfff2fa0, bOK=0xbfff2f9c)
    at trnio.c:215
#4  0x0806b44c in gmx_next_frame (status=0, fr=0x8214288) at trxio.c:349
#5  0x0806befa in read_next_frame (status=0, fr=0x8214288) at trxio.c:607
#6  0x0806c6af in read_next_x (status=0, t=0xbffff774, natoms=33191,
    x=0x4094c008, box=0xbfff34c0) at trxio.c:770
#7  0x0804c014 in main (argc=1, argv=0xbffff9c4) at g_rms.c:471
#8  0x402fd647 in __libc_start_main (main=0x804a4a4 <main>, argc=9,
    ubp_av=0xbffff9c4, init=0x8049a50 <_init>, fini=0x8146460 <_fini>,
    rtld_fini=0x4000dcd4 <_dl_fini>, stack_end=0xbffff9bc)
    at ../sysdeps/generic/libc-start.c:129

Any ideas what is happening?



            Andrew Horsfield          dr.horsfield at physics.org
                  Department of Physics and Astronomy,
                       University College London,
              Gower Street, London WC1E 6BT, United Kingdom
            Phone:+44-(0)20-7679-3500  FAX:+44-(0)20-7679-1360

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