[gmx-users] g_tcaf issue
Jones de Andrade
johannesrs at gmail.com
Wed Dec 18 19:21:58 CET 2013
Hi Justin.
Thanks for the suggestion.
Unfortunately, only today we could work on the problem again. We recompiled
it with option -DCMAKE_BUILD_TYPE=DEBUG on the cmake step. After, we ran
the gdb g_tcaf to get the following:
> gdb g_tcaf_mpi
GNU gdb (GDB) SUSE (7.3-0.6.1)
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html
>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from
/storage/home/taytyanne/bin/gromacs2/bin/g_tcaf_mpi...done.
(gdb) run
Starting program: /storage/home/taytyanne/bin/gromacs2/bin/g_tcaf_mpi
Missing separate debuginfo for /lib64/ld-linux-x86-64.so.2
Try: zypper install -C
"debuginfo(build-id)=181860a35c8e9a0456dd6675f85c2eb0f062e956"
Missing separate debuginfo for /lib64/libdl.so.2
Try: zypper install -C
"debuginfo(build-id)=3e4f6bfee9fdf77ca975b77b8c325347d9228bb8"
Missing separate debuginfo for /lib64/librt.so.1
Try: zypper install -C
"debuginfo(build-id)=44612b93c19e6567318299411987b113d2387081"
Missing separate debuginfo for /lib64/libpthread.so.0
Try: zypper install -C
"debuginfo(build-id)=09dae90d04b1e2e43758ce58845f026b4085aec9"
[Thread debugging using libthread_db enabled]
Missing separate debuginfo for /usr/lib64/libblas.so.3
Try: zypper install -C
"debuginfo(build-id)=685e344cfea9180ba1557a81cf584d7b1fe62eb4"
Missing separate debuginfo for /usr/lib64/liblapack.so.3
Try: zypper install -C
"debuginfo(build-id)=9f4fafa64bbde4ad346f3791ffaf394daf297424"
Missing separate debuginfo for /lib64/libm.so.6
Try: zypper install -C
"debuginfo(build-id)=e05f2e72f47391363a03eff3cde10ad4c007c045"
Missing separate debuginfo for /lib64/libc.so.6
Try: zypper install -C
"debuginfo(build-id)=469835eb7eeb4aa3f653537c36a72810e01fb602"
Missing separate debuginfo for /lib64/libgcc_s.so.1
Try: zypper install -C
"debuginfo(build-id)=fe7c25bfb3e605f9d6c1cb00b3c5f96ed95be6e5"
Missing separate debuginfo for /usr/lib64/libgfortran.so.3
Try: zypper install -C
"debuginfo(build-id)=c141baedf020fb494dc72929af873205e06651f8"
Missing separate debuginfo for /usr/lib64/libquadmath.so.0
Try: zypper install -C
"debuginfo(build-id)=35220c888c4243e2e3e2f11347ceb12236d3bc21"
:-) G R O M A C S (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) VERSION 4.6.3 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
:-) /storage/home/taytyanne/bin/gromacs2/bin/g_tcaf_mpi (-:
Option Filename Type Description
------------------------------------------------------------
-f traj.trr Input Full precision trajectory: trr trj cpt
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96
pdb
-n index.ndx Input, Opt. Index file
-ot transcur.xvg Output, Opt. xvgr/xmgr file
-oa tcaf_all.xvg Output xvgr/xmgr file
-o tcaf.xvg Output xvgr/xmgr file
-of tcaf_fit.xvg Output xvgr/xmgr file
-oc tcaf_cub.xvg Output, Opt. xvgr/xmgr file
-ov visc_k.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]mol bool no Calculate TCAF of molecules
-[no]k34 bool no Also use k=(3,0,0) and k=(4,0,0)
-wt real 5 Exponential decay time for the TCAF fit weights
-acflen int -1 Length of the ACF, default is half the number of
frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0
indicates
none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac,
exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of
correlation functions
-beginfit real 0 Time where to begin the exponential fit of the
correlation function
-endfit real -1 Time where to end the exponential fit of the
correlation function, -1 is until the end
Reading file topol.tpr, VERSION 4.6.3 (double precision)
Reading file topol.tpr, VERSION 4.6.3 (double precision)
Group 0 ( System) has 30000 elements
Group 1 ( Other) has 30000 elements
Group 2 ( BMI) has 25000 elements
Group 3 ( ANI) has 5000 elements
Select a group: 0
Selected 0: 'System'
trn version: GMX_trn_file (double precision)
Last frame -1 time 0.000
Last frame -1 time 4646.000
Density = 1229.95 (kg/m^3)
Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaca258d2 in *__strlen_sse42 () from /lib64/libc.so.6*
(gdb) backtrace
#0 0x00002aaaaca258d2 in __strlen_sse42 () from /lib64/libc.so.6
#1 0x0000000000429689 in bputs (msg=0x7fffffffb610* "Not enough memory.
Failed to calloc ld elements of size ld for "*, len=0x7fffffffb5a8,
s=0xffffffff80000001 <Address 0xffffffff80000001 out of bounds>, fld=0)
at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/gmxlib/gmx_fatal.c:151
#2 0x000000000042a297 in parse_printf_args (fmt=0xf87208 "Not enough
memory. Failed to calloc %lld elements of size %lld for %s\n(called from
file %s, line %d)",
ap=0x7fffffffc610, msg=0x7fffffffb610 "Not enough memory. Failed to
calloc ld elements of size ld for ")
at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/gmxlib/gmx_fatal.c:472
#3 0x000000000042a3d1 in gmx_fatal (f_errno=12, file=0xf871c0
"/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/gmxlib/smalloc.c",
line=191,
fmt=0xf87208 "Not enough memory. Failed to calloc %lld elements of size
%lld for %s\n(called from file %s, line %d)")
at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/gmxlib/gmx_fatal.c:495
#4 0x0000000000426ea8 in save_calloc (name=0xf8438c "tcaf[k]",
file=0xf84340
"/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/tools/gmx_tcaf.c",
line=118,
nelem=18446744071562067969, elsize=4) at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/gmxlib/smalloc.c:191
#5 0x00000000004190c0 in process_tcaf (nframes=1, dt=-nan(0x400000),
nkc=4, tc=0x123e000, kfac=0x7fffffffcb40, rho=1229.94922, wt=5,
fn_trans=0x0,
fn_tca=0x123d760 "tcaf_all.xvg", fn_tc=0x123d7a0 "tcaf.xvg",
fn_tcf=0x123d7e0 "tcaf_fit.xvg", fn_cub=0x0, fn_vk=0x123d860 "visc_k.xvg",
oenv=0x123d5d0)
at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/tools/gmx_tcaf.c:118
#6 0x000000000041af6c in gmx_tcaf (argc=1, argv=0x7fffffffdae8) at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/tools/gmx_tcaf.c:489
#7 0x0000000000418867 in main (argc=1, argv=0x7fffffffdae8) at
/storage/home/taytyanne/src/gromacs/gromacs-4.6.3/src/tools/g_tcaf.c:52
(gdb) quit
A debugging session is active.
Inferior 1 [process 748478] will be killed.
Quit anyway? (y or n) y
>
There are two strange things showing up here: first, it complains about
"__strlen_sse42 () from /lib64/libc.so.6", which is not only a very well
known library, but also the "more /proc/cpuinfo" clearly states:
model name : Intel(R) Xeon(R) CPU E7- 8837 @ 2.67GHz
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl
xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2
ssse3 cx16 xtpr pdcm dca sse4_1 *sse4_2* x2apic popcnt lahf_lm ida arat epb
dtherm tpr_shadow vnmi flexpriority ept vpid
So, this processor does have sse4.2 instructions available. :(
Second, it complains about "Not enough memory. Failed to calloc ld elements
of size ld for", but this for gdb usage was executed out of the queue,
meaning it should have about 1 terabyte available!
Is this still worth a redmine issue? Or is there some sort of really stupid
mistake for which I should already feel ashamed?
Thanks a lot for any help,
Jones
On Fri, Dec 13, 2013 at 9:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On Fri, Dec 13, 2013 at 2:01 PM, Jones de Andrade <johannesrs at gmail.com
> >wrote:
>
> > Hi all.
> >
> > We are having some problem running g_tcaf here. It keeps yielding
> > "segmentation faults".
> >
> > We first thought it was because of the single-precision calculations
> > of the first run, or the exceedingly large trajectory file. Both were
> > changed for a second trial, which still yielded the same error.
> >
> > Also, we are aware of the similar error posted in this thread at this
> > mail-list:
> >
> > http://www.mail-archive.com/gmx-users@gromacs.org/msg54295.html
> >
> > Unfortunately, it seems to be a different issue.
> >
> > We are also writing a full trajectory file in the .trr file, as can be
> > seen below on the excerpt from the .mdp file below:
> >
> > dt = 0.002
> > nsteps = 100000
> > nstcomm = 1
> > nstxout = 0
> > nstvout = 10
> > nstfout = 10
> > nstlog = 10
> > nstenergy = 100
> > nstlist = 5
> >
> > The precise line our cluster script is trying to execute is:
> >
> > echo 0 | g_tcaf -f BMIm.AlCl4.md14.trr -s BMIm.AlCl4.md14.tpr -oa
> > BMIm.AlCl4.md14.all.xvg -o BMIm.AlCl4.md14.tcaf.xvg -of
> > BMIm.AlCl4.md14.fit.xvg -ov BMIm.AlCl4.md14.visc.xvg >& md14.tcaf.out
> >
> > The "echo 0" assures that the needed parameter is passed to g_tcaf. By
> > the way, in our last test the pbs parameters for resources request
> > were:
> >
> > #PBS -l ncpus=8
> > #PBS -l mem=16GB
> >
> > We know that it's pointless to ask for extra cpus, it's in there just
> > for a matter involving the machine architecture. But the 16 GB of
> > memory, despite available, are just our guess on how much it will
> > need. We also tested it out of the queue to be certain, but it still
> > fails at the same point.
> >
> > Does anybody has any suggestion please? I would be really helpful.
> >
> >
> Seg faults from analysis tools are usually bugs. Feel free to file a bug
> report on redmine.gromacs.org with the smallest test case possible that
> reproduces the problem. Running the command through a debugger like gdb
> would help to find the solution even faster.
>
> -Justin
>
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
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