[gmx-users] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472
schlesi at uni-mainz.de
Fri Jan 24 18:45:25 CET 2014
I am having problems with GROMACS 4.6.5 and one type of CPU on our
cluster (other CPU-types make no problems). GROMACS was always compiled
on the master, which uses a different CPU-type (see below at the
beginning of the 'md.log'-file).
For the CPU type (partial output from 'cat /proc/cpuinfo'):
vendor_id : GenuineIntel
cpu family : 6
model : 23
model name : Intel(R) Xeon(R) CPU E5472 @ 3.00GHz
stepping : 6
cpu MHz : 3000.186
cache size : 6144 KB
'grompp' 'g_rdf' and 'pdb2gmx' all work fine, only 'mdrun' gives
problems (so I think only 'mdrun' is affected).
Error message is:
and i get a 'core dump'. (Didn't looked into the dumped file, since i
only know i can do this with 'gdb' but have absolute no idea how 'gdb'
works and for what i should look).
Last lines of the 'md.log' file before the crash (energy minimization of
a small water box with cut-offs):
Removing pbc first time
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
So, i get the impression, that the preparation for the simulation is
success full, and the crash happens when the actual simulation starts.
The same simulation works with gromacs 4.0.7 and 4.5.5 (on the same
machine). So I thought SSE4.1 or the internal MPI-stuff from gromacs
4.6.5 produces the problem.
So i compiled gromacs 4.6.5 with
-DGMX_CPU_ACCELERATION=SSE2 (or) None
and without any MPI support (and then running only a serial calculation).
Also tried for FFT the internal 'fftpack' (thought maybe the FFT part
might be the problem - for this i also ran the simulation without PME
and only plain cut-offs).
But the error still occurs in every case :(
I tried the compilation with two different compilers:
icc (ICC) 12.1.2 20111128
Copyright (C) 1985-2011 Intel Corporation. All rights reserved.
gcc (GCC) 4.6.4 20120511 (prerelease)
Copyright (C) 2011 Free Software Foundation, Inc.
but i makes no difference.
To give some more information:
Beginning of the 'md.log'-file:
Log file opened on Fri Jan 24 16:40:34 2014
Host: tc-3-12.local pid: 6755 nodeid: 0 nnodes: 1
Gromacs version: VERSION 4.6.5
Memory model: 64 bit
MPI library: none
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: SSE4.1
FFT library: fftpack (built-in)
Large file support: enabled
RDTSCP usage: enabled
Built on: Fr 24. Jan 16:26:42 CET 2014
Built by: schlesi at dirac.chemie.uni-mainz.de [CMAKE]
Build OS/arch: Linux 2.6.18-238.19.1.el5 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Build CPU family: 6 Model: 44 Stepping: 1
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
C compiler: /share/apps/gcc/gcc-4.6.4_20120511/bin/gcc GNU gcc
(GCC) 4.6.4 20120511 (prerelease)
C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
cmake-command for compilation (used for the last build):
(here i'm using line breaks to make it easier to read):
(Sidenote: the 'GMX_MPI_IN_PLACE' isn't used - cmake tells me this).
Till now i havn't tried to compile GROMACS on any of the problematic
machines, but i can try this on monday.
Has anyone any idea (for solving, or to better trace the error)? Since
i'm at the end with my knowledge (actually i'm quite happy that i came
so far, since about this 'hardcore' computer stuff my knowledge is very
If someone needs more informations (or the core dumped file), just tell me.
Greetings (and wish you a nice weekend)
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