[gmx-users] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472

Fri Jan 24 19:19:36 CET 2014

Please try setting GMX_DISTRIBUTABLE_BUILD=ON for CMake and see whether
that fixes the problem.

On Fri, Jan 24, 2014 at 6:18 PM, Thomas Schlesier <schlesi at uni-mainz.de>wrote:

> Hi all,
> 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:
> Illegal instruction
> 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
> Water Models
> 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:
> Intel:
> icc (ICC) 12.1.2 20111128
> Copyright (C) 1985-2011 Intel Corporation.  All rights reserved.
> and GNU:
> 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
> Precision:          single
> 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
> ssse3
> 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
> -DNDEBUG
>
> cmake-command for compilation (used for the last build):
> (here i'm using line breaks to make it easier to read):
>
> cmake
> -DCMAKE_C_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/gcc
> -DCMAKE_CXX_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/g++
> -DGMX_BUILD_OWN_FFTW=OFF
> -DCMAKE_INSTALL_PREFIX=/scrcluster/schlesi/bug465 -DBUILD_SHARED_LIBS=OFF
> -DGMX_PREFER_STATIC_LIBS=ON
> -DGMX_CPU_ACCELERATION=SSE4.1
> -DGMX_MPI_IN_PLACE=OFF
> -DGMX_OPENMP=OFF
> -DGMX_THREAD_MPI=OFF
> -DGMX_MPI=OFF
> -DGMX_FFT_LIBRARY=fftpack
> ..
> (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 limited).
> If someone needs more informations (or the core dumped file), just tell me.
>
> Greetings (and wish you a nice weekend)
> Thomas
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-- 
Teemu Murtola
<teemu.murtola at iki.fi>
+358 50 362 6829