[gmx-users] mdrun no error, but hangs no results

[Mark Abraham]

Perhaps you need a less prehistoric compiler. Or the affinity-setting bug
fix in 4.6.3. Or both.
On Jul 17, 2013 6:25 PM, "Shi, Yu (shiy4)" <shiy4 at mail.uc.edu> wrote:

> Dear gmx-users,
>
> My problem is weird.
> My mdrun worked well using the old  serial version 4.5.5 (about two years
> ago). And I have these top, ndx, mdp, and gro files.
> Basing on those old files, for the serial 4.6.2, the grompp works through,
> resulting the .tpr file successfully.
> After that when I make the mdrun,
>  mdrun -v -s em-nv.tpr -deffnm ss
> it only shows:
> Reading file em-nv.tpr, VERSION 4.6.2 (double precision)
> Using 8 MPI threads
> Killed
> and there is no further processing. Later, it is killed.
>
> Also, using cmake my installation process works well, so does anyone meet
> this problem before?
>
>
> And part of the logfile is:
> Log file opened on Wed Jul 17 12:17:30 2013
> Host: opt-login03.osc.edu  pid: 32177  nodeid: 0  nnodes:  1
> Gromacs version:    VERSION 4.6.2
> Precision:          double
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     disabled
> GPU support:        disabled
> invsqrt routine:    gmx_software_invsqrt(x)
> CPU acceleration:   SSE2
> FFT library:        fftw-3.3-sse2
> Large file support: enabled
> RDTSCP usage:       enabled
> Built on:           Wed Jul 17 10:51:22 EDT 2013
> Built by:           ucn1118 at opt-login03.osc.edu [CMAKE]
> Build OS/arch:      Linux 2.6.18-308.11.1.el5 x86_64
> Build CPU vendor:   AuthenticAMD
> Build CPU brand:    Dual-Core AMD Opteron(tm) Processor 8218
> Build CPU family:   15   Model: 65   Stepping: 2
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr pse
> rdtscp sse2 sse3
> C compiler:         /usr/bin/cc GNU cc (GCC) 4.1.2 20080704 (Red Hat
> 4.1.2-48)
> C compiler flags:   -msse2    -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
> -fomit-frame-pointer -funroll-all-loops  -O3 -DNDEBUG
> .
> .
> .
> .
> Initializing Domain Decomposition on 8 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Using 0 separate PME nodes, as there are too few total
>  nodes for efficient splitting
> Optimizing the DD grid for 8 cells with a minimum initial size of 0.000 nm
> Domain decomposition grid 8 x 1 x 1, separate PME nodes 0
> PME domain decomposition: 8 x 1 x 1
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Using 8 MPI threads
>
> Detecting CPU-specific acceleration.
> Present hardware specification:
> Vendor: AuthenticAMD
> Brand:  Dual-Core AMD Opteron(tm) Processor 8218
> Family: 15  Model: 65  Stepping:  2
> Features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr pse rdtscp sse2 sse3
> Acceleration most likely to fit this hardware: SSE2
> Acceleration selected at GROMACS compile time: SSE2
>
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G.
> Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
>
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