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)" <sh...@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: ucn1...@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 --- -------- -------- > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
