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
