[gmx-users] Segfault using Verlet-list with Gromacs 4.6.5 - MPI only

[Sébastien Côté]

Dear gmx developers, 
I am trying to use Verlet list for MD simulations using MPI parallelization only with Gromacs 4.6.5. However, I am getting a segfault during the initialization of my system before any time step is executed. The simulation runs perfectly when I am either using Group list or Gromacs 4.6.1 instead. 
Is their a problem known for verlet list in Gromacs 4.6.5 for some architecture?
Thanks for your help,
Sebastien 
Below, you can find more specific information:
The error message thrown by the system:
starting mdrun 'bla'100 steps,      0.2 ps.[node-c3-42:09559] *** Process received signal ***[node-c3-42:09559] Signal: Segmentation fault (11)[node-c3-42:09559] Signal code:  (128)[node-c3-42:09559] Failing at address: (nil)[node-c3-42:09559] [ 0] /lib64/libpthread.so.0() [0x3a05c0f500][node-c3-42:09559] [ 1] /home/apps/Logiciels/gromacs/gromacs-4.6.5-no-plumed/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x2223) [0x7f676aedc983][node-c3-42:09559] [ 2] /home/apps/Logiciels/gromacs/gromacs-4.6.5-no-plumed/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) [0x7f676aea9901][node-c3-42:09559] [ 3] /home/apps/intel/composerxe-2011.4.191/mkl/../compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x7f6768380323][node-c3-42:09559] *** End of error message ***[node-c3-42:09554] *** Process received signal ***
The log file finishes as follow:
Center of mass motion removal mode is LinearWe have the following groups for center of mass motion removal:  0:  Protein  1:  non-Protein
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++G. Bussi, D. Donadio and M. ParrinelloCanonical sampling through velocity rescalingJ. Chem. Phys. 126 (2007) pp. 014101-------- -------- --- Thank You --- -------- --------
System info in the log file:
Log file opened on Mon Apr 14 18:51:35 2014Host: node-c3-42  pid: 9551  nodeid: 0  nnodes:  12Gromacs version:    VERSION 4.6.5Precision:          singleMemory model:       64 bitMPI library:        MPIOpenMP support:     enabledGPU support:        disabledinvsqrt routine:    gmx_software_invsqrt(x)CPU acceleration:   SSE4.1FFT library:        MKLLarge file support: enabledRDTSCP usage:       enabledBuilt on:           Mon Apr 14 09:57:30 EDT 2014Built by:           rqchpbib at briaree1 [CMAKE]Build OS/arch:      Linux 2.6.32-71.el6.x86_64 x86_64Build CPU vendor:   GenuineIntelBuild CPU brand:    Intel(R) Xeon(R) CPU           X5650  @ 2.67GHzBuild CPU family:   6   Model: 44   Stepping: 2Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3C compiler:         /RQusagers/apps/intel/composerxe-2011.4.191/bin/intel64/icc Intel icc (ICC) 12.0.4 20110427C compiler flags:   -msse4.1    -mkl=sequential -std=gnu99 -Wall   -ip -funroll-all-loops  -O3 -DNDEBUGLinked with Intel MKL version 10.3.4.