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@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.
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