LAMMPS PPPM Problem

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1

All,

I get following error message while trying to run Peptide example. I have done the compilation using GCC compiler. The problem appears to be related to FFTW. I have fftw-2.1.5.

PPPM initialization …

G vector = 0.268721

grid = 15 15 15

stencil order = 5

RMS precision = 4.86052e-05

brick FFT buffer size/proc = 10648 3375 5808

Setting up run …

[hpc:08465] *** Process received signal ***

[hpc:08465] Signal: Segmentation fault (11)

[hpc:08465] Signal code: (128)

[hpc:08465] Failing at address: (nil)

[hpc:08465] [ 0] /lib64/libpthread.so.0 [0x2b8fe64bbfb0]

[hpc:08465] [ 1] …/…/src/lmp_openmpi(_Z6fft_3dP12fftw_complexS0_iP11fft_plan_3d+0x1e) [0x59b1be]

[hpc:08465] [ 2] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS4PPPM7poissonEii+0x1f0) [0x81c030]

[hpc:08465] [ 3] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS4PPPM7computeEii+0x24a) [0x8204ba]

[hpc:08465] [ 4] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS6Verlet5setupEv+0x244) [0x875f74]

[hpc:08465] [ 5] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x4c7) [0x847fe7]

[hpc:08465] [ 6] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xda2) [0x6c0482]

[hpc:08465] [ 7] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x341) [0x6c1961]

[hpc:08465] [ 8] …/…/src/lmp_openmpi(main+0x4a) [0x6cc7ea]

[hpc:08465] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b8fe66e6b54]

[hpc:08465] [10] …/…/src/lmp_openmpi(__gxx_personality_v0+0x339) [0x47e529]

[hpc:08465] *** End of error message ***

Segmentation fault

Can you please tell me how can this be resolved?

Thanks & Regards,

Kaushik

HPC Administrator

2

All,

I get following error message while trying to run Peptide example. I have done the compilation using GCC compiler. The problem appears to be related to FFTW. I have fftw-2.1.5.

PPPM initialization …

G vector = 0.268721

grid = 15 15 15

stencil order = 5

RMS precision = 4.86052e-05

brick FFT buffer size/proc = 10648 3375 5808

Setting up run …

[hpc:08465] *** Process received signal ***

[hpc:08465] Signal: Segmentation fault (11)

[hpc:08465] Signal code: (128)

[hpc:08465] Failing at address: (nil)

[hpc:08465] [ 0] /lib64/libpthread.so.0 [0x2b8fe64bbfb0]

[hpc:08465] [ 1] …/…/src/lmp_openmpi(_Z6fft_3dP12fftw_complexS0_iP11fft_plan_3d+0x1e) [0x59b1be]

[hpc:08465] [ 2] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS4PPPM7poissonEii+0x1f0) [0x81c030]

[hpc:08465] [ 3] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS4PPPM7computeEii+0x24a) [0x8204ba]

[hpc:08465] [ 4] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS6Verlet5setupEv+0x244) [0x875f74]

[hpc:08465] [ 5] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x4c7) [0x847fe7]

[hpc:08465] [ 6] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0xda2) [0x6c0482]

[hpc:08465] [ 7] …/…/src/lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x341) [0x6c1961]

[hpc:08465] [ 8] …/…/src/lmp_openmpi(main+0x4a) [0x6cc7ea]

[hpc:08465] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b8fe66e6b54]

[hpc:08465] [10] …/…/src/lmp_openmpi(__gxx_personality_v0+0x339) [0x47e529]

[hpc:08465] *** End of error message ***

Segmentation fault

Can you please tell me how can this be resolved?

most likely you have a mismatch of single and double
precision, e.g. are linking a single precision fftw-2.x library
with a LAMMPS compile configured for double precision.

you can avoid this by linking to the proper library or
configuring LAMMPS to use the different precision,
or better yet, use fftw-3.x where it is not possible to
link the wrong precision library. or configure LAMMPS
to use the internal fft library via -DFFT_NONE, that
one will always be correct.

axel.