Benchmarking LAMMPS

Hello list,

   I'd like to test LAMMPS for some benchmarking purposes. I'm particularly interested in the Rhodopsin protein benchmark [1]. I found that the input script references a file named data.rhodo, however I'm unable to find it in the LAMMPS webpage (or maybe I overlooked something). Googl'ing a bit, I found [2], but when I test it on my laptop it raises the error below, so I'm unsure whther this file is ok. Would you mind pointing out me where to find this file, please?

Thank you very much in advance.

# mpirun -np 8 ./lmp_mpi -in rhodopsin
LAMMPS (9 Dec 2014)
Reading data file ...
   orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
   2 by 2 by 2 MPI processor grid
   reading atoms ...
   32000 atoms
   reading velocities ...
   32000 velocities
   scanning bonds ...
   4 = max bonds/atom
   scanning angles ...
   8 = max angles/atom
   scanning dihedrals ...
   18 = max dihedrals/atom
   scanning impropers ...
   2 = max impropers/atom
   reading bonds ...
   27723 bonds
   reading angles ...
   40467 angles
   reading dihedrals ...
   56829 dihedrals
   reading impropers ...
   1034 impropers
Finding 1-2 1-3 1-4 neighbors ...
   4 = max # of 1-2 neighbors
   12 = max # of 1-3 neighbors
   24 = max # of 1-4 neighbors
   26 = max # of special neighbors
ERROR: Invalid fix style (../modify.cpp:762)

[1] http://lammps.sandia.gov/bench.html#rhodo
[2] https://code.google.com/p/lammps-hppi/source/browse/trunk/bench/data.rhodo?r=12

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Hello list,

   I'd like to test LAMMPS for some benchmarking purposes. I'm
particularly interested in the Rhodopsin protein benchmark [1]. I found
that the input script references a file named data.rhodo, however I'm
unable to find it in the LAMMPS webpage (or maybe I overlooked
something). Googl'ing a bit, I found [2], but when I test it on my

it is in the LAMMPS source distribution in the bench folder.

laptop it raises the error below, so I'm unsure whther this file is ok.
Would you mind pointing out me where to find this file, please?

the error is not due to the missing file, but due to a LAMMPS binary
that is missing features required by the input. most likely the RIGID
package. you can identify the offending input line by using the flag:
-echo screen
and then compare to the documentation where there is an error or an
additional requirement.

axel.

Hello Axel,

Hello list,

    I'd like to test LAMMPS for some benchmarking purposes. I'm
particularly interested in the Rhodopsin protein benchmark [1]. I found
that the input script references a file named data.rhodo, however I'm
unable to find it in the LAMMPS webpage (or maybe I overlooked
something). Googl'ing a bit, I found [2], but when I test it on my

it is in the LAMMPS source distribution in the bench folder.

   ah, great! I only google'd for lammps benchmark and I didn't notice that the package itself contained the benchs :wink:

laptop it raises the error below, so I'm unsure whther this file is ok.
Would you mind pointing out me where to find this file, please?

the error is not due to the missing file, but due to a LAMMPS binary
that is missing features required by the input. most likely the RIGID
package. you can identify the offending input line by using the flag:
-echo screen
and then compare to the documentation where there is an error or an
additional requirement.

   ok, I've rerun the application and I got this additional info on the screen:

fix 1 all shake 0.0001 5 0 m 1.0 a 232
ERROR: Invalid fix style (../modify.cpp:762)

   After googling a bit I found [1] and I enabled asphere, user-cg-cmm, kspace and molecule, but still not luck. The binary rejects to execute. What I'm missing to execute this benchmark?

Thank you!

[1] https://cmg.soton.ac.uk/community/wiki/support/HPC_Molecular_Dynamics_on_Emerald

axel.

Thank you very much in advance.

# mpirun -np 8 ./lmp_mpi -in rhodopsin
LAMMPS (9 Dec 2014)
Reading data file ...
    orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
    2 by 2 by 2 MPI processor grid
    reading atoms ...
    32000 atoms
    reading velocities ...
    32000 velocities
    scanning bonds ...
    4 = max bonds/atom
    scanning angles ...
    8 = max angles/atom
    scanning dihedrals ...
    18 = max dihedrals/atom
    scanning impropers ...
    2 = max impropers/atom
    reading bonds ...
    27723 bonds
    reading angles ...
    40467 angles
    reading dihedrals ...
    56829 dihedrals
    reading impropers ...
    1034 impropers
Finding 1-2 1-3 1-4 neighbors ...
    4 = max # of 1-2 neighbors
    12 = max # of 1-3 neighbors
    24 = max # of 1-4 neighbors
    26 = max # of special neighbors
ERROR: Invalid fix style (../modify.cpp:762)

[1] http://lammps.sandia.gov/bench.html#rhodo
[2]
https://code.google.com/p/lammps-hppi/source/browse/trunk/bench/data.rhodo?r=12

WARNING / LEGAL TEXT: This message is intended only for the use of the
individual or entity to which it is addressed and may contain
information which is privileged, confidential, proprietary, or exempt
from disclosure under applicable law. If you are not the intended
recipient or the person responsible for delivering the message to the
intended recipient, you are strictly prohibited from disclosing,
distributing, copying, or in any way using this message. If you have
received this communication in error, please notify the sender and
destroy and delete any copies you may have received.

http://www.bsc.es/disclaimer

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   ok, I've rerun the application and I got this additional info on the
screen:

fix 1 all shake 0.0001 5 0 m 1.0 a 232
ERROR: Invalid fix style (../modify.cpp:762)

   After googling a bit I found [1] and I enabled asphere, user-cg-cmm,
kspace and molecule, but still not luck. The binary rejects to execute.
What I'm missing to execute this benchmark?

[email protected]...:~/lammps/src$ find . -name '*shake*'
./USER-CUDA/fix_shake_cuda.cpp
./USER-CUDA/fix_shake_cuda.h
./RIGID/fix_shake.h
./RIGID/fix_shake.cpp

so, a "make yes-rigid" should help. Don't forget to recompile afterwards.

P