[geng]

Hi all,

I tried to install the GPU verison of spdyn. However, I failed to pass the test of REMD, while other tests passed. I confused whether the GPU spdyn cannot do REMD or my installation is not correct?

Best Regards,

Geng

 

[ckobayashi]

Hi Geng,

 

REMD in spdyn should work as well as cMD in GPU version.

Could you share error logs of the test of REMD?

 

Thank you.

 

Chigusa

[geng]

Sorry for so many messages.

I tried to use 4/8 parallel cpu cores. One GPU was used.

/Geng

[geng]

We now found that the GPU spdyn failed in REMD because of the cutoff : “Read Ctrl Energy: cutoff is not available with GPU”.

I do not understant this “cutoff”.

Best,

Geng

 

[geng]

Hi Chigusa,

<span style=”text-decoration: underline;”>The final report of test is</span>

Passed 0 / 10
Failed 0 / 10
Aborted 10 / 10

<span style=”text-decoration: underline;”>I then check the log file in tests-1.6.1/regression_test/test_remd_common/H-REMD_DIHED, and found </span>

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 45649 RUNNING AT g0001
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 45650 RUNNING AT g0001
= EXIT STATUS: 1
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 45651 RUNNING AT g0001
= KILLED BY SIGNAL: 9 (Killed)
=========================================================================

.

.

.

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 14 PID 45663 RUNNING AT g0001
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 15 PID 45664 RUNNING AT g0001
= EXIT STATUS: 1
===================================================================================

Thank you!

Best Regards,

Geng

[geng]

I tried again, and nothing was found in log file but

“/data/apps/intel/2019/compilers_and_libraries_2019.3.199/linux/mpi/intel64/bin/mpirun: line 103: 51908 Segmentation fault mpiexec.hydra “$@” 0<&0″

was shown in error file.

Best,

Geng

[tmori]

Could you try to execute spdyn in the subdirectory “./test_remd_common/H-REMD_DIHED”
without using “test_remd.py”?

For example, please type the following commands:
$ export OMP_NUM_THREADS=1
$ mpirun -np 8 /PATH_TO_GENESIS/bin/spdyn inp > test.log

If you could obtain output files, the problem might lie in the python script or command rather than GENESIS.

Bests,
Takaharu Mori

[geng]

The test.log file is empty, and I found “/data/apps/intel/2019/compilers_and_libraries_2019.3.199/linux/mpi/intel64/bin/mpirun: line 103: 68726 Segmentation fault mpiexec.hydra “$@” 0<&0′ in the slurm-55692.out file.

Best,

Geng

[geng]

Does it matter that I used the GPU card of V100?

Best Regards,

Geng

[tmori]

As shown in the user manual (p. 18 “Run the additional tests”),
there is an example command for GPU tests:

$ ./test.py “mpirun -np 8 ~/genesis/genesis-1.6.1/bin/spdyn” gpu

Did you successfully finish this test?

Bests,
Takaharu Mori

[geng]

Yes, we have successfully done the test.py.

I have successfully done the test_rpath.py, test_gamd.py and test_fep.py, but failed for test_remd.py.

Best,

Geng

[geng]

Does it matter that I used the GPU card of V100, which is not included in the manual (NVIDIA K20, K40, P100, TITAN V, GTX 1080, GTX 1080Ti, RTX 2080, RTX 2080Ti)

Best Regards,

Geng

[tmori]

I think in the regression tests for REMD, GPU version of spdyn is not available.
This is simply because we did not prepare such test options. We are sorry for the confusion.
Of course, you can perform REMD simulations with GPU spdyn.
Basically, GPGPU calculation in spdyn requires “electrostatic = PME” (not CUTOFF).

Best regards,
Takaharu Mori

[tmori]

For the REMD test using GPU version of spdyn,
“regression_test/test_remd_spdyn/T-REMD_RESPA” is available.
Please try this test set.

Thank you,
Takaharu Mori

[geng]

Thank you for your information.

I tried T-REMD_RESPA, and it passed.

Thank you.

Best,

Geng

[geng]

I can now run remd in gpu version. However, the GPU utilization rate is much low of 25-30%.

I run simulation with one GPU (V100) and 8 cores of CPU.  I tried with more cpu cores and less cpu cores, and these will lead to ever lower utilization rate of GPU.

Is it caused by the compilation, e.g. cuda version, intel compiler?

Do you have any suggestion for this? How do you compile Genesis?

Thank you very much!

Best,

Geng

[jwjung]

Dear Geng,

In GENESIS, we use GPU for real-space nonbonded interactions (van der Waals and electrostatic) while CPU is used for other parts (bond/angle/dihedral angle calculation and recprocal-space electrostatic). In fact, the performance of GPU is limited by CPU calculation of such parts and I guess it makes the low utilization of GPU.