Hi Zheyong,
Congratulations on your paper acceptance.
I have read them closely and found that they are really helpful for me.
I will do some tests using my data. If there is a problem, I am happy to give
you feedback if I may.
With best wishes,
Liang
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
________________________________
From: gpumd-bounce@xxxxxxxxxxxxx <gpumd-bounce@xxxxxxxxxxxxx> on behalf of
Bruce Fan <brucenju@xxxxxxxxx>
Sent: 06 October 2021 19:38:28
To: gpumd@xxxxxxxxxxxxx
Subject: [gpumd] Re: Compiling errors for the GPUMD code with NEP updates
Hello Liang,
I would like to tell you that there have been important improvements for the
NEP potential.
I first released GPUMD-v2.6, which corresponds to this published paper:
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.104.104309
Later, I released GPUMD-v2.7, which corresponds to this preprint:
https://arxiv.org/abs/2109.10643
In GPUMD-v2.7, the fitting accuracy for multi-component systems is
significantly improved.
Today, I have finished adding a feature to the master version of GPUMD, which
allows training with a mini-batch. This version has not been released yet, but
I will probably not change it any more. Here is a tutorial using the latest
master version:
https://github.com/brucefan1983/GPUMD/blob/master/examples/nep/PbTe_Fan_2021/train/nep_tutorial.ipynb
Using this version, you should be able to train a NEP potential with your large
training set (with 43162 structures). You can choose an appropriate batch size
such as 500.
Zheyong
On Wed, Sep 1, 2021 at 8:07 PM Yuan, Liang
<Liang.Yuan@xxxxxxxxxxxxxxx<mailto:Liang.Yuan@xxxxxxxxxxxxxxx>> wrote:
Hi Zheyong,
Thanks very much for the updates.
I am in the process of testing the GPUMD+NEP methods.
I will contact you with more details if there is trouble.
Thank you again for consistently providing me help.
With best regards,
Liang
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
________________________________
From: gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>
<gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>> on behalf of
Bruce Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
Sent: 31 August 2021 23:18
To: gpumd@xxxxxxxxxxxxx<mailto:gpumd@xxxxxxxxxxxxx>
Subject: [gpumd] Re: Compiling errors for the GPUMD code with NEP updates
Hello,
If you still have this memory problem, you can try to use this code
(https://github.com/brucefan1983/GPUMD/tree/master/tools/nep_related/train2train_plus_test)
to reduce the size of the training set.
See the beginning of the source file main.cpp (from the link above) for the
usage of the code.
My experience is that a training set with about 1000 structures is sufficient.
In your test above, you have 43162 structures with 9322992 atoms in total,
which is too much for GPUMD. Perhaps you have saved the full trajectories of
some AIMD runs?
As I mentioned in the previous email, if you want more suggestions, please
present more details about your calculations.
Zheyong
On Tue, Aug 10, 2021 at 6:11 AM Yuan, Liang
<Liang.Yuan@xxxxxxxxxxxxxxx<mailto:Liang.Yuan@xxxxxxxxxxxxxxx>> wrote:
Hello Zheyong,
Thank you very much for pointing out this error, but I have another more
serious problem.
The size of the dataset that I want to train is about 40000 (configurations).
An error shows "out of memory".
I would like to see if you can help on this issue.
Thanks very much!
The full information of the error is:
(base) liang@GPUWORKSTATION:~/code/GPUMD$ src/nep < examples/input_nep.txt
***************************************************************
* Welcome to use GPUMD *
* (Graphics Processing Units Molecular Dynamics) *
* Developing Version *
* This is the nep executable *
* Author: *
* Zheyong Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
*
***************************************************************
---------------------------------------------------------------
GPU information:
---------------------------------------------------------------
Device id: 0
Device name: NVIDIA TITAN Xp
Compute capability: 6.1
Amount of global memory: 11.9079 GB
Amount of constant memory: 64 KB
Maximum grid size: 2147483647 65535 65535
Maximum block size: 1024 1024 64
Number of SMs: 30
Maximum amount of shared memory per block: 48 KB
Maximum amount of shared memory per SM: 96 KB
Maximum number of registers per block: 64 K
Maximum number of registers per SM: 64 K
Maximum number of threads per block: 1024
Maximum number of threads per SM: 2048
---------------------------------------------------------------
Run simulation for 'examples/nep/mgo'.
---------------------------------------------------------------
---------------------------------------------------------------
Started reading nep.in<http://nep.in>.
---------------------------------------------------------------
radial cutoff = 6 A.
angular cutoff = 4 A.
n_max_radial = 12.
n_max_angular = 6.
l_max = 4.
ANN = 41-40-1.
number of parameters to be optimized = 1721.
regularization = 0.05, 0.05.
population_size = 50.
maximum_generation = 100000.
---------------------------------------------------------------
Started reading train.in<http://train.in>.
---------------------------------------------------------------
Number of configurations = 43162.
Total number of atoms = 9322992.
Number of atoms in the largest configuration = 216.
Number of configurations having virial = 43162.
Radial descriptor with a cutoff of 6 A:
Minimum number of neighbors for one atom = 79.
Maximum number of neighbors for one atom = 93.
Angular descriptor with a cutoff of 4 A:
Minimum number of neighbors for one atom = 21.
Maximum number of neighbors for one atom = 29.
CUDA Error:
File: ./utilities/gpu_vector.cuh
Line: 83
Error code: 2
Error text: out of memory
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
________________________________
From: gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>
<gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>> on behalf of
Bruce Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
Sent: 07 August 2021 21:37
To: gpumd@xxxxxxxxxxxxx<mailto:gpumd@xxxxxxxxxxxxx>
Subject: [gpumd] Re: Compiling errors for the GPUMD code with NEP updates
You have another problem in the xyz.in<http://xyz.in> input file:
This NEP potential for PbTe has a radial cutoff distance of 8 A, and you set
the initial neighbor list cutoff to 5 A only. This will definitely cause
problems. You can set the initial neighbor list cutoff to 9 A, and (optionally)
use the following command within each "run" in the run.in<http://run.in> input
file:
neighbor 1.0 # enable neighbor list updating with a skin distance of 1 A
By default, GPUMD does not update the neighbor list at all.
Suggestion: It is very important to read through the whole manual before using
GPUMD. Fortunately, this will only take a couple of days.
Zheyong
On Sun, Aug 8, 2021 at 12:23 AM Bruce Fan
<brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>> wrote:
For the NEP potential, use atomic number as the type in the first column of
xyz.in<http://xyz.in>.
I will add this to manual soon.
Zheyong
Yuan, Liang <Liang.Yuan@xxxxxxxxxxxxxxx<mailto:Liang.Yuan@xxxxxxxxxxxxxxx>> 于
2021年8月7日周六 18:51写道：
Hi Zheyong,
Thank you so much for your time.
I found that there are no examples of testing the NEP.
Therefore I prepared the two files (xyz.in<http://xyz.in> and
run.in<http://run.in>) for PbTe with nep potential in
/GPUMD/potentials/nep/PbTe_Fan_2021.txt.
But there is an error "Failed to open
examples/gpumd/a_pbte_gpumd_test/atomic_number.in<http://atomic_number.in>!"
It seems that there should be a file named
"atomic_number.in<http://atomic_number.in>" when run the MD with NEP.
I attached the xyz.in<http://xyz.in> and run.in<http://run.in> alongside this
email, and full information of the error is:
(base) liang@GPUWORKSTATION:~/code/GPUMD$ gpumd < examples/input_gpumd.txt
***************************************************************
* Welcome to use GPUMD *
* (Graphics Processing Units Molecular Dynamics) *
* Version 2.5.1 *
* This is the gpumd executable *
* Authors: *
* Zheyong Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
*
* Alexander J. Gabourie
<gabourie@xxxxxxxxxxxx<mailto:gabourie@xxxxxxxxxxxx>> *
* Ville Vierimaa *
* Mikko Ervasti *
* Ari Harju *
***************************************************************
---------------------------------------------------------------
Compiling options:
---------------------------------------------------------------
DEBUG is off: Use different PRNG seeds for different runs.
---------------------------------------------------------------
GPU information:
---------------------------------------------------------------
Device id: 0
Device name: NVIDIA TITAN Xp
Compute capability: 6.1
Amount of global memory: 11.9079 GB
Amount of constant memory: 64 KB
Maximum grid size: 2147483647 65535 65535
Maximum block size: 1024 1024 64
Number of SMs: 30
Maximum amount of shared memory per block: 48 KB
Maximum amount of shared memory per SM: 96 KB
Maximum number of registers per block: 64 K
Maximum number of registers per SM: 64 K
Maximum number of threads per block: 1024
Maximum number of threads per SM: 2048
---------------------------------------------------------------
Run simulation for 'examples/gpumd/a_pbte_gpumd_test'.
---------------------------------------------------------------
---------------------------------------------------------------
Started initializing positions and related parameters.
---------------------------------------------------------------
Number of atoms is 512.
Maximum number of neighbors is 1024.
Initial cutoff for neighbor list is 5 A.
Use orthogonal box.
Do not specify initial velocities here.
Have no grouping method.
Box lengths are
Lx = 2.5816400528e+01 A
Ly = 2.5816400528e+01 A
Lz = 2.5816400528e+01 A
Use periodic boundary conditions along x.
Use periodic boundary conditions along y.
Use periodic boundary conditions along z.
There are 2 atom types.
256 atoms of type 0.
256 atoms of type 1.
---------------------------------------------------------------
Finished initializing positions and related parameters.
---------------------------------------------------------------
---------------------------------------------------------------
Started executing the commands in run.in<http://run.in>.
---------------------------------------------------------------
Use the NEP potential.
radial cutoff = 8 A.
angular cutoff = 4 A.
n_max_radial = 12.
n_max_angular = 6.
l_max = 4.
ANN = 41-40-1.
Failed to open
examples/gpumd/a_pbte_gpumd_test/atomic_number.in<http://atomic_number.in>!
No such file or directory
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
________________________________
From: gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>
<gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>> on behalf of
Bruce Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
Sent: 06 August 2021 22:39:14
To: gpumd@xxxxxxxxxxxxx<mailto:gpumd@xxxxxxxxxxxxx>
Subject: [gpumd] Re: Compiling errors for the GPUMD code with NEP updates
To prepare for the train.in<http://train.in> file, you need to read the
document (https://gpumd.zheyongfan.org/index.php/The_train.in_input_file) and
write some code to generate it by yourself. This reflects the philosophy of
GPUMD: we assume that the user is a good programmer :-)
Zheyong
On Sat, Aug 7, 2021 at 4:21 AM Yuan, Liang
<Liang.Yuan@xxxxxxxxxxxxxxx<mailto:Liang.Yuan@xxxxxxxxxxxxxxx>> wrote:
Dear Zheyong,
Thank you so much for your help.
Yes, the error is related to my GCC as I successfully installed the code on
another workstation with a newer ubuntu system.
Now I can run "src/nep < examples/input_nep.txt". I expect that the input
training data for silicon is stored in the file "train.in<http://train.in>"(?)
May I ask, to produce it from VASP output, do I have some script?
With best regards,
Liang
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
________________________________
From: gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>
<gpumd-bounce@xxxxxxxxxxxxx<mailto:gpumd-bounce@xxxxxxxxxxxxx>> on behalf of
Bruce Fan <brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>>
Sent: 06 August 2021 21:49
To: gpumd@xxxxxxxxxxxxx<mailto:gpumd@xxxxxxxxxxxxx>
Subject: [gpumd] Re: Compiling errors for the GPUMD code with NEP updates
Another hint: perhaps you can also try to change the GCC optimization level in
the makefile (within the src/ folder):
CFLAGS = -std=c++11 -O3 -arch=sm_35
to
CFLAGS = -std=c++11 -O2 -arch=sm_35
Zheyong
On Sat, Aug 7, 2021 at 3:43 AM Bruce Fan
<brucenju@xxxxxxxxx<mailto:brucenju@xxxxxxxxx>> wrote:
Hi Liang,
Thanks for reporting this issue. I believe it is due to the GCC version. I
have found similar questions from the github repo of tensorflow. You can read
it and try to find some clue for the solution (might be just changing to use an
older GCC):
https://github.com/tensorflow/tensorflow/issues/10220
You can also try to build GPUMD in other machines with CUDA to see if it has
the same problem.
Anyway, welcome to post further questions if you cannot solve them.
Zheyong
On Sat, Aug 7, 2021 at 3:25 AM Yuan, Liang
<Liang.Yuan@xxxxxxxxxxxxxxx<mailto:Liang.Yuan@xxxxxxxxxxxxxxx>> wrote:
Hello Zheyong,
I read your paper (arXiv:2107.08119<https://arxiv.org/abs/2107.08119>) with
exceptional interest, which integrates neural network potential with molecular
dynamics within the GPUMD code.
It is an exciting update that comes out after a long wait.
There is just one little question which I will likely need your suggestions. I
found errors when compiling the code, and I attached them at the end of this
email. May I ask if you can help to figure what is going wrong?
Another related question about the neural network potential is how to prepare
the training dataset from VASP output?
Thank you very much for your help.
With best regards,
Liang
--------------
Liang Yuan
Bayerisches Geoinstitut
Universitätsstraße 30, 95447 Bayreuth, Germany
https://www.bgi.uni-bayreuth.de/?page=4&lng=en&mode=s&id=342
My Linux workstation information:
gcc --version:
gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
nvcc --version:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2017 NVIDIA Corporation
Built on Fri_Nov__3_21:07:56_CDT_2017
Cuda compilation tools, release 9.1, V9.1.85
The full information of the errors are:
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c main_gpumd/main.cu<http://main.cu> -o
main_gpumd/main.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
main_gpumd/velocity.cu<http://velocity.cu> -o main_gpumd/velocity.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c main_gpumd/run.cu<http://run.cu> -o
main_gpumd/run.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
minimize/minimizer_sd.cu<http://minimizer_sd.cu> -o minimize/minimizer_sd.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
minimize/minimizer.cu<http://minimizer.cu> -o minimize/minimizer.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
minimize/minimize.cu<http://minimize.cu> -o minimize/minimize.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble.cu<http://ensemble.cu> -o integrate/ensemble.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/integrate.cu<http://integrate.cu> -o integrate/integrate.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble_lan.cu<http://ensemble_lan.cu> -o integrate/ensemble_lan.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble_nve.cu<http://ensemble_nve.cu> -o integrate/ensemble_nve.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble_ber.cu<http://ensemble_ber.cu> -o integrate/ensemble_ber.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble_bdp.cu<http://ensemble_bdp.cu> -o integrate/ensemble_bdp.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
integrate/ensemble_nhc.cu<http://ensemble_nhc.cu> -o integrate/ensemble_nhc.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/tersoff1989.cu<http://tersoff1989.cu> -o force/tersoff1989.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/force.cu<http://force.cu> -o
force/force.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/nep.cu<http://nep.cu> -o
force/nep.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/vashishta.cu<http://vashishta.cu> -o force/vashishta.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/potential.cu<http://potential.cu> -o force/potential.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/fcp.cu<http://fcp.cu> -o
force/fcp.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/force_constant.cu<http://force_constant.cu> -o force/force_constant.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/sw.cu<http://sw.cu> -o force/sw.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/lj.cu<http://lj.cu> -o force/lj.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/tersoff1988.cu<http://tersoff1988.cu> -o force/tersoff1988.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/tersoff_mini.cu<http://tersoff_mini.cu> -o force/tersoff_mini.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
force/rebo_mos2.cu<http://rebo_mos2.cu> -o force/rebo_mos2.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/validate.cu<http://validate.cu>
-o force/validate.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/ri.cu<http://ri.cu> -o force/ri.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/limt.cu<http://limt.cu> -o
force/limt.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c force/eam.cu<http://eam.cu> -o
force/eam.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/cvac.cu<http://cvac.cu> -o
measure/cvac.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/compute_heat.cu<http://compute_heat.cu> -o measure/compute_heat.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/hnemd_kappa.cu<http://hnemd_kappa.cu> -o measure/hnemd_kappa.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/parse_utilities.cu<http://parse_utilities.cu> -o
measure/parse_utilities.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_restart.cu<http://dump_restart.cu> -o measure/dump_restart.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/dos.cu<http://dos.cu> -o
measure/dos.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_velocity.cu<http://dump_velocity.cu> -o measure/dump_velocity.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_thermo.cu<http://dump_thermo.cu> -o measure/dump_thermo.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/measure.cu<http://measure.cu>
-o measure/measure.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/modal_analysis.cu<http://modal_analysis.cu> -o measure/modal_analysis.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/shc_harmonic.cu<http://shc_harmonic.cu> -o measure/shc_harmonic.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/hac.cu<http://hac.cu> -o
measure/hac.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_force.cu<http://dump_force.cu> -o measure/dump_force.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_position.cu<http://dump_position.cu> -o measure/dump_position.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/sdc.cu<http://sdc.cu> -o
measure/sdc.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
measure/dump_netcdf.cu<http://dump_netcdf.cu> -o measure/dump_netcdf.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/shc.cu<http://shc.cu> -o
measure/shc.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c measure/compute.cu<http://compute.cu>
-o measure/compute.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/neighbor_ON1.cu -o
model/neighbor_ON1.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/neighbor.cu<http://neighbor.cu>
-o model/neighbor.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/read_xyz.cu<http://read_xyz.cu>
-o model/read_xyz.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/box.cu<http://box.cu> -o
model/box.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/group.cu<http://group.cu> -o
model/group.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c model/neighbor_ON2.cu -o
model/neighbor_ON2.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
utilities/cusolver_wrapper.cu<http://cusolver_wrapper.cu> -o
utilities/cusolver_wrapper.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c utilities/error.cu<http://error.cu> -o
utilities/error.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
utilities/read_file.cu<http://read_file.cu> -o utilities/read_file.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
utilities/main_common.cu<http://main_common.cu> -o utilities/main_common.o
nvcc main_gpumd/main.o main_gpumd/velocity.o main_gpumd/run.o
minimize/minimizer_sd.o minimize/minimizer.o minimize/minimize.o
integrate/ensemble.o integrate/integrate.o integrate/ensemble_lan.o
integrate/ensemble_nve.o integrate/ensemble_ber.o integrate/ensemble_bdp.o
integrate/ensemble_nhc.o force/tersoff1989.o force/force.o force/nep.o
force/vashishta.o force/potential.o force/fcp.o force/force_constant.o
force/sw.o force/lj.o force/tersoff1988.o force/tersoff_mini.o
force/rebo_mos2.o force/validate.o force/ri.o force/limt.o force/eam.o
measure/cvac.o measure/compute_heat.o measure/hnemd_kappa.o
measure/parse_utilities.o measure/dump_restart.o measure/dos.o
measure/dump_velocity.o measure/dump_thermo.o measure/measure.o
measure/modal_analysis.o measure/shc_harmonic.o measure/hac.o
measure/dump_force.o measure/dump_position.o measure/sdc.o
measure/dump_netcdf.o measure/shc.o measure/compute.o model/neighbor_ON1.o
model/neighbor.o model/read_xyz.o model/box.o model/group.o
model/neighbor_ON2.o utilities/cusolver_wrapper.o utilities/error.o
utilities/read_file.o utilities/main_common.o -o gpumd -lcublas -lcusolver
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
main_phonon/main_phonon.cu<http://main_phonon.cu> -o main_phonon/main_phonon.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
main_phonon/hessian.cu<http://hessian.cu> -o main_phonon/hessian.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c
main_phonon/phonon.cu<http://phonon.cu> -o main_phonon/phonon.o
nvcc main_phonon/main_phonon.o main_phonon/hessian.o main_phonon/phonon.o
minimize/minimizer_sd.o minimize/minimizer.o minimize/minimize.o
force/tersoff1989.o force/force.o force/nep.o force/vashishta.o
force/potential.o force/fcp.o force/force_constant.o force/sw.o force/lj.o
force/tersoff1988.o force/tersoff_mini.o force/rebo_mos2.o force/validate.o
force/ri.o force/limt.o force/eam.o model/neighbor_ON1.o model/neighbor.o
model/read_xyz.o model/box.o model/group.o model/neighbor_ON2.o
utilities/cusolver_wrapper.o utilities/error.o utilities/read_file.o
utilities/main_common.o -o phonon -lcublas -lcusolver
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c main_nep/nep.cu<http://nep.cu> -o
main_nep/nep.o
nvcc -std=c++11 -O3 -arch=sm_35 -I./ -c main_nep/fitness.cu<http://fitness.cu>
-o main_nep/fitness.o
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9220): error: argument
of type "const void *" is incompatible with parameter of type "const float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9231): error: argument
of type "const void *" is incompatible with parameter of type "const float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9244): error: argument
of type "const void *" is incompatible with parameter of type "const double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9255): error: argument
of type "const void *" is incompatible with parameter of type "const double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9268): error: argument
of type "const void *" is incompatible with parameter of type "const float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9279): error: argument
of type "const void *" is incompatible with parameter of type "const float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9292): error: argument
of type "const void *" is incompatible with parameter of type "const double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9303): error: argument
of type "const void *" is incompatible with parameter of type "const double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9316): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9327): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9340): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9352): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9365): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9376): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9389): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9401): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9410): error: argument
of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9419): error: argument
of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9428): error: argument
of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9437): error: argument
of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9445): error: argument
of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9454): error: argument
of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9463): error: argument
of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9472): error: argument
of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9481): error: argument
of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9490): error: argument
of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9499): error: argument
of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9508): error: argument
of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9517): error: argument
of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9526): error: argument
of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9535): error: argument
of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512fintrin.h(9544): error: argument
of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(55): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(63): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(73): error: argument
of type "const void *" is incompatible with parameter of type "const long long
*"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(81): error: argument
of type "const void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(91): error: argument
of type "void *" is incompatible with parameter of type "const long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(100): error: argument
of type "void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(109): error: argument
of type "void *" is incompatible with parameter of type "const long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(117): error: argument
of type "void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(127): error: argument
of type "void *" is incompatible with parameter of type "const long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(136): error: argument
of type "void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(145): error: argument
of type "void *" is incompatible with parameter of type "const long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512pfintrin.h(153): error: argument
of type "void *" is incompatible with parameter of type "const int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10799): error:
argument of type "const void *" is incompatible with parameter of type "const
float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10811): error:
argument of type "const void *" is incompatible with parameter of type "const
float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10823): error:
argument of type "const void *" is incompatible with parameter of type "const
double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10835): error:
argument of type "const void *" is incompatible with parameter of type "const
double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10847): error:
argument of type "const void *" is incompatible with parameter of type "const
float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10859): error:
argument of type "const void *" is incompatible with parameter of type "const
float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10871): error:
argument of type "const void *" is incompatible with parameter of type "const
double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10883): error:
argument of type "const void *" is incompatible with parameter of type "const
double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10895): error:
argument of type "const void *" is incompatible with parameter of type "const
int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10907): error:
argument of type "const void *" is incompatible with parameter of type "const
int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10919): error:
argument of type "const void *" is incompatible with parameter of type "const
long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10931): error:
argument of type "const void *" is incompatible with parameter of type "const
long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10943): error:
argument of type "const void *" is incompatible with parameter of type "const
int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10955): error:
argument of type "const void *" is incompatible with parameter of type "const
int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10967): error:
argument of type "const void *" is incompatible with parameter of type "const
long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10979): error:
argument of type "const void *" is incompatible with parameter of type "const
long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(10989): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11000): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11009): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11020): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11029): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11040): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11049): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11060): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11069): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11080): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11089): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11100): error:
argument of type "void *" is incompatible with parameter of type "float *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11109): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11120): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11129): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11140): error:
argument of type "void *" is incompatible with parameter of type "double *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11149): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11160): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11169): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11180): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11189): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11200): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11209): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11220): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11229): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11240): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11249): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11260): error:
argument of type "void *" is incompatible with parameter of type "int *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11269): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11280): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11289): error:
argument of type "void *" is incompatible with parameter of type "long long *"
/usr/lib/gcc/x86_64-linux-gnu/5/include/avx512vlintrin.h(11300): error:
argument of type "void *" is incompatible with parameter of type "long long *"
92 errors detected in the compilation of
"/tmp/tmpxft_00003047_00000000-6_fitness.cpp1.ii".
makefile:134: recipe for target 'main_nep/fitness.o' failed
make: *** [main_nep/fitness.o] Error 1
