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View Code? Open in Web Editor NEWBoris Computational Spintronics
Home Page: https://boris-spintronics.uk
License: GNU General Public License v3.0
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boris2's Issues
GPU select
Hi,
I would like to suggest that the user should be able to choose the GPU on which the calculations will be performed.
Regards,
Mateusz
Spherical shell
Hi, do you have a spherical shell option in Boris?
Like you do have the one Shape.ellipsoid. But I am not sure if you have an option for Shape.shell or anything like that?
Kind Regards
Compiling on Linux
Hi,
I'm trying to compile Boris on linux. For my sanity and the sake of reproducibility and portability, I'm using docker to compile with the following Dockerfile:
FROM nvidia/cuda:12.0.1-devel-ubuntu20.04
RUN DEBIAN_FRONTEND=noninteractive apt update && \
apt-get -qq install \
wget \
build-essential \
libomp-dev \
libtbb-dev \
python-dev \
git
RUN wget https://www.fftw.org/fftw-3.3.10.tar.gz && \
tar -xf fftw-3.3.10.tar.gz && \
cd fftw-3.3.10 && \
./configure && \
make && \
make install
RUN git clone https://github.com/SerbanL/Boris2 /src
CMD cd /src && \
make configure arch=80 sprec=1 python=3.8 cuda=12.0 && \
make compile -j 16
make installI run with docker build -t boris . && docker run -it --rm --gpus all --name borisc boris. I get the following result :
mkdir -p Boris/Boris_o
mkdir -p Boris/Boris_cuo
Configured for -arch=sm_80 and SINGLEPRECISION = 1. Python version 3.8. CUDA Toolkit version 12.0.
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/SMElastic.cpp -o Boris/Boris_o/SMElastic.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DiffEq_Iterate.cpp -o Boris/Boris_o/DiffEq_Iterate.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/TMRCUDA.cpp -o Boris/Boris_o/TMRCUDA.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/STransportCUDA.cpp -o Boris/Boris_o/STransportCUDA.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DipoleDipoleTFunc_Self.cpp -o Boris/Boris_o/DipoleDipoleTFunc_Self.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DemagTFunc_L.cpp -o Boris/Boris_o/DemagTFunc_L.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/Atom_Demag_N.cpp -o Boris/Boris_o/Atom_Demag_N.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DiffEqAFMCUDA.cpp -o Boris/Boris_o/DiffEqAFMCUDA.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DWRunTimeFit.cpp -o Boris/Boris_o/DWRunTimeFit.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DiffEqFMCUDA.cpp -o Boris/Boris_o/DiffEqFMCUDA.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/ModulesCUDA.cpp -o Boris/Boris_o/ModulesCUDA.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/SimFiles.cpp -o Boris/Boris_o/SimFiles.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/SurfExchange.cpp -o Boris/Boris_o/SurfExchange.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/DiffEqFM_Evals_RK4.cpp -o Boris/Boris_o/DiffEqFM_Evals_RK4.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/Demag.cpp -o Boris/Boris_o/Demag.o
g++ -I/usr/local/cuda-12.0/targets/x86_64-linux/include/ -c -Ofast -std=c++17 -I/usr/include/python3.8/ -IBorisLib -IBorisCUDALib -fopenmp Boris/STransport_Charge.cpp -o Boris/Boris_o/STransport_Charge.o
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/Simulation.h:36,
from Boris/SimFiles.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/SMElastic.h:3,
from Boris/SMElastic.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DiffEq.h:3,
from Boris/DiffEq_Iterate.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DipoleDipoleTFunc.h:3,
from Boris/DipoleDipoleTFunc_Self.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DemagTFunc.h:3,
from Boris/DemagTFunc_L.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/STransport.h:3,
from Boris/STransport_Charge.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DWRunTimeFit.h:5,
from Boris/DWRunTimeFit.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/SimFiles.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [makefile:78: Boris/Boris_o/SMElastic.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/Atom_Demag_N.h:3,
from Boris/Atom_Demag_N.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
make: *** [makefile:78: Boris/Boris_o/DiffEq_Iterate.o] Error 1
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/DemagTFunc_L.o] Error 1
make: *** [makefile:78: Boris/Boris_o/STransport_Charge.o] Error 1
make: *** [makefile:78: Boris/Boris_o/DipoleDipoleTFunc_Self.o] Error 1
make: *** [makefile:78: Boris/Boris_o/DWRunTimeFit.o] Error 1
make: *** [makefile:78: Boris/Boris_o/Atom_Demag_N.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DiffEq.h:3,
from Boris/DiffEqFM.h:3,
from Boris/DiffEqFM_Evals_RK4.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/DiffEqFM_Evals_RK4.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/Demag.h:3,
from Boris/Demag.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/Demag.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/SurfExchange.h:3,
from Boris/SurfExchange.cpp:2:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/SurfExchange.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/TMR.h:3,
from Boris/TMRCUDA.cpp:8:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/STransport.h:3,
from Boris/STransportCUDA.cpp:8:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/TMRCUDA.o] Error 1
make: *** [makefile:78: Boris/Boris_o/STransportCUDA.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DiffEq.h:3,
from Boris/DiffEqFM.h:3,
from Boris/DiffEqFMCUDA.cpp:7:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/DiffEqFMCUDA.o] Error 1
In file included from BorisLib/BLib_Funcs.h:10,
from BorisLib/BorisLib.h:15,
from Boris/DiffEq.h:3,
from Boris/DiffEqAFM.h:3,
from Boris/DiffEqAFMCUDA.cpp:7:
BorisLib/Funcs_Files_Linux.h:11:10: fatal error: X11/Xlib.h: No such file or directory
11 | #include <X11/Xlib.h>
| ^~~~~~~~~~~~
compilation terminated.
make: *** [makefile:78: Boris/Boris_o/DiffEqAFMCUDA.o] Error 1
I tried installing xorg but it doesn't change a thing.
Could not load embedded Python wrapper file : /src/EmbeddedPythonWrapper.py
Hi :),
I don't seem to be able to run a script:
./boris -s ./script.py
Script server running.
Console activated...
To open manual use the manual command.
Could not load embedded Python wrapper file : /src/EmbeddedPythonWrapper.py
Started Python script : ./script.py
Finished Python script : ./script.py
Terminated
Here is the inside of script.py directly from the manual page 17
from NetSocks import NSClient
import matplotlib.pyplot as plt
import numpy as np
ns = NSClient(); ns.configure(True)
########################################
#This is based on Exercise 8.3, done entirely using a Python script
Py = ns.Ferromagnet([160e-9, 80e-9, 10e-9], [5e-9, 5e-9, 5e-9])
Py.modules(['Zeeman', 'demag', 'exchange', 'transport'])
#set amr percentage of 2%
Py.param.amr = 2.0
#amr loop angle (deg.)
direction_deg = 5
ns.setangle(90, 180.0 + direction_deg)
#set electrodes at x-axis ends with a 1 mV potential drop
ns.setdefaultelectrodes()
ns.setpotential(1e-3)
#save applied field (A/m) and resistance (Ohms)
ns.setsavedata('amr_rawdata.txt', ['Ha', Py], ['R'])
#Run hysteresis loop
ns.setode('LLGStatic', 'SDesc')
ns.Hpolar_seq(
[Py, [-100e3, 90, direction_deg, 100e3, 90, direction_deg, 200],
'mxh', 1e-6, 'step'])
ns.Hpolar_seq(
[Py, [100e3, 90, direction_deg, -100e3, 90, direction_deg, 200],
'mxh', 1e-6, 'step'])
########################################
#Plot loop
#load all columns from file (0, 1, 2, 3) into internal arrays (0, 1, 2, 4)
ns.dp_load('amr_rawdata.txt', [0, 1, 2, 3, 0, 1, 2, 4])
#get field strength along loop direction and save it in internal array 3
ns.dp_dotprod(0, np.cos(np.radians(direction_deg)),
np.sin(np.radians(direction_deg)), 0, 3)
#save field strength and resistance in processed file, then plot it here
ns.dp_save('amr_loop.txt', [3, 4])
amr_data = ns.Get_Data_Columns('amr_loop.txt', [0, 1])
plt.axes(xlabel = 'H (kA/m)', ylabel = 'R (Ohms)', title = 'AMR Loop')
plt.plot(np.array(amr_data[0])/1e3, amr_data[1])
plt.show()What could be the issue ?
Consider Splitting this repo
Hi :),
The current breakdown of the disk usage of this repo is as follows (I used dust):
18M ┌── Boris_o │ ░░░████ │ 3%
33M ┌─┴ Boris │ ███████ │ 6%
8.9M │ ┌── Porter Comparison │ ░░░░░░░░▒▒██ │ 2%
8.9M │ ├── Spin Transport │ ░░░░░░░░▒▒██ │ 2%
19M │ ┌─┴ muMAG5 │ ░░░░░░░░████ │ 4%
11M │ │ ┌── ufsky_fm.bsm │ ░░░░░▒▒▒▒███ │ 2%
11M │ │ ┌─┴ High │ ░░░░░▒▒▒▒███ │ 2%
11M │ │ │ ┌── ufsky_fm.bsm │ ░░░░░▒▒▒▒███ │ 2%
11M │ │ ├─┴ Low │ ░░░░░▒▒▒▒███ │ 2%
11M │ │ │ ┌── ufsky_fm.bsm │ ░░░░░▒▒▒▒███ │ 2%
11M │ │ ├─┴ Medium │ ░░░░░▒▒▒▒███ │ 2%
35M │ ├─┴ UFSky_FM │ ░░░░░███████ │ 7%
61M ├─┴ BorisArticle │ ████████████ │ 11%
8.7M │ ┌── skyrmion_x3.out │ ░▒▓▓▓▓▓▓▓▓██ │ 2%
10.0M │ ├── skyrmion_x4.out │ ░▒▓▓▓▓▓▓▓▓██ │ 2%
10M │ ├── skyrmion_x6.out │ ░▒▓▓▓▓▓▓▓▓██ │ 2%
10M │ ├── skyrmion_x5.out │ ░▒▓▓▓▓▓▓▓▓██ │ 2%
50M │ ┌─┴ mumax3 │ ░▒██████████ │ 9%
59M │ ┌─┴ 2D │ ░███████████ │ 11%
64M ├─┴ MLConv Paper │ ████████████ │ 12%
8.7M │ ┌── BorisManual-v340.pdf │ ░░░░░░░░░░░██ │ 2%
8.3M │ │ ┌── Tutorial 29 │ ░░░▒▒▒▒▒▒▒▒██ │ 2%
8.6M │ │ ├── Tutorial 24 │ ░░░▒▒▒▒▒▒▒▒██ │ 2%
10.0M │ │ ├── Tutorial 23 │ ░░░▒▒▒▒▒▒▒▒██ │ 2%
52M │ ├─┴ Examples │ ░░░██████████ │ 10%
69M ├─┴ Manual │ █████████████ │ 13%
9.3M │ ┌── Boris │ ░░░░░░░░░░░░░██ │ 2%
8.3M │ │ ┌── Tutorial 29 │ ░░░▒▒▓▓▓▓▓▓▓▓██ │ 2%
8.6M │ │ ├── Tutorial 24 │ ░░░▒▒▓▓▓▓▓▓▓▓██ │ 2%
10.0M │ │ ├── Tutorial 23 │ ░░░▒▒▓▓▓▓▓▓▓▓██ │ 2%
52M │ │ ┌─┴ Examples │ ░░░▒▒██████████ │ 10%
60M │ ├─┴ Boris_Data │ ░░░████████████ │ 11%
79M ├─┴ BorisLin │ ███████████████ │ 15%
215M │ ┌── pack-6e2dba985484ef1466014b7238341112b0c5ecb1.pack│ ████████████████████████████████████████ │ 40%
215M │ ┌─┴ pack │ ████████████████████████████████████████ │ 40%
215M │ ┌─┴ objects │ ████████████████████████████████████████ │ 40%
215M ├─┴ .git │ ████████████████████████████████████████ │ 40%
534M ┌─┴ . │█████████████████████████████████████████████████████████████████████████████████████████████████ │ 100%
Many git tools will time out for such a large repo. Also only a small part of it is source code. I think it would be possible to move the Manual, Papers, etc to different repos. What do you think ?
Asynchronous data saving
Hi,
I have found one more issue - I think in Boris is missing asynchronous data saving procedure -
I noticed that when Boris needs to save a lot of data on the disk (and there is a connection problem or the disk is busy), calculations are stopped. Is writing files in Boris asynchronous (e.g. writing files on disk is queued in RAM and a separate process is responsible for writing them on disk)? If not, maybe it is worth to do it?
Boris2 in Docker
Hello together,
currently, I am trying to make Boris2 run in a docker container, since it is supposed to be used in a simulation plattform that automatizes simulations and the analysis.
The issue I am facing is that Boris2 seems to not compile correctly?
On a system using a GPU that has an Ampere architecture Boris is compiled in docker with the arch setting being 80.
Afterwards, Boris starts successfully.
If I use a different setup, with a GPU that has a Volta or Turing architecture and using arch=70 the container is build successfully, without errors. Same concerning the compiling process of Boris.
Unfortunately, Boris2 will not start in this configuration, if docker is forwarding GPUs. There is no error message.
If Boris2 is started without forwarding GPUs to the container, Boris2 starts.
Here is the docker file I am using:
FROM nvidia/cuda:11.4.3-devel-ubuntu20.04
WORKDIR /app
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ="Europe/Berlin"
RUN apt-get update
RUN apt-get install build-essential -y
RUN apt-get install libomp-dev -y
RUN apt-get install libtbb-dev -y
RUN apt-get install wget -y
RUN apt-get install libx11-dev -y
RUN apt-get install nano
RUN apt-get install python3.8-dev -y
RUN apt-get install python3-pip -y
RUN apt-get install git -y
RUN python3.8 -m pip install --upgrade pip
RUN pip3 install matplotlib numpy notebook
RUN wget www.fftw.org/fftw-3.3.10.tar.gz
RUN tar -xzf fftw-3.3.10.tar.gz
RUN cd fftw-3.3.10
RUN chmod +x fftw-3.3.10/configure
RUN bash fftw-3.3.10/configure
RUN make
RUN make install
RUN git clone https://github.com/SerbanL/Boris2.git /Boris2
RUN cd /Boris2
RUN make -C /Boris2 configure arch=70 sprec=1 python=3.8 cuda=11.4
RUN make -C /Boris2 compile -j 30
RUN make -C /Boris2 install
RUN chmod ugo+rwx /Boris2/BorisLin
RUN cp -r /Boris2/BorisPythonScripts/* /Boris2/
WORKDIR /Boris2/BorisPythonScripts
ENV PATH=${PATH}:/Boris2/BorisLin
RUN cp -r /Boris2/src/NetSocks /usr/lib/python3.8/
Thank you for your help
Yours faithfully
Tim Vogel
Bugs Status
NOT SOLVED:
Saving simulation file sometimes sets dT to zero (to a floating point error). I've only seen it happen with CUDA enabled. Very rare, no apparent cause found yet.
LIKELY SOLVED:
Using a python script may result in program hanging if issuing a flood of commands.
If heat solver diverges (e.g. due to too high a time step), and at least 1 material parameter has a temperature dependence, when in CUDA mode out of gpu memory errors can result requiring a program restart. I seem to have fixed it using extra checks on Temperature when getting updated parameter values, but I don't understand why this happens without the checks so the solution seems like a hack. Not happy with this!
SOLVED:
Drag and drop simulation file sometimes crashes program. Found bad conversion function - I'm certain that was the problem, so consider this solved but keep an eye on this for a while.
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