Compiling on Linux

Question

Compiling on Linux

MathieuMoalic opened this issue 2 years ago · 2 comments

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 install

I 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.

Answer 1 · 2023-03-09T16:38:18.000Z

Hi Mathieu,

First, try to find if X11 is on your system: "find /usr/include/X11 -name Xlib.h"
If, not then install it: "sudo apt-get install libx11-dev"
Let me know if it works.

Serban

Answer 2 · 2023-03-09T19:10:35.000Z

This worked. Other changes I had to make:

python-dev -> python3.9-dev ( I think it's python2 if you don't specify the version)
g++ $(OBJ_DIR)/*.o $(CUOBJ_DIR)/*.o -fopenmp -lpython$(python) -ltbb -lfftw3 -lX11 -L/usr/local/cuda-$(cuda)/targets/x86_64-linux/lib/ -lcudart -lcufft -lcudadevrt -o BorisLin -> -o BorisLin2 because 'BorisLin' already exists and is a directory.

Here is a working Dockerfile:

FROM nvidia/cuda:12.0.1-devel-ubuntu20.04

RUN apt update && \
    DEBIAN_FRONTEND=noninteractive apt-get -qq install \
    wget \
    build-essential \
    libomp-dev \
    libtbb-dev \
    libx11-dev \
    python3.9-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=3.9 cuda=12.0 && \
    make compile -j 16 && \
    make install