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mrc-ide / sircovid-gpu-hack

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Add 2nd link #3

Open richfitz opened 4 years ago

richfitz commented 4 years ago 
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/cpp11/include" -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/dust/include"  -DHAVE_INLINE -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/cpp11/include" -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/dust/include"  -DHAVE_INLINE -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sirs.cpp -o sirs.o
nvcc -g -G --relocatable-device-code=true -I. -I/usr/share/R/include -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/cpp11/include" -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/dust/include" -Xcompiler -fPIC -x cu -c sirs_gpu.cu -o sirs_gpu.o
nvcc -g -G --relocatable-device-code=true -I. -I/usr/share/R/include -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/cpp11/include" -I"/home/jlees/R/x86_64-pc-linux-gnu-library/3.6/dust/include" -Xcompiler -fPIC  -dlink cpp11.o sirs.o sirs_gpu.o -o device_link.o -Xnvlink -L/usr/local/cuda-11.0/lib64 -lcudart -lcudadevrt -Xcompiler -fopenmp -L/usr/lib/R/lib -lR
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o prototype.so cpp11.o sirs.o sirs_gpu.o device_link.o -L/usr/local/cuda-11.0/lib64 -lcudart -lcudadevrt -fopenmp -L/usr/lib/R/lib -lR
richfitz commented 4 years ago

on the raplab we get:

g++ -std=gnu++11 -I"$R_HOME/R/include" -DNDEBUG  -I'$R_LIB_HOME/cpp11/include' -I'$R_LIB_HOME/dust/include' -I/usr/local/include  -DHAVE_INLINE -fopenmp -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"$R_HOME/R/include" -DNDEBUG  -I'$R_LIB_HOME/cpp11/include' -I'$R_LIB_HOME/dust/include' -I/usr/local/include  -DHAVE_INLINE -fopenmp -fpic  -g -O2  -c sirs.cpp -o sirs.o
nvcc -O2 -I. -I$R_HOME/R/include -I'$R_LIB_HOME/cpp11/include' -I'$R_LIB_HOME/dust/include' -Xcompiler -fPIC -x cu -c sirs_gpu.cu -o sirs_gpu.o
g++ -std=gnu++11 -shared -L$R_HOME/R/lib -L$R_HOME/R/lib -Wl,-rpath,$R_HOME/R/lib -o prototype.so cpp11.o sirs.o sirs_gpu.o -lcudart -fopenmp -L$R_HOME/R/lib -lR