diff options
Diffstat (limited to '005-fix_cuda_thrust_include.patch')
| -rw-r--r-- | 005-fix_cuda_thrust_include.patch | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/005-fix_cuda_thrust_include.patch b/005-fix_cuda_thrust_include.patch new file mode 100644 index 000000000000..1870755c2f0c --- /dev/null +++ b/005-fix_cuda_thrust_include.patch @@ -0,0 +1,76 @@ +# Author: Caspar van Leeuwen (SURF) +# FSL includes thrust headers by doing #include <device_vector.h> +# and then include -I$CUDA_ROOT/include/thrust +# This results in errors like +# /sw/arch/Debian10/EB_production/2019/software/CUDA/10.1.243/include/cuda_runtime_api.h(7397): +# error: identifier "UINT_MAX" is undefined +# This is normally defined in the standard C header 'limits.h'. +# However, by doing -I$CUDA_ROOT/include/thrust, the limits.h from Thrust is picked up instead! +# According to the Thrust docs, includes should be done as #include <thrust/device_vector.h> +# This way, -I$CUDA_ROOT/include is sufficient, and the limits.h from thrust +# no longer erroneously gets picked up. +diff -Nru a/fsl/src/fdt/CUDA/diffmodels.cuh fsl/src/fdt/CUDA/diffmodels.cuh +--- a/fsl/src/fdt/CUDA/diffmodels.cuh 2020-06-09 20:41:17.117128671 +0200 ++++ b/fsl/src/fdt/CUDA/diffmodels.cuh 2020-06-09 20:42:44.045211731 +0200 +@@ -66,7 +66,7 @@ + University, to negotiate a licence. Contact details are: + <a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind2006%26L%3DFSL%26E%3Dbase64%26P%3D3480627%26B%3D------%253D_Part_434001_1485233425.1591892113317%26T%3Dtext%252Fx-patch%3B%2520name%3D%2522FSL-6.0.2_thrust.patch%2522%26N%3DFSL-6.0.2_thrust.patch%26attachment%3Dq%26XSS%3D3" target="_parent" >[log in to unmask]</a> quoting Reference Project 9564, FSL.*/ + +-#include <device_vector.h> ++#include <thrust/device_vector.h> + + void fit_PVM_single( //INPUT + const vector<ColumnVector> datam_vec, +diff -Nru a/fsl/src/fdt/CUDA/runmcmc.cu fsl/src/fdt/CUDA/runmcmc.cu +--- a/fsl/src/fdt/CUDA/runmcmc.cu 2020-06-09 20:41:17.101128655 +0200 ++++ b/fsl/src/fdt/CUDA/runmcmc.cu 2020-06-09 20:43:13.649240030 +0200 +@@ -71,8 +71,8 @@ + #include "runmcmc_kernels.cu" + #include "sync_check.h" + +-#include <host_vector.h> +-#include <device_vector.h> ++#include <thrust/host_vector.h> ++#include <thrust/device_vector.h> + + #include <time.h> + #include <sys/time.h> +diff -Nru a/fsl/src/fdt/CUDA/xfibres_gpu.cu fsl/src/fdt/CUDA/xfibres_gpu.cu +--- a/fsl/src/fdt/CUDA/xfibres_gpu.cu 2020-06-09 20:41:17.117128671 +0200 ++++ b/fsl/src/fdt/CUDA/xfibres_gpu.cu 2020-06-09 20:44:00.621284957 +0200 +@@ -76,8 +76,8 @@ + #include "samples.h" + #include "options.h" + +-#include <host_vector.h> +-#include <device_vector.h> ++#include <thrust/host_vector.h> ++#include <thrust/device_vector.h> + + #include <time.h> + #include <sys/time.h> +diff -Nru a/fsl/src/fdt/CUDA/xfibres_gpu.cuh fsl/src/fdt/CUDA/xfibres_gpu.cuh +--- a/fsl/src/fdt/CUDA/xfibres_gpu.cuh 2020-06-09 20:41:17.113128667 +0200 ++++ b/fsl/src/fdt/CUDA/xfibres_gpu.cuh 2020-06-09 20:43:38.469263769 +0200 +@@ -67,8 +67,8 @@ + <a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind2006%26L%3DFSL%26E%3Dbase64%26P%3D3480627%26B%3D------%253D_Part_434001_1485233425.1591892113317%26T%3Dtext%252Fx-patch%3B%2520name%3D%2522FSL-6.0.2_thrust.patch%2522%26N%3DFSL-6.0.2_thrust.patch%26attachment%3Dq%26XSS%3D3" target="_parent" >[log in to unmask]</a> quoting Reference Project 9564, FSL.*/ + + #include "newimage/newimageall.h" +-#include <host_vector.h> +-#include <device_vector.h> ++#include <thrust/host_vector.h> ++#include <thrust/device_vector.h> + + #include "fibre_gpu.h" + #include <curand_kernel.h> +--- a/fsl/src/fdt/Makefile 2020-08-25 21:32:15.316740340 +0200 ++++ b/fsl/src/fdt/Makefile 2020-08-25 21:34:28.163670755 +0200 +@@ -171,7 +171,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${EDDYCOMBINEOBJS} ${DLIBS} + + ${LIBBEDPOSTX_CUDA}: +- ${NVCC} --shared --compiler-options '-fPIC' -o CUDA/libbedpostx_cuda.so CUDA/init_gpu.cu CUDA/samples.cu CUDA/diffmodels.cu CUDA/runmcmc.cu CUDA/xfibres_gpu.cu -O3 ${GENCODE_FLAGS} -lcudart -lcuda -lcurand -I. -L${LIB_CUDA} -L${LIB_CUDA}/stubs -ICUDA/options -I${INC_NEWMAT} -I${FSLDIR}/include -I${INC_BOOST} -I${INC_CUDA} -I${INC_CUDA}/thrust -maxrregcount=64 ++ ${NVCC} --shared --compiler-options '-fPIC' -o CUDA/libbedpostx_cuda.so CUDA/init_gpu.cu CUDA/samples.cu CUDA/diffmodels.cu CUDA/runmcmc.cu CUDA/xfibres_gpu.cu -O3 ${GENCODE_FLAGS} -lcudart -lcuda -lcurand -I. -L${LIB_CUDA} -L${LIB_CUDA}/stubs -ICUDA/options -I${INC_NEWMAT} -I${FSLDIR}/include -I${INC_BOOST} -I${INC_CUDA} -I${INC_CUDA} -maxrregcount=64 + @if [ ! -d ${FSLDEVDIR}/lib/ ] ; then ${MKDIR} ${FSLDEVDIR}/lib ; fi + ${CP} -rf CUDA/libbedpostx_cuda.so ${FSLDEVDIR}/lib + |