Build error

[chenxuhao]

Hello,

I got this error when building:

~/work/DEDUKT/build$ make
[ 1%] Retrieving git version
[ 1%] Built target GET_GIT_VERSION
[ 3%] Building /home/cxh/work/DEDUKT/version.h
Building DIBELLA version 93504aa
[ 3%] Built target REPLACE_VERSION_H
[ 12%] Built target common
[ 14%] Built target fqreader
[ 16%] Built target loadfq_objs
[ 17%] Built target MPIType
[ 20%] Built target KmerObjects-32
[ 24%] Built target gpu_kmer
[ 25%] Built target readufx-4-32
[ 27%] Building CXX object kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/spmer_kmrCnt.cpp.o
In file included from /home/cxh/work/DEDUKT/kmercount/spmer_kmrCnt.h:13,
from /home/cxh/work/DEDUKT/kmercount/spmer_kmrCnt.cpp:11:
/home/cxh/work/DEDUKT/kmercount/common_gpu.h:4:10: fatal error: cuda_runtime_api.h: No such file or directory
#include <cuda_runtime_api.h>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/build.make:89: recipe for target 'kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/spmer_kmrCnt.cpp.o' failed
make[2]: *** [kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/spmer_kmrCnt.cpp.o] Error 1
CMakeFiles/Makefile2:467: recipe for target 'kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/all' failed
make[1]: *** [kmercount/CMakeFiles/kmermatch-4-32-NOUPC.dir/all] Error 2
Makefile:135: recipe for target 'all' failed
make: *** [all] Error 2

Any idea?

Thanks!

[zach-ucb]

I got the same error when compiling. I was able to resolve it and get the build process working again by:

1. Downgrading from CUDA 11.1 to CUDA 10.2.
2. Because of the way my environment is set up, adding an include_directories directive to CMakeLists.txt. On other systems, I think you may need to add $CUDA_HOME/include instead of the specific directory I added, or you may not need to add the directive at all.