cudaglmnet fails to compile

[PDDeane]

When I try to compile cudaglmnet, I get the following error sequence. I include outputs of ./configure and system information after the error log.

What gives? What's going wrong, and how to fix? I'm not an expert on configuration issues with CUDA/nvcc, so I haven't much of a clue here, and any pointers would be helpful.

Thanks!

Paul Deane

Starting after cloning sudaglmnet and cding to the installation directory:

sudo R CMD INSTALL ./

• installing to library ‘/usr/local/lib/R/site-library’
• installing source package ‘cudaglmnet’ ...
  ** using staged installation
  configure: checking for critical tools used by configure
  checking "environment variable COMPILER_BINDIR"... "COMPILER_BINDIR not set; using user's default path"
  checking "environment variable CUDA_HOME"... "CUDA_HOME not set; using default /usr/local/cuda"
  checking "environment variable CULA_HOME"... "CULA_HOME not set; using default /usr/local/cula"
  checking for /usr/local/cuda/bin/nvcc... yes
  "nvcc found"
  checking "whether this is the 64 bit linux version of CUDA"... checking for /usr/local/cuda/lib64/libcublas.so... yes
  "yes -- using /usr/local/cuda/lib64 for CUDA libs"
  "using -I/usr/share/R/include for R header files"
  "using -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n for R shared libraries"
  checking "whether this is the 64 bit version of CULA"... checking for /usr/local/cula/lib64/libcula.so... no
  checking for /usr/local/cula/lib64/libcula.dylib... no
  "no"
  checking "checking whether cula is present at all"... checking for /usr/local/cula/lib/libcula.so... no
  checking for /usr/local/cula/lib/libcula.dylib... no
  "cula is not installed"
  configure: determining host platform
  checking build system type... x86_64-unknown-linux-gnu
  checking host system type... x86_64-unknown-linux-gnu
  configure: creating ./config.status
  config.status: creating src/Makefile
  ** libs
  ** arch -
  /usr/local/cuda/bin/nvcc -O2 -shared -Xlinker -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n -L/usr/local/cuda/lib64 -lcublas main.o -o cudaglmnet.so
  nvcc fatal : Unknown option '-fopenmp'
  make: *** [Makefile:24: cudaglmnet.so] Error 1
  ERROR: compilation failed for package ‘cudaglmnet’
• removing ‘/usr/local/lib/R/site-library/cudaglmnet’
• restoring previous ‘/usr/local/lib/R/site-library/cudaglmnet’

SYSTEM INFORMATION

Description: Ubuntu 20.04 LTS
Release: 20.04
Codename: focal

GPU: NVIDIA GeForce RTX 3070
R version: 4.2.2 Patched (2022-11-10 r83330)

./configure
configure: checking for critical tools used by configure
checking "environment variable COMPILER_BINDIR"... "COMPILER_BINDIR not set; using user's default path"
checking "environment variable CUDA_HOME"... "using CUDA_HOME=/usr/local/cuda-12.0"
checking "environment variable CULA_HOME"... "CULA_HOME not set; using default /usr/local/cula"
checking for /usr/local/cuda-12.0/bin/nvcc... yes
"nvcc found"
checking "whether this is the 64 bit linux version of CUDA"... checking for /usr/local/cuda-12.0/lib64/libcublas.so... yes
"yes -- using /usr/local/cuda-12.0/lib64 for CUDA libs"
"using -I/usr/share/R/include for R header files"
"using -L/usr/local/R/lib -lR for R shared libraries"
checking "whether this is the 64 bit version of CULA"... checking for /usr/local/cula/lib64/libcula.so... no
checking for /usr/local/cula/lib64/libcula.dylib... no
"no"
checking "checking whether cula is present at all"... checking for /usr/local/cula/lib/libcula.so... no
checking for /usr/local/cula/lib/libcula.dylib... no
"cula is not installed"
configure: determining host platform
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makefile

/usr/local/cuda-12.0/bin/nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2022 NVIDIA Corporation
Built on Mon_Oct_24_19:12:58_PDT_2022
Cuda compilation tools, release 12.0, V12.0.76
Build cuda_12.0.r12.0/compiler.31968024_0

cat /usr/local/cuda-12.0/version.json
{
"cuda" : {
"name" : "CUDA SDK",
"version" : "12.0.20221203"
},
"cuda_cccl" : {
"name" : "CUDA C++ Core Compute Libraries",
"version" : "12.0.90"
},
"cuda_cudart" : {
"name" : "CUDA Runtime (cudart)",
"version" : "12.0.107"
},
"cuda_cuobjdump" : {
"name" : "cuobjdump",
"version" : "12.0.76"
},
"cuda_cupti" : {
"name" : "CUPTI",
"version" : "12.0.90"
},
"cuda_cuxxfilt" : {
"name" : "CUDA cu++ filt",
"version" : "12.0.76"
},
"cuda_demo_suite" : {
"name" : "CUDA Demo Suite",
"version" : "12.0.76"
},
"cuda_gdb" : {
"name" : "CUDA GDB",
"version" : "12.0.90"
},
"cuda_nsight" : {
"name" : "Nsight Eclipse Plugins",
"version" : "12.0.78"
},
"cuda_nvcc" : {
"name" : "CUDA NVCC",
"version" : "12.0.76"
},
"cuda_nvdisasm" : {
"name" : "CUDA nvdisasm",
"version" : "12.0.76"
},
"cuda_nvml_dev" : {
"name" : "CUDA NVML Headers",
"version" : "12.0.76"
},
"cuda_nvprof" : {
"name" : "CUDA nvprof",
"version" : "12.0.90"
},
"cuda_nvprune" : {
"name" : "CUDA nvprune",
"version" : "12.0.76"
},
"cuda_nvrtc" : {
"name" : "CUDA NVRTC",
"version" : "12.0.76"
},
"cuda_nvtx" : {
"name" : "CUDA NVTX",
"version" : "12.0.76"
},
"cuda_nvvp" : {
"name" : "CUDA NVVP",
"version" : "12.0.90"
},
"cuda_opencl" : {
"name" : "CUDA OpenCL",
"version" : "12.0.76"
},
"cuda_sanitizer_api" : {
"name" : "CUDA Compute Sanitizer API",
"version" : "12.0.90"
},
"libcublas" : {
"name" : "CUDA cuBLAS",
"version" : "12.0.1.189"
},
"libcufft" : {
"name" : "CUDA cuFFT",
"version" : "11.0.0.21"
},
"libcufile" : {
"name" : "GPUDirect Storage (cufile)",
"version" : "1.5.0.59"
},
"libcurand" : {
"name" : "CUDA cuRAND",
"version" : "10.3.1.50"
},
"libcusolver" : {
"name" : "CUDA cuSOLVER",
"version" : "11.4.2.57"
},
"libcusparse" : {
"name" : "CUDA cuSPARSE",
"version" : "12.0.0.76"
},
"libnpp" : {
"name" : "CUDA NPP",
"version" : "12.0.0.30"
},
"libnvjitlink" : {
"name" : "JIT Linker Library",
"version" : "12.0.76"
},
"libnvjpeg" : {
"name" : "CUDA nvJPEG",
"version" : "12.0.0.28"
},
"libnvvm_samples" : {
"name" : "NVVM Samples",
"version" : "12.0.94"
},
"nsight_compute" : {
"name" : "Nsight Compute",
"version" : "2022.4.0.15"
},
"nsight_systems" : {
"name" : "Nsight Systems",
"version" : "2022.4.2.18"
},
"nvidia_driver" : {
"name" : "NVIDIA Linux Driver",
"version" : "525.60.13"
},
"nvidia_fs" : {
"name" : "NVIDIA file-system",
"version" : "2.14.12"
}
}