Error in R package installation

[Filippo-Rambelli]

Dear ExaGeoStatCPP team,

I am attempting to install the ExaGeoStatCPP R package on our academic HPC cluster following the instructions in the ReadMe.

Because of the discussions in issue #48, I am using GCC 8.5.0. However, the installation currently fails with the following error:
`---------------------------------------- GSL
-- Checking for GSL with Version 2.7.1
Can't find GSL, Installing it instead ..
-- Fetching gsl v2.7.1 from https://ftp.gnu.org/gnu/gsl/gsl-2.7.1.tar.gz
[ 11%] Creating directories for 'gsl-populate'
[ 22%] Performing download step (download, verify and extract) for 'gsl-populate'
-- Downloading...
dst='/cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/GSL/gsl-subbuild/gsl-populate-prefix/src/gsl-2.7.1.tar.gz'
timeout='none'
inactivity timeout='none'
-- Using src='https://ftp.gnu.org/gnu/gsl/gsl-2.7.1.tar.gz'
CMake Error at gsl-subbuild/gsl-populate-prefix/src/gsl-populate-stamp/download-gsl-populate.cmake:170 (message):
Each download failed!

error: downloading 'https://ftp.gnu.org/gnu/gsl/gsl-2.7.1.tar.gz' failed
      status_code: 1
      status_string: "Unsupported protocol"
      log:
      --- LOG BEGIN ---
      Protocol "https" not supported or disabled in libcurl

Closing connection

      --- LOG END ---

make[2]: *** [CMakeFiles/gsl-populate.dir/build.make:100: gsl-populate-prefix/src/gsl-populate-stamp/gsl-populate-download] Error 1
make[1]: *** [CMakeFiles/Makefile2:83: CMakeFiles/gsl-populate.dir/all] Error 2
gmake: *** [Makefile:91: all] Error 2

CMake Error at installdir/_deps/CMAKE/share/cmake-3.28/Modules/FetchContent.cmake:1679 (message):
Build step for gsl failed: 2
Call Stack (most recent call first):
installdir/_deps/CMAKE/share/cmake-3.28/Modules/FetchContent.cmake:1819:EVAL:2 (__FetchContent_directPopulate)
installdir/_deps/CMAKE/share/cmake-3.28/Modules/FetchContent.cmake:1819 (cmake_language)
cmake/macros/BuildDependency.cmake:59 (FetchContent_Populate)
cmake/macros/ImportDependency.cmake:61 (BuildDependency)
cmake/ImportGSL.cmake:34 (ImportDependency)
CMakeLists.txt:150 (include)

-- Configuring incomplete, errors occurred!
gmake: Makefile: No such file or directory
gmake: *** No rule to make target 'Makefile'. Stop.
cp: cannot stat '/cluster/home/fabiopc/software/ExaGeoStatCPP/bin/src/libExaGeoStatCPP.so': No such file or directory
Failed: libExaGeoStatCPP.so -> src
** libs
make: Nothing to be done for 'all'.
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘ExaGeoStatCPP’ in library.dynam(lib, package, package.lib):
shared object ‘ExaGeoStatCPP.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/cluster/home/fabiopc/R/x86_64-pc-linux-gnu-library/4.3/ExaGeoStatCPP’`

It appears that the curl version available in the GCC 8.5.0 software stack does not support HTTPS.
Do you have any suggestions?
Thank you very much for your help.

[SAbdulah]

Hi @Filippo-Rambelli

This restriction likely comes from the cluster itself. ExaGeoStatCPP attempts to install all missing dependencies by automatically downloading and building them. You can either ask the cluster support team to enable this for you or manually install the dependencies listed in the README file and export their paths to your environment.

[Filippo-Rambelli]

Hi @SAbdulah, Many thanks for your reponse. I installed the required dependencies manually and I am currently getting this error:

/cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:102:45: note: in definition o f macro 'LOGGER_CONTROL' #define LOGGER_CONTROL(x, A, B, FUNC, ...) FUNC ^~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:110:24: note: in expansion of macro 'LOGGER_1' LOGGER_1(__VA_ARGS__), \ ^~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/src/predi ction/Prediction.cpp:166:9: note: in expansion of macr o 'LOGGER' LOGGER("\t---- Using Prediction Function MSPE ----") ^~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:84:46: note: suggested altern ative: 'set_union' oss << "\t\t " << std::fixed << std::setpreci sion(DEFAULT_PRECISION) << msg << std::endl; \ ^~~~~~~~ ~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:102:45: note: in definition o f macro 'LOGGER_CONTROL' #define LOGGER_CONTROL(x, A, B, FUNC, ...) FUNC ^~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:110:24: note: in expansion of macro 'LOGGER_1' LOGGER_1(__VA_ARGS__), \ ^~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/src/predi ction/Prediction.cpp:166:9: note: in expansion of macr o 'LOGGER' LOGGER("\t---- Using Prediction Function MSPE ----") ^~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:84:46: error: 'setprecision' is not a member of 'std' oss << "\t\t " << std::fixed << std::setpreci sion(DEFAULT_PRECISION) << msg << std::endl; \ ^~~~~~~~ ~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:102:45: note: in definition o f macro 'LOGGER_CONTROL' #define LOGGER_CONTROL(x, A, B, FUNC, ...) FUNC ^~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:110:24: note: in expansion of macro 'LOGGER_1' LOGGER_1(__VA_ARGS__), \ ^~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/src/predi ction/Prediction.cpp:194:13: note: in expansion of mac ro 'LOGGER' LOGGER("\t\t- Prediction value: " << avg_ pred_value[0]) ^~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:84:46: note: suggested altern ative: 'set_union' oss << "\t\t " << std::fixed << std::setpreci sion(DEFAULT_PRECISION) << msg << std::endl; \ ^~~~~~~~ ~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:102:45: note: in definition o f macro 'LOGGER_CONTROL' #define LOGGER_CONTROL(x, A, B, FUNC, ...) FUNC ^~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/incl ude/utilities/Logger.hpp:110:24: note: in expansion of macro 'LOGGER_1' LOGGER_1(__VA_ARGS__), \ ^~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/src/predi ction/Prediction.cpp:194:13: note: in expansion of mac ro 'LOGGER' LOGGER("\t\t- Prediction value: " << avg_ pred_value[0]) ^~~~~~ gmake[2]: *** [src/CMakeFiles/ExaGeoStatCPP.dir/build. make:216: src/CMakeFiles/ExaGeoStatCPP.dir/prediction/ Prediction.cpp.o] Error 1 gmake[1]: *** [CMakeFiles/Makefile2:513: src/CMakeFile s/ExaGeoStatCPP.dir/all] Error 2 gmake: *** [Makefile:136: all] Error 2 cp: cannot stat '/cluster/home/fabiopc/software/ExaGeo StatCPP/bin/src/libExaGeoStatCPP.so': No such file or directory Failed: libExaGeoStatCPP.so -> src

[alihakam830]

Hi @Filippo-Rambelli , can you inform us which GCC version do you use?

[Filippo-Rambelli]

Hi @alihakam830, I use GCC 8.5.0

[alihakam830]

Hi @Filippo-Rambelli ,
Could you upgrade it to GCC 10.2.0

[Filippo-Rambelli]

@alihakam830 the available options in our cluster are GCC 8.5.0, GCC 12.2.0 and GCC 13.2.0

[alihakam830]

@Filippo-Rambelli Could you kindly attempt the build using GCC 12.2.0?

[Filippo-Rambelli]

Hi @alihakam830, I tried with GCC 12.2.0 and I now get this error:

[ 55%] Building CXX object src/CMakeFiles/ExaGeoStatCPP.dir/linear-algebra-solvers/LinearAlgebraMethods.cpp.o [ 55%] Building CXX object src/CMakeFiles/ExaGeoStatCPP.dir/runtime-solver/concrete/StarpuRuntimeSolver.cpp.o [ 55%] Building CXX object src/CMakeFiles/ExaGeoStatCPP.dir/linear-algebra-solvers/concrete/chameleon/dst/ChameleonDST.cpp.o [ 56%] Building CXX object src/CMakeFiles/ExaGeoStatCPP.dir/runtime-solver/RuntimeSolverFactory.cpp.o In file included from /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas.h:39, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/linear-algebra-solvers/concrete/ChameleonHeaders.hpp:19, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/data-units/descriptor/ExaGeoStatDescriptor.hpp:20, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/data-units/DescriptorData.hpp:20, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/data-units/ExaGeoStatData.hpp:18, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/linear-algebra-solvers/LinearAlgebraMethods.hpp:30, from /cluster/home/fabiopc/software/ExaGeoStatCPP/inst/include/linear-algebra-solvers/concrete/chameleon/ChameleonImplementation.hpp:19, from /cluster/home/fabiopc/software/ExaGeoStatCPP/src/linear-algebra-solvers/concrete/chameleon/ChameleonImplementation.cpp:24: /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas/cblas.h:30:6: error: multiple definition of 'enum CBLAS_ORDER' 30 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102}; | ^~~~~~~~~~~ In file included from /cluster/home/fabiopc/software/ExaGeoStatCPP/src/linear-algebra-solvers/concrete/chameleon/ChameleonImplementation.cpp:22: /cluster/software/stacks/2024-06/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.2.0/openblas-0.3.24-eiewhivju2io7doutnqmhj7rmisarv4b/include/cblas.h:56:14: note: previous definition here 56 | typedef enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102} CBLAS_ORDER; | ^~~~~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas/cblas.h:31:6: error: multiple definition of 'enum CBLAS_TRANSPOSE' 31 | enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113}; | ^~~~~~~~~~~~~~~ /cluster/software/stacks/2024-06/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.2.0/openblas-0.3.24-eiewhivju2io7doutnqmhj7rmisarv4b/include/cblas.h:57:14: note: previous definition here 57 | typedef enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113, CblasConjNoTrans=114} CBLAS_TRANSPOSE; | ^~~~~~~~~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas/cblas.h:32:6: error: multiple definition of 'enum CBLAS_UPLO' 32 | enum CBLAS_UPLO {CblasUpper=121, CblasLower=122}; | ^~~~~~~~~~ /cluster/software/stacks/2024-06/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.2.0/openblas-0.3.24-eiewhivju2io7doutnqmhj7rmisarv4b/include/cblas.h:58:14: note: previous definition here 58 | typedef enum CBLAS_UPLO {CblasUpper=121, CblasLower=122} CBLAS_UPLO; | ^~~~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas/cblas.h:33:6: error: multiple definition of 'enum CBLAS_DIAG' 33 | enum CBLAS_DIAG {CblasNonUnit=131, CblasUnit=132}; | ^~~~~~~~~~ /cluster/software/stacks/2024-06/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.2.0/openblas-0.3.24-eiewhivju2io7doutnqmhj7rmisarv4b/include/cblas.h:59:14: note: previous definition here 59 | typedef enum CBLAS_DIAG {CblasNonUnit=131, CblasUnit=132} CBLAS_DIAG; | ^~~~~~~~~~ /cluster/home/fabiopc/software/ExaGeoStatCPP/installdir/_deps/CHAMELEON/include/coreblas/cblas.h:34:6: error: multiple definition of 'enum CBLAS_SIDE' 34 | enum CBLAS_SIDE {CblasLeft=141, CblasRight=142}; | ^~~~~~~~~~ /cluster/software/stacks/2024-06/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.2.0/openblas-0.3.24-eiewhivju2io7doutnqmhj7rmisarv4b/include/cblas.h:60:14: note: previous definition here 60 | typedef enum CBLAS_SIDE {CblasLeft=141, CblasRight=142} CBLAS_SIDE; | ^~~~~~~~~~ make[2]: *** [src/CMakeFiles/ExaGeoStatCPP.dir/build.make:174: src/CMakeFiles/ExaGeoStatCPP.dir/linear-algebra-solvers/concrete/chameleon/ChameleonImplementation.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [CMakeFiles/Makefile2:513: src/CMakeFiles/ExaGeoStatCPP.dir/all] Error 2 gmake: *** [Makefile:136: all] Error 2 cp: cannot stat '/cluster/home/fabiopc/software/ExaGeoStatCPP/bin/src/libExaGeoStatCPP.so': No such file or directory Failed: libExaGeoStatCPP.so -> src ** libs make: Nothing to be done for 'all'. ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘ExaGeoStatCPP’ in library.dynam(lib, package, package.lib): shared object ‘ExaGeoStatCPP.so’ not found Error: loading failed Execution halted ERROR: loading failed

[alihakam830]

Hello @Filippo-Rambelli, please remove installdir/_deps, then reconfigure and rebuild. If the error persists with your current GCC, it’s likely a BLAS/CBLAS mismatch. Please load MKL and rebuild so CHAMELEON and ExaGeoStat both use MKL, and ensure no other cblas.h (e.g., OpenBLAS) is picked up in the include path.

[alihakam830]

Hello @Filippo-Rambelli ,

We hope you’re doing well. We wanted to check in and see whether the installation issues have been fully resolved and everything is now running smoothly, or if there is still anything blocking or causing trouble.