Error in offline installation of ABACUS on supercomputing servers using toolchain

Details

I am using toolchain to install abacus-3.7.5 offline on a supercomputing server that is not connected to an extranet. after toolchain_gnu.sh, I encountered errors when executing build_abacus_gnu.sh. What can be done about these errors？

This is the part where the message starts：

-- The CXX compiler identification is GNU 9.4.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- RapidJSON found. Headers: @INCLUDE_INSTALL_DIR@ -- Found Git: /usr/bin/git (found version "2.25.1") -- Found git: attempting to get commit info... fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). CMake Warning at CMakeLists.txt:102 (message): Failed to get git commit info

-- Found Cereal: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/cereal-1.3.2/include/cereal -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Found ELPA: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/elpa-2024.03.001/cpu/lib/libelpa_openmp.so -- Performing Test ELPA_VERSION_SATISFIES -- Performing Test ELPA_VERSION_SATISFIES - Success -- Found MPI_CXX: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/openmpi-4.1.6/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Looking for a CUDA compiler -- Looking for a CUDA compiler - NOTFOUND -- Found FFTW3: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/fftw-3.3.10/lib/libfftw3omp.so -- Looking for sgemm -- Looking for sgemm - not found -- Looking for sgemm -- Looking for sgemm_ - found -- Found BLAS: /vol8/home/hnuchn/software/abacus-develop-3.7.5/toolchain/install/openblas-0.3.27/lib/libopenblas.so -- Looking for cheev -- Looking for cheev_ - found -- Found LAPACK: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/openblas-0.3.27/lib/libopenblas.so;-lpthread;-lm;-ldl CMake Warning (dev) at CMakeLists.txt:418 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Environment variable SCALAPACK_ROOT is set to:

/vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/scalapack-2.2.1

For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. This warning is for project developers. Use -Wno-dev to suppress it.

-- Found ScaLAPACK: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/scalapack-2.2.1/lib/libscalapack.so -- Could NOT find MKL (missing: MKL_DIR) -- Found MKL_SCALAPACK: MKL_SCALAPACK-NOTFOUND -- Found Torch: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/libtorch-2.1.2/lib/libtorch.so -- Checking for one of the modules 'libxc' -- Found Libxc: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/toolchain/install/libxc-6.2.2/lib/libxc.so -- Found Libxc: version 6.2.2 -- Configuring done (8.7s) -- Generating done (3.8s) -- Build files have been written to: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/build_abacus_gnu shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied

This is the end of the error message： [ 67%] Built target gint shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied [ 67%] Built target cell make[2]: [source/module_hamilt_lcao/hamilt_lcaodft/CMakeFiles/hamilt_lcao.dir/build.make:76: source/module_hamilt_lcao/hamilt_lcaodft/CMakeFiles/hamilt_lcao.dir/hamilt_lcao.cpp.o] Error 1 make[2]: [source/module_hamilt_lcao/hamilt_lcaodft/CMakeFiles/hamilt_lcao.dir/build.make:272: source/module_hamilt_lcao/hamilt_lcaodft/CMakeFiles/hamilt_lcao.dir/FORCE_STRESS.cpp.o] Error 1 /vol8/home/hnu_chn/software/abacus-develop-3.7.5/source/module_hamilt_lcao/module_deepks/cal_gedm.cpp: In member function ‘void LCAO_Deepks::cal_gedm_equiv(int)’: /vol8/home/hnu_chn/software/abacus-develop-3.7.5/source/module_hamilt_lcao/module_deepks/cal_gedm.cpp:99:16: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 99 | std::system(cmd.c_str()); | ~~~^~~~~ make[1]: [CMakeFiles/Makefile2:1217: source/module_elecstate/CMakeFiles/elecstate.dir/all] Error 2 make[1]: [CMakeFiles/Makefile2:1451: source/module_hamilt_lcao/hamilt_lcaodft/CMakeFiles/hamilt_lcao.dir/all] Error 2 shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied [ 67%] Built target deepks make: *** [Makefile:136: all] Error 2 -- Install configuration: ""

Have you read FAQ on the online manual http://abacus.deepmodeling.com/en/latest/community/faq.html

[x] Yes, I have read the FAQ part on online manual.

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deepmodeling / abacus-develop