GROMACS version: 2023
GROMACS modification: No
Here post your question
I’m very much beginner of Linux from windows
in the installation process
“cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON” typed and incompletion goes through.
_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at /usr/share/cmake-3.22/Modules/CMakeDetermineSystem.cmake:193 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:56 (project)
– The C compiler identification is GNU 11.3.0
CMake Error at /usr/share/cmake-3.22/Modules/CMakeDetermineCCompiler.cmake:226 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:56 (project)
– The CXX compiler identification is GNU 11.3.0
CMake Error at /usr/share/cmake-3.22/Modules/CMakeDetermineCXXCompiler.cmake:226 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:56 (project)
– Detecting C compiler ABI info
– Detecting C compiler ABI info - failed
– Check for working C compiler: /usr/bin/cc
– Check for working C compiler: /usr/bin/cc - works
– Detecting C compile features
– Detecting C compile features - done
CMake Error at /usr/share/cmake-3.22/Modules/CMakeTestCCompiler.cmake:85 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:56 (project)
– Detecting CXX compiler ABI info
– Detecting CXX compiler ABI info - failed
– Check for working CXX compiler: /usr/bin/c++
– Check for working CXX compiler: /usr/bin/c++ - works
– Detecting CXX compile features
– Detecting CXX compile features - done
CMake Error at /usr/share/cmake-3.22/Modules/CMakeTestCXXCompiler.cmake:78 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:56 (project)
– Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Development Development.Module Development.Embed) (found suitable version “3.10.6”, minimum required is “3.7”)
CMake Error at cmake/gmxVersionInfo.cmake:432 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:78 (include)
CMake Error at /usr/share/cmake-3.22/Modules/CTestTargets.cmake:28 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CTest.cmake:264 (include)
cmake/gmxCTestUtilities.cmake:51 (include)
CMakeLists.txt:116 (gmx_ctest_init)
CMake Error at /usr/share/cmake-3.22/Modules/FindOpenMP.cmake:396 (try_compile):
Cannot copy output executable
'/mnt/c/Users/User/Desktop/Gromacs/gromacs-2022.3/build/CMakeFiles/CMakeTmp/cmTC_8e687'
to destination specified by COPY_FILE:
'/mnt/c/Users/User/Desktop/Gromacs/gromacs-2022.3/build/CMakeFiles/FindOpenMP/ompver_C.bin'
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindOpenMP.cmake:524 (_OPENMP_GET_SPEC_DATE)
cmake/gmxManageOpenMP.cmake:41 (find_package)
CMakeLists.txt:295 (include)
– Found OpenMP_C: -fopenmp
CMake Error at /usr/share/cmake-3.22/Modules/FindOpenMP.cmake:396 (try_compile):
Cannot copy output executable
'/mnt/c/Users/User/Desktop/Gromacs/gromacs-2022.3/build/CMakeFiles/CMakeTmp/cmTC_3a932'
to destination specified by COPY_FILE:
'/mnt/c/Users/User/Desktop/Gromacs/gromacs-2022.3/build/CMakeFiles/FindOpenMP/ompver_CXX.bin'
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindOpenMP.cmake:524 (_OPENMP_GET_SPEC_DATE)
cmake/gmxManageOpenMP.cmake:41 (find_package)
CMakeLists.txt:295 (include)
– Found OpenMP_CXX: -fopenmp
– Found OpenMP: TRUE
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CFLAGS_EXCESS_PREC
– Performing Test CFLAGS_EXCESS_PREC - Success
– Performing Test CFLAGS_COPT
– Performing Test CFLAGS_COPT - Success
– Performing Test CFLAGS_NOINLINE
– Performing Test CFLAGS_NOINLINE - Success
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS
– Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success
– Performing Test CXXFLAGS_EXCESS_PREC
– Performing Test CXXFLAGS_EXCESS_PREC - Success
– Performing Test CXXFLAGS_COPT
– Performing Test CXXFLAGS_COPT - Success
– Performing Test CXXFLAGS_NOINLINE
– Performing Test CXXFLAGS_NOINLINE - Success
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:367 (check_include_files)
– Looking for include file unistd.h
– Looking for include file unistd.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:368 (check_include_files)
– Looking for include file pwd.h
– Looking for include file pwd.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:369 (check_include_files)
– Looking for include file dirent.h
– Looking for include file dirent.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:370 (check_include_files)
– Looking for include file time.h
– Looking for include file time.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:371 (check_include_files)
– Looking for include file sys/time.h
– Looking for include file sys/time.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:372 (check_include_files)
– Looking for include file io.h
– Looking for include file io.h - not found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:373 (check_include_files)
– Looking for include file sched.h
– Looking for include file sched.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
CMakeLists.txt:374 (check_include_files)
– Looking for include file xmmintrin.h
– Looking for include file xmmintrin.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:377 (check_cxx_symbol_exists)
– Looking for gettimeofday
– Looking for gettimeofday - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:378 (check_cxx_symbol_exists)
– Looking for sysconf
– Looking for sysconf - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:379 (check_cxx_symbol_exists)
– Looking for nice
– Looking for nice - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:380 (check_cxx_symbol_exists)
– Looking for fsync
– Looking for fsync - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:381 (check_cxx_symbol_exists)
– Looking for _fileno
– Looking for _fileno - not found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:382 (check_cxx_symbol_exists)
– Looking for fileno
– Looking for fileno - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:383 (check_cxx_symbol_exists)
– Looking for _commit
– Looking for _commit - not found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:384 (check_cxx_symbol_exists)
– Looking for sigaction
– Looking for sigaction - found
– Performing Test HAVE_BUILTIN_CLZ
– Performing Test HAVE_BUILTIN_CLZ - Success
– Performing Test HAVE_BUILTIN_CLZLL
– Performing Test HAVE_BUILTIN_CLZLL - Success
– Looking for clock_gettime in rt
– Looking for clock_gettime in rt - found
– Looking for feenableexcept in m
– Looking for feenableexcept in m - found
– Looking for fedisableexcept in m
– Looking for fedisableexcept in m - found
– Checking for sched.h GNU affinity API
– Performing Test sched_affinity_compile
– Performing Test sched_affinity_compile - Success
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
cmake/gmxTestMMMalloc.cmake:46 (check_include_files)
CMakeLists.txt:410 (gmx_test_mm_malloc)
– Looking for include file mm_malloc.h
– Looking for include file mm_malloc.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFiles.cmake:94 (configure_file):
Operation not permitted
Call Stack (most recent call first):
cmake/gmxTestMMMalloc.cmake:47 (check_include_files)
CMakeLists.txt:410 (gmx_test_mm_malloc)
– Looking for include file malloc.h
– Looking for include file malloc.h - found
– Checking for _mm_malloc()
– Checking for _mm_malloc() - supported
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:411 (check_cxx_symbol_exists)
– Looking for posix_memalign
– Looking for posix_memalign - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckSymbolExists.cmake:142 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckCXXSymbolExists.cmake:77 (__CHECK_SYMBOL_EXISTS_IMPL)
CMakeLists.txt:412 (check_cxx_symbol_exists)
– Looking for memalign
– Looking for memalign - not found
– Check if the system is big endian
– Searching 16 bit integer
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFile.cmake:57 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:249 (check_include_file)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:55 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
– Looking for sys/types.h
– Looking for sys/types.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFile.cmake:57 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:250 (check_include_file)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:55 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
– Looking for stdint.h
– Looking for stdint.h - found
CMake Error at /usr/share/cmake-3.22/Modules/CheckIncludeFile.cmake:57 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:251 (check_include_file)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:55 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
– Looking for stddef.h
– Looking for stddef.h - found
– Check size of unsigned short
CMake Error at /usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:138 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:270 (__check_type_size_impl)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:55 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
– Check size of unsigned int
CMake Error at /usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:138 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:270 (__check_type_size_impl)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:60 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
– Check size of unsigned long
CMake Error at /usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:138 (configure_file):
Operation not permitted
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/CheckTypeSize.cmake:270 (__check_type_size_impl)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:67 (CHECK_TYPE_SIZE)
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
CMake Error at /usr/share/cmake-3.22/Modules/TestBigEndian.cmake:72 (message):
no suitable type found
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/TestBigEndian.cmake:37 (__TEST_BIG_ENDIAN_LEGACY_IMPL)
CMakeLists.txt:419 (test_big_endian)
too much issues are going on and I have no idea what I can do…
Please help me masters!!!