# Installation issue **URL:** \ **Category:** User discussions\ **Tags:** cmake-error\ **Created:** [November 5, 2022, 8:04am UTC](https://gromacs.bioexcel.eu/t/installation-issue/5178 "2022-11-05T08:04:14Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Cliff](https://avatars.discourse-cdn.com/v4/letter/c/b38774/32.png) [@Cliff](https://gromacs.bioexcel.eu/u/Cliff)\ **Post date:** [November 5, 2022, 8:04am UTC](https://gromacs.bioexcel.eu/t/installation-issue/5178/1 "2022-11-05T08:04:14Z")
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!!! ---
**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\ **Post date:** [November 5, 2022, 5:51pm UTC](https://gromacs.bioexcel.eu/t/installation-issue/5178/2 "2022-11-05T17:51:03Z")
Hi! It looks like either some directories are read-only or belong to another user. Please check the permissions on the build directory and the source directory.