# Gromacs +cp2k installation **URL:** \ **Category:** User discussions\ **Tags:** installation-error\ **Created:** [September 19, 2023, 10:44pm UTC](https://gromacs.bioexcel.eu/t/gromacs-cp2k-installation/7221 "2023-09-19T22:44:57Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![edivaldosrodrigues](https://avatars.discourse-cdn.com/v4/letter/e/2acd7d/32.png) [@edivaldosrodrigues](https://gromacs.bioexcel.eu/u/edivaldosrodrigues)\ **Post date:** [September 19, 2023, 10:44pm UTC](https://gromacs.bioexcel.eu/t/gromacs-cp2k-installation/7221/1 "2023-09-19T22:44:57Z")
GROMACS version: 2023.1 Hello. I am trying to compile gromacs-2023.1 with cp2k-2023.2, but I am not being able to link the fftwf3 library. So when I run the following command: cmake … -DBUILD\_SHARED\_LIBS=OFF -DGMXAPI=OFF -DGMX\_INSTALL\_NBLIB\_API=OFF -DGMX\_DOUBLE=ON -DGMX\_FFT\_LIBRARY=fftw3 -DFFTWF\_LIBRARY=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/lib -DFFTWF\_INCLUDE\_DIR=/home/edivaldo/cp2k/tools/toolchain/install/fftw-3.3.10/include -DGMX\_BLAS\_USER=/home/edivaldo/cp2k/tools/toolchain/install/openblas-0.3.23/lib/libopenblas.a -DGMX\_LAPACK\_USER=/home/edivaldo/cp2k/tools/toolchain/install/scalapack-2.2.1/lib/libscalapack.a -DGMX\_CP2K=ON -DCP2K\_DIR=“/home/edivaldo/cp2k/lib/local/psmp” -DGMX\_MPI=on I keep getting this warning: – The C compiler identification is GNU 11.4.0 – The CXX compiler identification is GNU 11.4.0 – Detecting C compiler ABI info – Detecting C compiler ABI info - done – Check for working C compiler: /usr/bin/cc - skipped – Detecting C compile features – Detecting C compile features - done – Detecting CXX compiler ABI info – Detecting CXX compiler ABI info - done – Check for working CXX compiler: /usr/bin/c++ - skipped – Detecting CXX compile features – Detecting CXX compile features - done – Found Python3: /home/edivaldo/anaconda3/bin/python3.10 (found suitable version “3.10.9”, minimum required is “3.7”) found components: Interpreter Development Development.Module Development.Embed – The Fortran compiler identification is GNU 11.4.0 – Detecting Fortran compiler ABI info – Detecting Fortran compiler ABI info - done – Check for working Fortran compiler: /usr/bin/gfortran - skipped – Found OpenMP\_C: -fopenmp (found version “4.5”) – Found OpenMP\_CXX: -fopenmp (found version “4.5”) – Found OpenMP\_Fortran: -fopenmp (found version “4.5”) – Found OpenMP: TRUE (found version “4.5”) – 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 – Looking for include file unistd.h – Looking for include file unistd.h - found – Looking for include file pwd.h – Looking for include file pwd.h - found – Looking for include file dirent.h – Looking for include file dirent.h - found – Looking for include file time.h – Looking for include file time.h - found – Looking for include file sys/time.h – Looking for include file sys/time.h - found – Looking for include file io.h – Looking for include file io.h - not found – Looking for include file sched.h – Looking for include file sched.h - found – Looking for include file xmmintrin.h – Looking for include file xmmintrin.h - found – Looking for gettimeofday – Looking for gettimeofday - found – Looking for sysconf – Looking for sysconf - found – Looking for nice – Looking for nice - found – Looking for fsync – Looking for fsync - found – Looking for \_fileno – Looking for \_fileno - not found – Looking for fileno – Looking for fileno - found – Looking for \_commit – Looking for \_commit - not found – 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 – Looking for include file mm\_malloc.h – Looking for include file mm\_malloc.h - found – Looking for include file malloc.h – Looking for include file malloc.h - found – Checking for \_mm\_malloc() – Checking for \_mm\_malloc() - supported – Looking for posix\_memalign – Looking for posix\_memalign - found – Looking for memalign – Looking for memalign - not found – MPI is not compatible with thread-MPI. Disabling thread-MPI. – Found MPI\_CXX: /home/edivaldo/openmpi/lib/libmpi.so (found version “3.1”) – Found MPI\_Fortran: /home/edivaldo/openmpi/lib/libmpi\_usempif08.so (found version “3.1”) – Found MPI: TRUE (found version “3.1”) found components: CXX Fortran – GROMACS library will use OpenMPI 4.1.5 – Found libcp2k in /home/edivaldo/cp2k/lib/local/psmp – Using default binary suffix: “\_mpi\_d” – Using default library suffix: “\_mpi\_d” – Looking for pthread.h – Looking for pthread.h - found – Performing Test CMAKE\_HAVE\_LIBC\_PTHREAD – Performing Test CMAKE\_HAVE\_LIBC\_PTHREAD - Success – Found Threads: TRUE – Looking for C++ include pthread.h – Looking for C++ include pthread.h - found – Performing Test TEST\_ATOMICS – Performing Test TEST\_ATOMICS - Success – Atomic operations found – Performing Test PTHREAD\_SETAFFINITY – Performing Test PTHREAD\_SETAFFINITY - Success – Detecting best SIMD instructions for this CPU – Checking for GCC x86 inline asm – Checking for GCC x86 inline asm - supported – Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic – Detected best SIMD instructions for this CPU - AVX2\_256 – Performing Test C\_mavx2\_mfma\_FLAG\_ACCEPTED – Performing Test C\_mavx2\_mfma\_FLAG\_ACCEPTED - Success – Performing Test C\_mavx2\_mfma\_COMPILE\_WORKS – Performing Test C\_mavx2\_mfma\_COMPILE\_WORKS - Success – Performing Test CXX\_mavx2\_mfma\_FLAG\_ACCEPTED – Performing Test CXX\_mavx2\_mfma\_FLAG\_ACCEPTED - Success – Performing Test CXX\_mavx2\_mfma\_COMPILE\_WORKS – Performing Test CXX\_mavx2\_mfma\_COMPILE\_WORKS - Success – Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma – Detecting flags to enable runtime detection of AVX-512 units on newer CPUs – Performing Test C\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED – Performing Test C\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED - Failed – Performing Test C\_xCORE\_AVX512\_FLAG\_ACCEPTED – Performing Test C\_xCORE\_AVX512\_FLAG\_ACCEPTED - Failed – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED - Success – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS - Success – Performing Test CXX\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED – Performing Test CXX\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED - Failed – Performing Test CXX\_xCORE\_AVX512\_FLAG\_ACCEPTED – Performing Test CXX\_xCORE\_AVX512\_FLAG\_ACCEPTED - Failed – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED - Success – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS - Success – Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw – Performing Test \_Wno\_unused\_command\_line\_argument\_FLAG\_ACCEPTED – Performing Test \_Wno\_unused\_command\_line\_argument\_FLAG\_ACCEPTED - Success – Performing Test \_callconv\_\_\_vectorcall – Performing Test \_callconv\_\_\_vectorcall - Failed – Performing Test _callconv\_\_\_regcall – Performing Test callconv\_\_\_regcall - Failed – Performing Test callconv – Performing Test callconv - Success – Detected build CPU vendor - Intel – Detected build CPU brand - Intel(R) Core™ i5-8400 CPU @ 2.80GHz – Detected build CPU family - 6 – Detected build CPU model - 158 – Detected build CPU stepping - 10 – Checking for 64-bit off\_t – Checking for 64-bit off\_t - present – Checking for fseeko/ftello – Checking for fseeko/ftello - present – Checking for SIGUSR1 – Checking for SIGUSR1 - found – Checking for pipe support – Checking for system XDR support – Checking for system XDR support - not present – Checking for module ‘fftw3’ – Found fftw3, version 3.3.8 – Looking for fftw\_plan\_many\_dft in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_plan\_many\_dft in /usr/lib/x86\_64-linux-gnu/libfftw3.so - found – Looking for fftw\_plan\_many\_dft\_r2c in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_plan\_many\_dft\_r2c in /usr/lib/x86\_64-linux-gnu/libfftw3.so - found – Looking for fftw\_plan\_many\_dft\_c2r in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_plan\_many\_dft\_c2r in /usr/lib/x86\_64-linux-gnu/libfftw3.so - found – Looking for fftw\_have\_simd\_sse in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_have\_simd\_sse in /usr/lib/x86\_64-linux-gnu/libfftw3.so - not found – Looking for fftw\_have\_sse in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_have\_sse in /usr/lib/x86\_64-linux-gnu/libfftw3.so - not found – Looking for fftw\_have\_simd\_sse2 in /usr/lib/x86\_64-linux-gnu/libfftw3.so – Looking for fftw\_have\_simd\_sse2 in /usr/lib/x86\_64-linux-gnu/libfftw3.so - found – Using external FFT library - FFTW3 – Checking that user BLAS library /home/edivaldo/cp2k/tools/toolchain/install/openblas-0.3.23/lib/libopenblas.a works – Looking for dgemm – Looking for dgemm_ - not found CMake Warning at cmake/gmxManageLinearAlgebraLibraries.cmake:77 (message): GMX\_BLAS\_USER library /home/edivaldo/cp2k/tools/toolchain/install/openblas-0.3.23/lib/libopenblas.a was specified, but it may not provide BLAS. We are proceeding by assuming you know what you are doing and that linking F77-style to this library will work. Call Stack (most recent call first): cmake/gmxManageLinearAlgebraLibraries.cmake:195 (manage\_linear\_algebra\_library) cmake/gmxManageLinearAlgebraLibraries.cmake:205 (gmxManageLinearAlgebraLibraries) CMakeLists.txt:846 (include) – Checking that user LAPACK library /home/edivaldo/cp2k/tools/toolchain/install/scalapack-2.2.1/lib/libscalapack.a works – Looking for cheev\_ – Looking for cheev\_ - not found CMake Warning at cmake/gmxManageLinearAlgebraLibraries.cmake:77 (message): GMX\_LAPACK\_USER library /home/edivaldo/cp2k/tools/toolchain/install/scalapack-2.2.1/lib/libscalapack.a was specified, but it may not provide LAPACK. We are proceeding by assuming you know what you are doing and that linking F77-style to this library will work. Call Stack (most recent call first): cmake/gmxManageLinearAlgebraLibraries.cmake:197 (manage\_linear\_algebra\_library) cmake/gmxManageLinearAlgebraLibraries.cmake:205 (gmxManageLinearAlgebraLibraries) CMakeLists.txt:846 (include) – Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: [Fixing Imagick's “not authorized” exception — Alex Vanderbist](https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized) – Found Doxygen: /usr/bin/doxygen (found version “1.9.1”) found components: doxygen missing components: dot – Found Python: /home/edivaldo/anaconda3/bin/python3.10 (found version “3.10.9”) found components: Interpreter – Performing Test HAVE\_NO\_DEPRECATED\_COPY – Performing Test HAVE\_NO\_DEPRECATED\_COPY - Success – Performing Test HAS\_WARNING\_EVERYTHING – Performing Test HAS\_WARNING\_EVERYTHING - Failed – Performing Test HAS\_NO\_STRINGOP\_TRUNCATION – Performing Test HAS\_NO\_STRINGOP\_TRUNCATION - Success – Performing Test HAS\_NO\_REDUNDANT\_MOVE – Performing Test HAS\_NO\_REDUNDANT\_MOVE - Success – Performing Test HAS\_WARNING\_NO\_CAST\_FUNCTION\_TYPE\_STRICT – Performing Test HAS\_WARNING\_NO\_CAST\_FUNCTION\_TYPE\_STRICT - Success – Performing Test HAS\_NO\_UNUSED – Performing Test HAS\_NO\_UNUSED - Success – Performing Test HAS\_NO\_UNUSED\_PARAMETER – Performing Test HAS\_NO\_UNUSED\_PARAMETER - Success – Performing Test HAS\_NO\_MISSING\_DECLARATIONS – Performing Test HAS\_NO\_MISSING\_DECLARATIONS - Success – Performing Test HAS\_NO\_NULL\_CONVERSIONS – Performing Test HAS\_NO\_NULL\_CONVERSIONS - Success – Looking for inttypes.h – Looking for inttypes.h - found – Performing Test HAS\_WARNING\_NO\_ARRAY\_BOUNDS – Performing Test HAS\_WARNING\_NO\_ARRAY\_BOUNDS - Success – Performing Test HAS\_WARNING\_NO\_DEPRECATED\_NON\_PROTOTYPE – Performing Test HAS\_WARNING\_NO\_DEPRECATED\_NON\_PROTOTYPE - Success – Performing Test COMPILER\_HAS\_HIDDEN\_VISIBILITY – Performing Test COMPILER\_HAS\_HIDDEN\_VISIBILITY - Success – Performing Test COMPILER\_HAS\_HIDDEN\_INLINE\_VISIBILITY – Performing Test COMPILER\_HAS\_HIDDEN\_INLINE\_VISIBILITY - Success – Performing Test COMPILER\_HAS\_DEPRECATED\_ATTR – Performing Test COMPILER\_HAS\_DEPRECATED\_ATTR - Success – Could NOT find Sphinx (missing: SPHINX\_EXECUTABLE) (Required is at least version “4.0.0”) – Configuring done – Generating done CMake Warning: Manually-specified variables were not used by the project: ``` FFTWF_INCLUDE_DIR FFTWF_LIBRARY ``` – Build files have been written to: /home/edivaldo/gromacs-2023.1/build So if I proceed if the installation ( runing make and …) I don´t get the gromacs installed with cp2k support. Even though I don’t get any trouble after runing make install, the command gmx doesn’t works. If any of you could help me, I would appreciate very much. Att, Edivaldo SR.