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
– 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.