Hi all, I am having trouble to make install Gromacs 5.0x under Linux. make install fails with:
CMake Error at src/programs/cmake_install.cmake:42 (FILE): file INSTALL cannot find "/home/waxs/opt/gmx/5.03-rotmax/bin/gmx". Call Stack (most recent call first): src/cmake_install.cmake:40 (INCLUDE) cmake_install.cmake:44 (INCLUDE) I have this trouble this on different machines (AMD, Intel), on our computing cluster, and on a webserver that we are running. With icc and gcc. The install directly is empty before the cmake. My cmake (version 2.8.12) call is, e.g.: cmake /home/waxs/src/gmx/gromacs-5.0.3 /path/to/gmxsrc -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=$(pwd) && make -j12 && make install (so totally standard) but this happens with other cmake calls as well (using FFTW or so). I am kind of stuck. Did anyone else have similar trouble? Below I pasted the cmake output (generated on an Ubuntu), but that looks all very standard to me. Many thanks for any hints, Jochen -- The C compiler identification is GNU 4.8.2 -- The CXX compiler identification is GNU 4.8.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detecting best SIMD instructions for this CPU -- Detected best SIMD instructions for this CPU - AVX_128_FMA -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Performing Test CFLAGS_WARN -- Performing Test CFLAGS_WARN - Success -- Performing Test CFLAGS_WARN_EXTRA -- Performing Test CFLAGS_WARN_EXTRA - Success -- Performing Test CFLAGS_WARN_REL -- Performing Test CFLAGS_WARN_REL - Success -- Performing Test CFLAGS_WARN_UNINIT -- Performing Test CFLAGS_WARN_UNINIT - 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 -- Performing Test CXXFLAGS_WARN - Success -- Performing Test CXXFLAGS_WARN_EXTRA -- Performing Test CXXFLAGS_WARN_EXTRA - Success -- Performing Test CXXFLAGS_WARN_REL -- Performing Test CXXFLAGS_WARN_REL - 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 regex.h -- Looking for include file regex.h - found -- Looking for C++ include regex -- Looking for C++ include regex - not found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - found -- Looking for _aligned_malloc -- Looking for _aligned_malloc - not found -- Looking for gettimeofday -- Looking for gettimeofday - 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 -- Looking for sysconf -- Looking for sysconf - found -- Looking for rsqrt -- Looking for rsqrt - not found -- Looking for rsqrtf -- Looking for rsqrtf - not found -- Looking for sqrtf -- Looking for sqrtf - not found -- Looking for sqrt in m -- Looking for sqrt in m - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.1") -- Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so -- Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so - found -- Looking for include file libxml/parser.h -- Looking for include file libxml/parser.h - found -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- 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 -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Boost version: 1.54.0 -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Setting build user/date/host/cpu information -- Setting build user & time - OK -- Checking floating point format -- Checking floating point format - IEEE754 (LE byte, LE word) -- 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 isfinite -- Performing Test isfinite_compile_ok -- Performing Test isfinite_compile_ok - Success -- Checking for isfinite - yes -- Checking for _isfinite -- Performing Test _isfinite_compile_ok -- Performing Test _isfinite_compile_ok - Failed -- Checking for _isfinite - no -- Checking for _finite -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Failed -- Checking for _finite - no -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test GMX_CXX11_SUPPORTED -- Performing Test GMX_CXX11_SUPPORTED - Success -- Checking for system XDR support -- Checking for system XDR support - present -- Try C compiler AVX (128 bit) flag = [-mavx] -- Performing Test C_FLAG_mavx -- Performing Test C_FLAG_mavx - Success -- Performing Test C_SIMD_COMPILES_FLAG_mavx -- Performing Test C_SIMD_COMPILES_FLAG_mavx - Success -- Try C++ compiler AVX (128 bit) flag = [-mavx] -- Performing Test CXX_FLAG_mavx -- Performing Test CXX_FLAG_mavx - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx -- Performing Test CXX_SIMD_COMPILES_FLAG_mavx - Success -- Looking for x86intrin.h -- Looking for x86intrin.h - found -- Looking for intrin.h -- Looking for intrin.h - not found -- Try C compiler AVX (128 bit) FMA4 flag = [-mfma4] -- Performing Test C_FLAG_mfma4 -- Performing Test C_FLAG_mfma4 - Success -- Performing Test C_SIMD_COMPILES_FLAG_mfma4 -- Performing Test C_SIMD_COMPILES_FLAG_mfma4 - Success -- Try C++ compiler AVX (128 bit) FMA4 flag = [-mfma4] -- Performing Test CXX_FLAG_mfma4 -- Performing Test CXX_FLAG_mfma4 - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mfma4 -- Performing Test CXX_SIMD_COMPILES_FLAG_mfma4 - Success -- Try C compiler AVX (128 bit) XOP flag = [-mxop] -- Performing Test C_FLAG_mxop -- Performing Test C_FLAG_mxop - Success -- Performing Test C_SIMD_COMPILES_FLAG_mxop -- Performing Test C_SIMD_COMPILES_FLAG_mxop - Success -- Try C++ compiler AVX (128 bit) XOP flag = [-mxop] -- Performing Test CXX_FLAG_mxop -- Performing Test CXX_FLAG_mxop - Success -- Performing Test CXX_SIMD_COMPILES_FLAG_mxop -- Performing Test CXX_SIMD_COMPILES_FLAG_mxop - Success -- Checking for gcc AVX maskload bug -- Checking for gcc AVX maskload bug - not present -- Enabling 128-bit AVX SIMD Gromacs SIMD (with fused-multiply add) -- 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 -- Using internal FFT library - fftpack -- Looking for sgemm_ -- Looking for sgemm_ - found -- A library with BLAS API found. -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could NOT find Pandoc (missing: PANDOC_EXECUTABLE) -- Found PythonInterp: /usr/bin/python (found version "2.7.6") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_DEPRECATED_REGISTER -- Performing Test HAS_NO_DEPRECATED_REGISTER - Success -- Configuring done -- Generating done -- Build files have been written to: /home/waxs/opt/gmx/5.03-rotmax -- --------------------------------------------------- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --------------------------------------------------- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
