[gmx-users] with 5.0: file INSTALL cannot find gmx

[Jochen Hub]

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/
---------------------------------------------------