[gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

[Mark Abraham]

Today, I have made similar observations and recorded them in the Bugzilla database here http://bugzilla.gromacs.org/show_bug.cgi?id=539

For now, I do not think cmake works properly. autotools have been fine for me, however.

Mark

----- Original Message -----
From: Christian Mücksch <muecksch at rhrk.uni-kl.de>
Date: Thursday, September 2, 2010 19:26
Subject: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5
To: gmx-users at gromacs.org

>  Dear all,
> 
> so I downloaded Gromacs-4.5 and tried to compile the gpu-version 
> with cmake version 2.8.0 as stated in the gpu installation 
> instructions as
> 
> export OPENMM_ROOT_DIR=/usr/local/openmm
> cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=$HOME/GROMACS_4.5
> make mdrun
> make install-mdrun
> 
> But I get a few errors:
> 
> -----------------------------------------------------------------
> --------------------
> -- The C compiler identification is GNU
> -- The CXX compiler identification is GNU
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- 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
> -- CTest cannot determine repository type. Please set 
> UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work.
> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
>   CPack license resource file:
>   "/home/c_muecksch/gpu_Install_Linux/gromacs-
> 4.5/admin/InstallLicense.txt"  could not be found.
> Call Stack (most recent call first):
>   /usr/share/cmake-2.8/Modules/CPack.cmake:707 
> (cpack_check_file_exists)  CMakeLists.txt:40 (include)
> 
> 
> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
>   CPack readme resource file:
>   "/home/c_muecksch/gpu_Install_Linux/gromacs-
> 4.5/admin/InstallInfo.txt"  could not be found.
> Call Stack (most recent call first):
>   /usr/share/cmake-2.8/Modules/CPack.cmake:708 
> (cpack_check_file_exists)  CMakeLists.txt:40 (include)
> 
> 
> CMake Error at /usr/share/cmake-2.8/Modules/CPack.cmake:702 (message):
>   CPack welcome resource file:
>   "/home/c_muecksch/gpu_Install_Linux/gromacs-
> 4.5/admin/InstallWelcome.txt"  could not be found.
> Call Stack (most recent call first):
>   /usr/share/cmake-2.8/Modules/CPack.cmake:709 
> (cpack_check_file_exists)  CMakeLists.txt:40 (include)
> 
> 
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Failed
> -- 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_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- No external FFT libraries needed for the OpenMM build, using 
> fftpack!-- Threads not compatible with OpenMM build, disabled!
> CMake Warning at CMakeLists.txt:183 (message):
>   CPU-based acceleration turned off, OpenMM does not 
> support/need any!
> 
> 
> -- Looking for include files HAVE_STRING_H
> -- Looking for include files HAVE_STRING_H - found
> -- Looking for include files HAVE_MATH_H
> -- Looking for include files HAVE_MATH_H - found
> -- Looking for include files HAVE_LIMITS_H
> -- Looking for include files HAVE_LIMITS_H - found
> -- Looking for include files HAVE_MEMORY_H
> -- Looking for include files HAVE_MEMORY_H - found
> -- Looking for include files HAVE_UNISTD_H
> -- Looking for include files HAVE_UNISTD_H - found
> -- Looking for include files HAVE_PWD_H
> -- Looking for include files HAVE_PWD_H - found
> -- Looking for include files HAVE_STDINT_H
> -- Looking for include files HAVE_STDINT_H - found
> -- Looking for include files HAVE_STDLIB_H
> -- Looking for include files HAVE_STDLIB_H - found
> -- Looking for include files HAVE_PTHREAD_H
> -- Looking for include files HAVE_PTHREAD_H - found
> -- Looking for include files HAVE_DIRENT_H
> -- Looking for include files HAVE_DIRENT_H - found
> -- Looking for include files HAVE_INTTYPES_H
> -- Looking for include files HAVE_INTTYPES_H - found
> -- Looking for include files HAVE_REGEX_H
> -- Looking for include files HAVE_REGEX_H - found
> -- Looking for include files HAVE_SYS_TYPES_H
> -- Looking for include files HAVE_SYS_TYPES_H - found
> -- Looking for include files HAVE_SYS_STAT_H
> -- Looking for include files HAVE_SYS_STAT_H - found
> -- Looking for include files HAVE_SYS_TIME_H
> -- Looking for include files HAVE_SYS_TIME_H - found
> -- Looking for include files HAVE_RPC_RPC_H
> -- Looking for include files HAVE_RPC_RPC_H - found
> -- Looking for include files HAVE_RPC_XDR_H
> -- Looking for include files HAVE_RPC_XDR_H - found
> -- Looking for include files HAVE_XMMINTRIN_H
> -- Looking for include files HAVE_XMMINTRIN_H - found
> -- Looking for include files HAVE_EMMINTRIN_H
> -- Looking for include files HAVE_EMMINTRIN_H - found
> -- Looking for include files HAVE_PMMINTRIN_H
> -- Looking for include files HAVE_PMMINTRIN_H - not found.
> -- Looking for include files HAVE_SMMINTRIN_H
> -- Looking for include files HAVE_SMMINTRIN_H - not found.
> -- Looking for include files HAVE_IO_H
> -- Looking for include files HAVE_IO_H - not found.
> -- Looking for strcasecmp
> -- Looking for strcasecmp - found
> -- Looking for strdup
> -- Looking for strdup - found
> -- Looking for vprintf
> -- Looking for vprintf - found
> -- Looking for memcmp
> -- Looking for memcmp - 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 isnan
> -- Looking for isnan - found
> -- Looking for _isnan
> -- Looking for _isnan - not found
> -- Looking for isfinite
> -- Looking for isfinite - not found
> -- Looking for _isfinite
> -- Looking for _isfinite - not 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 sqrt in m
> -- Looking for sqrt in m - found
> -- Looking for cbrt in m
> -- Looking for cbrt in m - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of bool
> -- Check size of bool - failed
> -- Check size of int
> -- Check size of int - done
> -- Check size of long int
> -- Check size of long int - done
> -- Check size of long long int
> -- Check size of long long int - done
> -- Check size of off_t
> -- Check size of off_t - done
> -- Check size of void *
> -- Check size of void * - done
> -- Check size of uid_t
> -- Check size of uid_t - done
> -- Check size of gid_t
> -- Check size of gid_t - done
> -- Check size of size_t
> -- Check size of size_t - done
> -- Check size of off_t
> -- Check size of off_t - done
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- checking for module 'libxml-2.0'
> --   package 'libxml-2.0' not found
> -- Could NOT find LibXml2  (missing:  
> LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
> -- Looking for XOpenDisplay in /usr/lib/libX11.so;/usr/lib/libXext.so
> -- Looking for XOpenDisplay in 
> /usr/lib/libX11.so;/usr/lib/libXext.so - found
> -- Looking for gethostbyname
> -- Looking for gethostbyname - found
> -- Looking for connect
> -- Looking for connect - found
> -- Looking for remove
> -- Looking for remove - found
> -- Looking for shmat
> -- Looking for shmat - found
> -- Looking for IceConnectionNumber in ICE
> -- Looking for IceConnectionNumber in ICE - found
> -- Found X11: /usr/lib/libX11.so
> -- Found CUDA: /usr/local/cuda
> -- Found OpenMM: /usr/local/openmm
> -- Setting build user & time
> -- Setting build user & time - OK
> -- Checking floating point format
> -- Checking floating point format - unknown
> -- Checking for 64-bit off_t
> -- Checking for 64-bit off_t - present
> -- Checking for fseeko/ftello
> -- Checking for fseeko/ftello - present
> -- Checking for return type of signals
> -- Checking for return type of signals - void
> -- Checking for SIGUSR1
> -- Checking for SIGUSR1 - found
> -- Checking for inline keyword
> -- Checking for inline keyword - inline
> -- Checking for inline keyword
> -- Checking for inline keyword - inline
> -- Checking for pipe support
> -- Checking for GCC x86 inline asm
> -- Checking for GCC x86 inline asm - supported
> -- Checking for MSVC x86 inline asm
> -- Checking for MSVC x86 inline asm - not supported
> -- Checking for system XDR support
> -- Checking for system XDR support - present
> -- Using internal FFT library - fftpack
> CMake Warning (dev) at CMakeLists.txt:664 (add_subdirectory):
>   The source directory
> 
>     /home/c_muecksch/gpu_Install_Linux/gromacs-
> 4.5/scripts
>   does not contain a CMakeLists.txt file.
> 
>   CMake does not support this case but it used to work 
> accidentally and is
>   being allowed for compatibility.
> 
>   Policy CMP0014 is not set: Input directories must have 
> CMakeLists.txt.  Run
>   "cmake --help-policy CMP0014" for policy details.  
> Use the cmake_policy
>   command to set the policy and suppress this warning.
> This warning is for project developers.  Use -Wno-dev to 
> suppress it.
> 
> -- Configuring incomplete, errors occurred!
> -----------------------------------------------------------------
> --------------------
> 
> 
> When I use this -Wno-dev it does not work either. What am I 
> doing wrong?
> 
> 
> Kind regards,
> Christian Muecksch
> -- 
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