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

[Carsten Kutzner]

On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote:

> 
> Hi,
> 
> Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf).
> 
> I'll release a 4.5.1 right now.
Hi Rossen,

in ./src/tools/CMakeLists.txt the program gmx_rmsdist.c is doubly listed.
Maybe you want to fix that also. It gives a warning only, though.

Carsten

> 
> A very short lived 4.5 (RIP) :)
> 
> Rossen
> 
> On 9/2/10 11:23 AM, Christian Mücksch wrote:
>> 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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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne