<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi, there:<div><br></div><div>I was trying to compile gromacs4.5.1 on a GPU cluster (<a href="https://secure.nersc.gov/nusers/systems/dirac/">https://secure.nersc.gov/nusers/systems/dirac/</a>). </div><div><br></div><div>The compilation seems to work fine, but in the installation folder, only "bin/mdrun-gpu" presents. Is it supposed to be so? </div><div><br></div><div>When I type "./mdrun-gpu -h", the following error occurs:</div><div>./mdrun-gpu: error while loading shared libraries: libgmxpreprocess.so.6: cannot open shared object file: No such file or directory</div><div><br></div><div>Do you have any idea what this means?</div><div><br></div><div>Thanks a lot,</div><div>Bin</div><div><br></div><div>=====================================</div><div>Here are steps I did for compiling:</div><div>export OPENMM_ROOT_DIR=/global/homes/b/bingo/Program/OpenMM2.0-Linux64</div><div>cmake -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=/global/homes/b/bingo/Program/gromacs_gpu</div><div>make mdrun</div><div>make install-mdrun</div><div><br></div><div>======================================</div><div>Here are the outputs from the cmake</div><div><br></div><div><div>-- The C compiler identification is GNU</div><div>-- The CXX compiler identification is GNU</div><div>-- Check for working C compiler: /usr/bin/gcc</div><div>-- Check for working C compiler: /usr/bin/gcc -- works</div><div>-- Detecting C compiler ABI info</div><div>-- Detecting C compiler ABI info - done</div><div>-- Check for working CXX compiler: /usr/bin/c++</div><div>-- Check for working CXX compiler: /usr/bin/c++ -- works</div><div>-- Detecting CXX compiler ABI info</div><div>-- Detecting CXX compiler ABI info - done</div><div>-- CTest cannot determine repository type. Please set UPDATE_TYPE to 'cvs' or 'svn'. CTest update will not work.</div><div>-- Performing Test CFLAGS_WARN</div><div>-- Performing Test CFLAGS_WARN - Success</div><div>-- Performing Test CFLAGS_EXCESS_PREC</div><div>-- Performing Test CFLAGS_EXCESS_PREC - Failed</div><div>-- Performing Test CFLAGS_COPT</div><div>-- Performing Test CFLAGS_COPT - Success</div><div>-- Performing Test CFLAGS_NOINLINE</div><div>-- Performing Test CFLAGS_NOINLINE - Success</div><div>-- Performing Test CXXFLAGS_WARN</div><div>-- Performing Test CXXFLAGS_WARN - Success</div><div>-- Performing Test CXXFLAGS_EXCESS_PREC</div><div>-- Performing Test CXXFLAGS_EXCESS_PREC - Failed</div><div>-- Performing Test CXXFLAGS_COPT</div><div>-- Performing Test CXXFLAGS_COPT - Success</div><div>-- Performing Test CXXFLAGS_NOINLINE</div><div>-- Performing Test CXXFLAGS_NOINLINE - Success</div><div>-- No external FFT libraries needed for the OpenMM build, using fftpack!</div><div>-- Threads not compatible with OpenMM build, disabled!</div><div>CMake Warning at CMakeLists.txt:183 (message):</div><div> CPU-based acceleration turned off, OpenMM does not support/need any!</div><div><br></div><div><br></div><div>-- Looking for include files HAVE_STRING_H</div><div>-- Looking for include files HAVE_STRING_H - found</div><div>-- Looking for include files HAVE_MATH_H</div><div>-- Looking for include files HAVE_MATH_H - found</div><div>-- Looking for include files HAVE_LIMITS_H</div><div>-- Looking for include files HAVE_LIMITS_H - found</div><div>-- Looking for include files HAVE_MEMORY_H</div><div>-- Looking for include files HAVE_MEMORY_H - found</div><div>-- Looking for include files HAVE_UNISTD_H</div><div>-- Looking for include files HAVE_UNISTD_H - found</div><div>-- Looking for include files HAVE_PWD_H</div><div>-- Looking for include files HAVE_PWD_H - found</div><div>-- Looking for include files HAVE_STDINT_H</div><div>-- Looking for include files HAVE_STDINT_H - found</div><div>-- Looking for include files HAVE_STDLIB_H</div><div>-- Looking for include files HAVE_STDLIB_H - found</div><div>-- Looking for include files HAVE_PTHREAD_H</div><div>-- Looking for include files HAVE_PTHREAD_H - found</div><div>-- Looking for include files HAVE_DIRENT_H</div><div>-- Looking for include files HAVE_DIRENT_H - found</div><div>-- Looking for include files HAVE_INTTYPES_H</div><div>-- Looking for include files HAVE_INTTYPES_H - found</div><div>-- Looking for include files HAVE_REGEX_H</div><div>-- Looking for include files HAVE_REGEX_H - found</div><div>-- Looking for include files HAVE_SYS_TYPES_H</div><div>-- Looking for include files HAVE_SYS_TYPES_H - found</div><div>-- Looking for include files HAVE_SYS_STAT_H</div><div>-- Looking for include files HAVE_SYS_STAT_H - found</div><div>-- Looking for include files HAVE_SYS_TIME_H</div><div>-- Looking for include files HAVE_SYS_TIME_H - found</div><div>-- Looking for include files HAVE_RPC_RPC_H</div><div>-- Looking for include files HAVE_RPC_RPC_H - found</div><div>-- Looking for include files HAVE_RPC_XDR_H</div><div>-- Looking for include files HAVE_RPC_XDR_H - found</div><div>-- Looking for include files HAVE_XMMINTRIN_H</div><div>-- Looking for include files HAVE_XMMINTRIN_H - found</div><div>-- Looking for include files HAVE_EMMINTRIN_H</div><div>-- Looking for include files HAVE_EMMINTRIN_H - found</div><div>-- Looking for include files HAVE_PMMINTRIN_H</div><div>-- Looking for include files HAVE_PMMINTRIN_H - not found.</div><div>-- Looking for include files HAVE_SMMINTRIN_H</div><div>-- Looking for include files HAVE_SMMINTRIN_H - not found.</div><div>-- Looking for include files HAVE_IO_H</div><div>-- Looking for include files HAVE_IO_H - not found.</div><div>-- Looking for strcasecmp</div><div>-- Looking for strcasecmp - found</div><div>-- Looking for strdup</div><div>-- Looking for strdup - found</div><div>-- Looking for vprintf</div><div>-- Looking for vprintf - found</div><div>-- Looking for memcmp</div><div>-- Looking for memcmp - found</div><div>-- Looking for posix_memalign</div><div>-- Looking for posix_memalign - found</div><div>-- Looking for memalign</div><div>-- Looking for memalign - found</div><div>-- Looking for _aligned_malloc</div><div>-- Looking for _aligned_malloc - not found</div><div>-- Looking for gettimeofday</div><div>-- Looking for gettimeofday - found</div><div>-- Looking for isnan</div><div>-- Looking for isnan - found</div><div>-- Looking for _isnan</div><div>-- Looking for _isnan - not found</div><div>-- Looking for isfinite</div><div>-- Looking for isfinite - not found</div><div>-- Looking for _isfinite</div><div>-- Looking for _isfinite - not found</div><div>-- Looking for fsync</div><div>-- Looking for fsync - found</div><div>-- Looking for _fileno</div><div>-- Looking for _fileno - not found</div><div>-- Looking for fileno</div><div>-- Looking for fileno - found</div><div>-- Looking for _commit</div><div>-- Looking for _commit - not found</div><div>-- Looking for sqrt in m</div><div>-- Looking for sqrt in m - found</div><div>-- Looking for cbrt in m</div><div>-- Looking for cbrt in m - found</div><div>-- Looking for stddef.h</div><div>-- Looking for stddef.h - found</div><div>-- Check size of bool</div><div>-- Check size of bool - failed</div><div>-- Check size of int</div><div>-- Check size of int - done</div><div>-- Check size of long int</div><div>-- Check size of long int - done</div><div>-- Check size of long long int</div><div>-- Check size of long long int - done</div><div>-- Check size of off_t</div><div>-- Check size of off_t - done</div><div>-- Check size of void *</div><div>-- Check size of void * - done</div><div>-- Check size of uid_t</div><div>-- Check size of uid_t - done</div><div>-- Check size of gid_t</div><div>-- Check size of gid_t - done</div><div>-- Check size of size_t</div><div>-- Check size of size_t - done</div><div>-- Check size of off_t</div><div>-- Check size of off_t - done</div><div>-- Check if the system is big endian</div><div>-- Searching 16 bit integer</div><div>-- Check size of unsigned short</div><div>-- Check size of unsigned short - done</div><div>-- Using unsigned short</div><div>-- Check if the system is big endian - little endian</div><div>-- checking for module 'libxml-2.0'</div><div>-- package 'libxml-2.0' not found</div><div>-- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)</div><div>-- Found CUDA: /global/common/carver/usg/cuda/3.1</div><div>-- Found OpenMM: /global/homes/b/bingo/Program/OpenMM2.0-Linux64</div><div>-- Setting build user & time</div><div>-- Setting build user & time - OK</div><div>-- Checking floating point format</div><div>-- Checking floating point format - unknown</div><div>-- Checking for 64-bit off_t</div><div>-- Checking for 64-bit off_t - present</div><div>-- Checking for fseeko/ftello</div><div>-- Checking for fseeko/ftello - present</div><div>-- Checking for return type of signals</div><div>-- Checking for return type of signals - void</div><div>-- Checking for SIGUSR1</div><div>-- Checking for SIGUSR1 - found</div><div>-- Checking for inline keyword</div><div>-- Checking for inline keyword - inline</div><div>-- Checking for inline keyword</div><div>-- Checking for inline keyword - inline</div><div>-- Checking for pipe support</div><div>-- Checking for GCC x86 inline asm</div><div>-- Checking for GCC x86 inline asm - supported</div><div>-- Checking for MSVC x86 inline asm</div><div>-- Checking for MSVC x86 inline asm - not supported</div><div>-- Checking for system XDR support</div><div>-- Checking for system XDR support - present</div><div>-- Using internal FFT library - fftpack</div><div>-- Configuring done</div><div>-- Generating done</div><div>-- Build files have been written to: /global/homes/b/bingo/Program/gromacs-4.5.1</div><div><br></div></div></body></html>