Hello,
I'm trying to install gromacs-2019.4 with GPU support, but was always wrong.
I ran cmake as
cmake3 .. -DCMAKE_INSTALL_PREFIX=~/gromacs/gmx2019.4 -DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_HWLOC=ON
It works but when installing always get error messages. (Attached please find
the messages I got after running cmake and the error messages for installing.)
Sorry for posting so much information, I really want to know how to solve this.
Thanks.
Wen
cmake3 .. -DCMAKE_INSTALL_PREFIX=~/gromacs/gmx2019.4 -DGMX_BUILD_OWN_FFTW=ON
-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_HWLOC=ON
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for 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
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Number of NVIDIA GPUs detected: 5
-- Found CUDA: /usr/local/cuda (found suitable version "10.1", minimum required
is "7.0")
-- Found OpenMP_C: -fopenmp (found version "3.1")
-- Found OpenMP_CXX: -fopenmp (found version "3.1")
-- Found OpenMP: TRUE (found version "3.1")
-- 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_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 gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - 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
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- 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
-- hwloc version: 1.11.8
-- Found Hwloc: /usr/lib64/libhwloc.so (found suitable version "1.11.8",
minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Check for working NVCC/C++ compiler combination with nvcc
'/usr/local/cuda/bin/nvcc'
-- Check for working NVCC/C++ compiler combination - works
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detected build CPU vendor - Intel
-- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2697A v4 @ 2.60GHz
-- Detected build CPU family - 6
-- Detected build CPU model - 79
-- Detected build CPU stepping - 1
-- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma
hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse
rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
-- Enabling RDTSCP support - detected on the build host
-- 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
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- Detecting best SIMD instructions for this CPU
-- Detected best SIMD instructions for this CPU - AVX2_256
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -mavx2 -mfma
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test C_mavx512f_FLAG_ACCEPTED
-- Performing Test C_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test C_arch_AVX_FLAG_ACCEPTED
-- Performing Test C_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test C_hgnu_FLAG_ACCEPTED
-- Performing Test C_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either
the compiler or binutils)
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED
-- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Failed
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED
-- Performing Test CXX_mavx512f_FLAG_ACCEPTED - Failed
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED
-- Performing Test CXX_arch_AVX_FLAG_ACCEPTED - Failed
-- Performing Test CXX_hgnu_FLAG_ACCEPTED
-- Performing Test CXX_hgnu_FLAG_ACCEPTED - Failed
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS
-- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Failed
-- Could not find any flag to build test source (this could be due to either
the compiler or binutils)
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -
not supported
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- 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
-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2;--enable-avx;--enable-avx2
-- Using external FFT library - FFTW3 build managed by GROMACS
-- Could NOT find BLAS (missing: BLAS_LIBRARIES)
-- Using GROMACS built-in BLAS.
-- LAPACK requires BLAS
-- A library with LAPACK API not found. Please specify library location.
-- Using GROMACS built-in LAPACK.
-- 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 convert sample image, ImageMagick convert can not be used
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.5",
minimum required is "2.7")
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- 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
-- Configuring done
-- Generating done
-- Build files have been written to:
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/build
#######ERROR MESSAGES######
[ 96%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:
In function âbool gmx::{anonymous}::parseHwLocCache(hwloc_topology_t,
gmx::HardwareTopology::Machine*)â:
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:314:66:
error: âHWLOC_OBJ_CACHE_DATAâ was not declared in this scope
int depth = hwloc_get_cache_type_depth(topo, cachelevel,
HWLOC_OBJ_CACHE_DATA);
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:314:86:
error: âhwloc_get_cache_type_depthâ was not declared in this scope
int depth = hwloc_get_cache_type_depth(topo, cachelevel,
HWLOC_OBJ_CACHE_DATA);
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:327:84:
error: âstruct hwloc_obj_attr_u::hwloc_cache_attr_sâ has no member named
âassociativityâ
static_cast<int>(cache->attr->cache.associativity),
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:329:46:
error: no matching function for call to
âstd::vector<gmx::HardwareTopology::Cache>::push_back(<brace-enclosed
initializer list>)â
} );
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:329:46:
note: candidates are:
In file included from /usr/include/c++/4.8.2/vector:64:0,
from
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.h:48,
from
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:46:
/usr/include/c++/4.8.2/bits/stl_vector.h:901:7: note: void std::vector<_Tp,
_Alloc>::push_back(const value_type&) [with _Tp = gmx::HardwareTopology::Cache;
_Alloc = std::allocator<gmx::HardwareTopology::Cache>; std::vector<_Tp,
_Alloc>::value_type = gmx::HardwareTopology::Cache]
push_back(const value_type& __x)
^
/usr/include/c++/4.8.2/bits/stl_vector.h:901:7: note: no known conversion for
argument 1 from â<brace-enclosed initializer list>â to âconst value_type&
{aka const gmx::HardwareTopology::Cache&}â
/usr/include/c++/4.8.2/bits/stl_vector.h:919:7: note: void std::vector<_Tp,
_Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp =
gmx::HardwareTopology::Cache; _Alloc =
std::allocator<gmx::HardwareTopology::Cache>; std::vector<_Tp,
_Alloc>::value_type = gmx::HardwareTopology::Cache]
push_back(value_type&& __x)
^
/usr/include/c++/4.8.2/bits/stl_vector.h:919:7: note: no known conversion for
argument 1 from â<brace-enclosed initializer list>â to
âstd::vector<gmx::HardwareTopology::Cache>::value_type&& {aka
gmx::HardwareTopology::Cache&&}â
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:
In function âbool gmx::{anonymous}::parseHwLocDevices(hwloc_topology_t,
gmx::HardwareTopology::Machine*)â:
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:545:83:
error: âHWLOC_OBJ_PCI_DEVICEâ was not declared in this scope
std::vector<const hwloc_obj*> pcidevs = getHwLocDescendantsByType(topo,
root, HWLOC_OBJ_PCI_DEVICE);
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:580:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.vendor_id,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:581:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.device_id,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:582:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.class_id,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:583:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.domain,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:584:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.bus,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:585:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.dev,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:586:50:
error: âunion hwloc_obj_attr_uâ has no member named âpcidevâ
p->attr->pcidev.func,
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:588:39:
error: no matching function for call to
âstd::vector<gmx::HardwareTopology::Device>::push_back(<brace-enclosed
initializer list>)â
} );
^
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:588:39:
note: candidates are:
In file included from /usr/include/c++/4.8.2/vector:64:0,
from
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.h:48,
from
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:46:
/usr/include/c++/4.8.2/bits/stl_vector.h:901:7: note: void std::vector<_Tp,
_Alloc>::push_back(const value_type&) [with _Tp =
gmx::HardwareTopology::Device; _Alloc =
std::allocator<gmx::HardwareTopology::Device>; std::vector<_Tp,
_Alloc>::value_type = gmx::HardwareTopology::Device]
push_back(const value_type& __x)
^
/usr/include/c++/4.8.2/bits/stl_vector.h:901:7: note: no known conversion for
argument 1 from â<brace-enclosed initializer list>â to âconst value_type&
{aka const gmx::HardwareTopology::Device&}â
/usr/include/c++/4.8.2/bits/stl_vector.h:919:7: note: void std::vector<_Tp,
_Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp =
gmx::HardwareTopology::Device; _Alloc =
std::allocator<gmx::HardwareTopology::Device>; std::vector<_Tp,
_Alloc>::value_type = gmx::HardwareTopology::Device]
push_back(value_type&& __x)
^
/usr/include/c++/4.8.2/bits/stl_vector.h:919:7: note: no known conversion for
argument 1 from â<brace-enclosed initializer list>â to
âstd::vector<gmx::HardwareTopology::Device>::value_type&& {aka
gmx::HardwareTopology::Device&&}â
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:
In function âvoid
gmx::{anonymous}::parseHwLoc(gmx::HardwareTopology::Machine*,
gmx::HardwareTopology::SupportLevel*, bool*)â:
/mnt/mbi/home/mbiyum/gromacs/gromacs-2019.4/src/gromacs/hardware/hardwaretopology.cpp:613:36:
error: âHWLOC_TOPOLOGY_FLAG_IO_DEVICESâ was not declared in this scope
hwloc_topology_set_flags(topo, HWLOC_TOPOLOGY_FLAG_IO_DEVICES);
^
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
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