[gmx-users] Error when compiling 2019.2 with -DGMX_MPI=ON

[Dallas Warren]

Realise I should provide some output etc for each of these:

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cmake .. -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromas-2019.2
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- 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: 1
-- Found CUDA: /usr/local/cuda (found suitable version "10.1", minimum
required is "7.0")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 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
-- Defaulting to building static libraries
-- Could NOT find Hwloc (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS)
(Required is at least version "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
-- Adding work-around for issue compiling CUDA code with glibc 2.23 string.h
-- 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) Core(TM) i7-3930K CPU @ 3.20GHz
-- Detected build CPU family - 6
-- Detected build CPU model - 45
-- Detected build CPU stepping - 7
-- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse
rdtscp 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 - AVX_256
-- Performing Test C_mavx_FLAG_ACCEPTED
-- Performing Test C_mavx_FLAG_ACCEPTED - Success
-- Performing Test C_mavx_COMPILE_WORKS
-- Performing Test C_mavx_COMPILE_WORKS - Success
-- Performing Test CXX_mavx_FLAG_ACCEPTED
-- Performing Test CXX_mavx_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx_COMPILE_WORKS
-- Performing Test CXX_mavx_COMPILE_WORKS - Success
-- Enabling 256-bit AVX SIMD instructions using CXX flags:  -mavx
-- 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 - Success
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success
-- 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 - Success
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on
newer CPUs -  -mavx512f -mfma
-- 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
-- Checking for module 'fftw3f'
--   Found fftw3f, version 3.3.8
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- 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
-- GROMACS only supports plugins in a build that uses shared
libraries, which can be disabled for various reasons.
BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is
required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can
influence the default BUILD_SHARED_LIBS, so if you need plugins,
reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- 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

make
Scanning dependencies of target tng_io_zlib
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inflate.c.o
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o

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Then I delete the build directory and do this:

cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromas-2019.2
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- 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: 1
-- Found CUDA: /usr/local/cuda (found suitable version "10.1", minimum
required is "7.0")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 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
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Found MPI_C: /usr/lib64/mpi/gcc/mvapich2/lib64/libmpi.so (found
version "3.0")
-- Found MPI_CXX: /usr/lib64/mpi/gcc/mvapich2/lib64/libmpicxx.so
(found version "3.0")
-- Found MPI: TRUE (found version "3.0")
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Could NOT find Hwloc (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS)
(Required is at least version "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
-- Adding work-around for issue compiling CUDA code with glibc 2.23 string.h
-- 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) Core(TM) i7-3930K CPU @ 3.20GHz
-- Detected build CPU family - 6
-- Detected build CPU model - 45
-- Detected build CPU stepping - 7
-- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse
rdtscp 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 - AVX_256
-- Performing Test C_mavx_FLAG_ACCEPTED
-- Performing Test C_mavx_FLAG_ACCEPTED - Success
-- Performing Test C_mavx_COMPILE_WORKS
-- Performing Test C_mavx_COMPILE_WORKS - Success
-- Performing Test CXX_mavx_FLAG_ACCEPTED
-- Performing Test CXX_mavx_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx_COMPILE_WORKS
-- Performing Test CXX_mavx_COMPILE_WORKS - Success
-- Enabling 256-bit AVX SIMD instructions using CXX flags:  -mavx
-- 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 - Success
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS
-- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success
-- 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 - Success
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on
newer CPUs -  -mavx512f -mfma
-- 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
-- Checking for module 'fftw3f'
--   Found fftw3f, version 3.3.8
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- 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
-- GROMACS only supports plugins in a build that uses shared
libraries, which can be disabled for various reasons.
BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is
required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can
influence the default BUILD_SHARED_LIBS, so if you need plugins,
reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using default binary suffix: "_mpi"
-- Using default library suffix: "_mpi"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Failed
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Failed
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Failed
-- 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 - failed
-- Looking for inttypes.h
-- Looking for inttypes.h - not found
-- Configuring done
-- Generating done

make
Scanning dependencies of target tng_io_zlib
[  0%] Building C object
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o
cc: fatal error: no input files
compilation terminated.
/bin/sh: -funwind-tables: command not found
/bin/sh: -fasynchronous-unwind-tables: command not found
/bin/sh: -fstack-clash-protection: command not found
make[2]: *** [src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make:63:
src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o]
Error 127
make[1]: *** [CMakeFiles/Makefile2:1760:
src/gromacs/CMakeFiles/tng_io_zlib.dir/all] Error 2
make: *** [Makefile:163: all] Error 2


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 6 May 2019 at 10:37, Dallas Warren <dallas.warren at monash.edu> wrote:
>
> I can compiling the entire package of 2019.2 fine, without MPI on.
>
> But as soon as I go to compile with MPI, I get a fatal error.
>
> The following works fine:
> cmake .. -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromas-2019.2
>
> But the following does not:
> cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromas-2019.2
>
> Gives the following error:
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/dallas/Downloads/gromacs/gromacs-2019.2/build
> [  0%] Building C object
> src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o
> cc: fatal error: no input files
> compilation terminated.
> /bin/sh: -funwind-tables: command not found
> /bin/sh: -fasynchronous-unwind-tables: command not found
> /bin/sh: -fstack-clash-protection: command not found
> make[2]: *** [src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make:63:
> src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o]
> Error 127
> make[1]: *** [CMakeFiles/Makefile2:1760:
> src/gromacs/CMakeFiles/tng_io_zlib.dir/all] Error 2
> make: *** [Makefile:163: all] Error 2
>
> Did think it might have been an issue with having TNG on, and the zlib
> etc, so even when you turn off TNG off (-DGMX_USE_TNG=OFF) then get
> the same error:
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/dallas/Downloads/gromacs/gromacs-2019.2/build
> Scanning dependencies of target libgromacs_generated
> [  0%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o
> c++: fatal error: no input files
> compilation terminated.
> /bin/sh: -funwind-tables: command not found
> /bin/sh: -fasynchronous-unwind-tables: command not found
> /bin/sh: -fstack-clash-protection: command not found
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make:63:
> src/gromacs/CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o]
> Error 127
> make[1]: *** [CMakeFiles/Makefile2:1756:
> src/gromacs/CMakeFiles/libgromacs_generated.dir/all] Error 2
> make: *** [Makefile:163: all] Error 2
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.