[gmx-users] gromacs 2018 compilation problem with stdlib
Manoel Barrionuevo
manoelvfb at gmail.com
Mon Jul 16 17:02:13 CEST 2018
Hi Mark,
On 16/07/2018 05:09, Mark Abraham wrote:
> Hi,
>
> On Sat, Jul 14, 2018 at 4:58 AM Manoel Barrionuevo <manoelvfb at gmail.com>
> wrote:
>
>> Hi all,
>>
>> I'm trying to compile gromacs 2018.2 and I would like to use intel
>> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop
>> computer with a intel i5 quad-core cpu (the only purpose of it is for
>> learning), in order to do so I was first following the suggested
>> procedures at the INSTALL file distributed along with gromacs, and got
>> the command bellow:
>>
>> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group
>> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a
>> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a
>> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp
>> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include"
>> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
>> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g -O2
>> -std=c++11"
>>
> You're doing a few things that make your life hard (or are brittle) and
> some that make things slow. Source the appropriate script for the intel
> compiler that you want, and then leave MKL details up to it. Choosing -O2
> for optimization overrides the defaults for no good reason. Thus
>
> source /path/to/compiler/bin/compilervars.sh intel64
> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DGMX_GPU=on
> -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/"
> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc
Well, I may not get all details you pointed me however I have attached
two files to show you what exactly happens when I do as said, first you
will see "cmaking" file where you can find the output of cmake. I
noticed some failures, I would be happy to hear from you what could them be.
> It worths to say that the OS under current operation is Lubuntu (16.04)
>> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly
>> without problems, however I noticed a std failure after issuing the
>> "make" command, it says:
>>
>> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250):
>>
>> error: namespace "std" has no member "_Exit"
>> std:: _Exit(returnValue);
>> ^
>>
>> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251):
>>
>> warning #1628: function declared with "noreturn" does retu
>> rn
>> }
>> ^
>>
>> The same problem can be seen if I start from a very simple "cmake ../"
>> and "make". What am I doing wrong? Is there some environment preparation
>> step to be done prior to everything else, and what should it be?
>>
> On Linux, Intel compilers rely on having and finding a suitable gcc for the
> standard library, so I can only presume something is messed up there. For
> example, gcc was installed or updated after icc. Try the advice at
> http://manual.gromacs.org/documentation/current/install-guide/index.html#compiler
>
> Mark
Next, you will see in "making" attached file the output of "make".
Again, I still seeing the issue I reported before. I haven't, however,
set up what you suggested by looking at gromacs manual
(http://manual.gromacs.org/documentation/current/install-guide/index.html#compile).
I'm aware of what you just said, but I can get how should it be the
problem since the current OS have g++-5, gcc-5, gfortran-5 and clang-5
available, and no other gcc, g++, gfortran or clang installed and/or
updated/available as alternative for the system.
I may also point out that it would be of great help if you clarify some
points that I got stuck since, as I said, I'm not an expert (that's why
I got so many dumb things with my first attempt with cmake). Here they are:
1) Gromacs manual suggests this:
|-DGMX_STDLIB_CXX_FLAGS=-gcc-name=/path/to/gcc/binary
|
Where we read "-gcc-name" should I change to "-gcc-5" and give it
the expected path. Is it?
2) Also we get this:
|-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/path/to/gcc/lib64 -L/path/to/gcc/lib64"
|
Where we read "-rpath", should I keep it as it is or change it to
something else? (here you can realize how much I don't know about
compiling stuff).
3) Finally we get the last one:
|-DCMAKE_CXX_FLAGS=--gcc-toolchain=/path/to/gcc/folder|
Where we read "-gcc-toolchain" should it be changed too? And so,
for what?
Well, I told since my very first email that the purpose of it is
learning. I hope I will learn something from my mistakes and I do
appreciate the kind help you provided me till now.
Thanks a lot.
|
|
||
>> I must say that I'm not an expert on compiling things up and I got
>> stuck. Could someone help me out? It would be of great help to know some
>> tips from you guys.
>>
>> Thank you all.
>>
>> Kind regards,
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
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src/gromacs/CMakeFiles/libgromacs.dir/build.make:2800: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o' failed
CMakeFiles/Makefile2:2632: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250): error: namespace "std" has no member "_Exit"
std::_Exit(returnValue);
^
/home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251): warning #1628: function declared with "noreturn" does return
} ^
compilation aborted for /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp (code 2)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o] Error 2
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
Makefile:162: recipe for target 'all' failed
-------------- next part --------------
-- The C compiler identification is Intel 17.0.0.20160721
-- The CXX compiler identification is Intel 17.0.0.20160721
-- Check for working C compiler: /opt/intel17/compilers_and_libraries_2017.0.098/linux/bin/intel64/icc
-- Check for working C compiler: /opt/intel17/compilers_and_libraries_2017.0.098/linux/bin/intel64/icc -- 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: /opt/intel17/compilers_and_libraries_2017.0.098/linux/bin/intel64/icpc
-- Check for working CXX compiler: /opt/intel17/compilers_and_libraries_2017.0.098/linux/bin/intel64/icpc -- 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-9.1/ (found suitable version "9.1", minimum required is "7.0")
-- Found NVML: /usr/lib/x86_64-linux-gnu/libnvidia-ml.so
-- Found OpenMP_C: -qopenmp (found version "4.5")
-- Found OpenMP_CXX: -qopenmp (found version "4.5")
-- Performing Test CFLAGS_STDGNU
-- Performing Test CFLAGS_STDGNU - Success
-- Performing Test CFLAGS_OPT
-- Performing Test CFLAGS_OPT - Success
-- Performing Test CFLAGS_DEBUG
-- Performing Test CFLAGS_DEBUG - Success
-- Performing Test CFLAGS_FP_RELASSERT
-- Performing Test CFLAGS_FP_RELASSERT - Success
-- Performing Test CXXFLAGS_OPT
-- Performing Test CXXFLAGS_OPT - Success
-- Performing Test CXXFLAGS_DEBUG
-- Performing Test CXXFLAGS_DEBUG - Success
-- Performing Test CXXFLAGS_FP_RELASSERT
-- Performing Test CXXFLAGS_FP_RELASSERT - 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
-- 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
-- Could NOT find Hwloc (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS) (Required is at least version "1.5")
-- Looking for include file pthread.h
-- Looking for include file 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
-- Check for working NVCC/C compiler combination - works
-- Enabling single compilation unit for the CUDA non-bonded module. Multiple compilation units are not compatible with CC 2.x devices, to enable the feature specify only CC >=3.0 target architectures in GMX_CUDA_TARGET_SM/GMX_CUDA_TARGET_COMPUTE.
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Setting build user - yokai at yokai [CMAKE]
-- Setting build time - 2018-07-16 14:45:48
-- Setting build host - Linux 4.13.0-36-generic x86_64
-- Detected build CPU vendor - Intel
-- Detected build CPU brand - Intel(R) Core(TM) i5-7400 CPU @ 3.00GHz
-- Detected build CPU family - 6
-- Detected build CPU model - 158
-- Detected build CPU stepping - 9
-- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 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 - AVX2_256
-- Performing Test C_march_core_avx2_FLAG_ACCEPTED
-- Performing Test C_march_core_avx2_FLAG_ACCEPTED - Success
-- Performing Test C_march_core_avx2_COMPILE_WORKS
-- Performing Test C_march_core_avx2_COMPILE_WORKS - Success
-- Performing Test CXX_march_core_avx2_FLAG_ACCEPTED
-- Performing Test CXX_march_core_avx2_FLAG_ACCEPTED - Success
-- Performing Test CXX_march_core_avx2_COMPILE_WORKS
-- Performing Test CXX_march_core_avx2_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags: -march=core-avx2
-- 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 - Success
-- Performing Test C_xCORE_AVX512_COMPILE_WORKS
-- Performing Test C_xCORE_AVX512_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 - Success
-- Performing Test CXX_xCORE_AVX512_COMPILE_WORKS
-- Performing Test CXX_xCORE_AVX512_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -xCORE-AVX512
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Failed
-- Performing Test _wd10121_FLAG_ACCEPTED
-- Performing Test _wd10121_FLAG_ACCEPTED - Success
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Success
-- Looking for DftiCreateDescriptor
-- Looking for DftiCreateDescriptor - found
-- Using external FFT library - Intel MKL
-- Looking for dgemm_
-- Looking for dgemm_ - found
-- Looking for cheev_
-- Looking for cheev_ - found
-- 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: ""
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.14", 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
-- 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: /home/yokai/Programs/gromacs-2018.2/build
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