[gmx-users] Regarding installation problem

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 23 15:42:57 CET 2016 

Hi,

That's still going to need an updated binutils, though.

Mark

On Tue, Feb 23, 2016 at 3:40 PM Szilárd Páll <pall.szilard at gmail.com> wrote:

> AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if
> it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will
> waste your hardware a bit less.
>
> --
> Szilárd
>
> On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You can probably use any GROMACS version, if you want it to run slowly
> and
> > generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1.
> >
> > Mark
> >
> > On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL <m.souvik at iitkgp.ac.in>
> > wrote:
> >
> > > Which version of gromacs will be suitable for gcc version 4.4.7?
> > >
> > >
> > >
> > > ----- Original Message -----
> > > From: "Mark Abraham" <mark.j.abraham at gmail.com>
> > > To: gmx-users at gromacs.org
> > > Sent: Tuesday, February 23, 2016 6:05:13 PM
> > > Subject: Re: [gmx-users] Regarding installation problem
> > >
> > > Hi,
> > >
> > > The simplest thing is to get the latest version of gcc that your
> > operating
> > > system (e.g. Linux distribution) supports. Sadly, people often sell
> > compute
> > > systems based on "mature, stable, reliable" versions of software, but
> > with
> > > modern hardware, which automatically means that everything is out of
> date
> > > and their users have to do all of this useless work. But do talk to
> your
> > > system administrators to get some up to date tools installed for you.
> > >
> > > Mark
> > >
> > > On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL <m.souvik at iitkgp.ac.in>
> > > wrote:
> > >
> > > > Can u tell what are compilers I need to up-to-date?
> > > >
> > > > ----- Original Message -----
> > > > From: "Mark Abraham" <mark.j.abraham at gmail.com>
> > > > To: gmx-users at gromacs.org
> > > > Sent: Tuesday, February 23, 2016 4:50:52 PM
> > > > Subject: Re: [gmx-users] Regarding installation problem
> > > >
> > > > Hi,
> > > >
> > > > On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL <
> m.souvik at iitkgp.ac.in>
> > > > wrote:
> > > >
> > > > > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON
> > > > > the output in that ternimal comes as follows
> > > > >
> > > > > - The C compiler identification is GNU 4.4.7
> > > > > -- The CXX compiler identification is GNU 4.4.7
> > > > >
> > > >
> > > > This compiler version was designed several years before your hardware
> > > model
> > > > was released, so it will not work very well. Please get an up-to-date
> > > > compiler for your distribution, as the install guide suggests :-)
> > > >
> > > > -- 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 NVIDIA GPUs present in the system
> > > > > -- Could not detect NVIDIA GPUs
> > > > > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > > > acceleration
> > > > > -- Checking for GCC x86 inline asm
> > > > > -- Checking for GCC x86 inline asm - supported
> > > > > -- Detecting best SIMD instructions for this CPU
> > > > > -- Detected best SIMD instructions for this CPU - AVX2_256
> > > > > -- Try OpenMP C flag = [-fopenmp]
> > > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > > -- Try OpenMP CXX flag = [-fopenmp]
> > > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > > -- Found OpenMP: -fopenmp
> > > > > -- Performing Test CFLAGS_WARN
> > > > > -- Performing Test CFLAGS_WARN - Success
> > > > > -- Performing Test CFLAGS_WARN_EXTRA
> > > > > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > > > > -- Performing Test CFLAGS_WARN_UNDEF
> > > > > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > > > > -- Performing Test CFLAGS_WARN_REL
> > > > > -- Performing Test CFLAGS_WARN_REL - 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_WARN_EXTRA
> > > > > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > > > > -- Performing Test CXXFLAGS_WARN_UNDEF
> > > > > -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> > > > > -- Performing Test CXXFLAGS_WARN_REL
> > > > > -- Performing Test CXXFLAGS_WARN_REL - 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
> > > > > -- gcc 4.4.7 detected, using -O3, will apply workaround for
> > > optimization
> > > > > bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> > > > > -- 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 posix_memalign
> > > > > -- Looking for posix_memalign - found
> > > > > -- Looking for memalign
> > > > > -- Looking for memalign - not found
> > > > > -- Looking for _aligned_malloc
> > > > > -- Looking for _aligned_malloc - not 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
> > > > > -- Looking for rsqrt
> > > > > -- Looking for rsqrt - not found
> > > > > -- Looking for rsqrtf
> > > > > -- Looking for rsqrtf - not found
> > > > > -- Looking for sqrtf
> > > > > -- Looking for sqrtf - found
> > > > > -- 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
> > > > > -- 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
> > > > > -- Looking for zlibVersion in /usr/lib64/libz.so
> > > > > -- Looking for zlibVersion in /usr/lib64/libz.so - found
> > > > > -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
> > > > > -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so
> > > > > -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so -
> > > found
> > > > > -- Looking for include file libxml/parser.h
> > > > > -- Looking for include file libxml/parser.h - found
> > > > > -- 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
> > > > > -- 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
> > > > > -- Could NOT find Boost
> > > > > Boost >= 1.44 not found. Using minimal internal version. This may
> > cause
> > > > > trouble if you plan on compiling/linking other software that uses
> > Boost
> > > > > against GROMACS.
> > > > > -- Setting build user/date/host/cpu information
> > > > > -- Setting build user & time - OK
> > > > > -- Checking floating point format
> > > > > -- Checking floating point format - IEEE754 (LE byte, LE word)
> > > > > -- 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
> > > > > -- Checking for isfinite
> > > > > -- Performing Test isfinite_compile_ok
> > > > > -- Performing Test isfinite_compile_ok - Success
> > > > > -- Checking for isfinite - yes
> > > > > -- Checking for _isfinite
> > > > > -- Performing Test _isfinite_compile_ok
> > > > > -- Performing Test _isfinite_compile_ok - Failed
> > > > > -- Checking for _isfinite - no
> > > > > -- Checking for _finite
> > > > > -- Performing Test _finite_compile_ok
> > > > > -- Performing Test _finite_compile_ok - Failed
> > > > > -- Checking for _finite - no
> > > > > -- Performing Test CXXFLAG_STD_CXX0X
> > > > > -- Performing Test CXXFLAG_STD_CXX0X - Success
> > > > > -- Performing Test GMX_CXX11_SUPPORTED
> > > > > -- Performing Test GMX_CXX11_SUPPORTED - Failed
> > > > > -- Looking for C++ include regex
> > > > > -- Looking for C++ include regex - not found
> > > > > -- Checking for system XDR support
> > > > > -- Checking for system XDR support - present
> > > > > -- Try C compiler AVX2 flag = [-march=core-avx2]
> > > > > -- Performing Test C_FLAG_march_core_avx2
> > > > > -- Performing Test C_FLAG_march_core_avx2 - Failed
> > > > > -- Try C compiler AVX2 flag = [-mavx2]
> > > > > -- Performing Test C_FLAG_mavx2
> > > > > -- Performing Test C_FLAG_mavx2 - Failed
> > > > > -- Try C compiler AVX2 flag = [/arch:AVX]
> > > > > -- Performing Test C_FLAG_arch_AVX
> > > > > -- Performing Test C_FLAG_arch_AVX - Failed
> > > > > -- Try C compiler AVX2 flag = [-hgnu]
> > > > > -- Performing Test C_FLAG_hgnu
> > > > > -- Performing Test C_FLAG_hgnu - Failed
> > > > > -- Try C compiler AVX2 flag = []
> > > > > -- Performing Test C_FLAG_
> > > > > -- Performing Test C_FLAG_ - Success
> > > > > -- Performing Test C_SIMD_COMPILES_FLAG_
> > > > > -- Performing Test C_SIMD_COMPILES_FLAG_ - Failed
> > > > > -- Compiler flag was valid, but executable did not build - perhaps
> > > update
> > > > > the binutils package
> > > > > -- Try C++ compiler AVX2 flag = [-march=core-avx2]
> > > > > -- Performing Test CXX_FLAG_march_core_avx2
> > > > > -- Performing Test CXX_FLAG_march_core_avx2 - Failed
> > > > > -- Try C++ compiler AVX2 flag = [-mavx2]
> > > > > -- Performing Test CXX_FLAG_mavx2
> > > > > -- Performing Test CXX_FLAG_mavx2 - Failed
> > > > > -- Try C++ compiler AVX2 flag = [/arch:AVX]
> > > > > -- Performing Test CXX_FLAG_arch_AVX
> > > > > -- Performing Test CXX_FLAG_arch_AVX - Failed
> > > > > -- Try C++ compiler AVX2 flag = [-hgnu]
> > > > > -- Performing Test CXX_FLAG_hgnu
> > > > > -- Performing Test CXX_FLAG_hgnu - Failed
> > > > > -- Try C++ compiler AVX2 flag = []
> > > > > -- Performing Test CXX_FLAG_
> > > > > -- Performing Test CXX_FLAG_ - Success
> > > > > -- Performing Test CXX_SIMD_COMPILES_FLAG_
> > > > > -- Performing Test CXX_SIMD_COMPILES_FLAG_ - Failed
> > > > > -- Compiler flag was valid, but executable did not build - perhaps
> > > update
> > > > > the binutils package
> > > > > CMake Error at cmake/gmxManageSimd.cmake:67 (message):
> > > > >   Found a compiler flag for AVX2 support, but some other problem
> > > exists.
> > > > >   Update your assembler and/or linker, e.g.  in the binutils
> package
> > of
> > > > > your
> > > > >   distribution.
> > > > >
> > > >
> > > > Here's the diagnosis of the problem. But if you're anyway updating
> your
> > > > infrastructure, get a new compiler first.
> > > >
> > > > Mark
> > > >
> > > >
> > > > > Call Stack (most recent call first):
> > > > >   cmake/gmxManageSimd.cmake:285
> > > > > (gmx_give_fatal_error_when_simd_support_not_found)
> > > > >   CMakeLists.txt:645 (gmx_manage_simd)
> > > > >
> > > > >
> > > > > -- Configuring incomplete, errors occurred!
> > > > > See also
> > > > "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeOutput.log".
> > > > > See also
> > > "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeError.log".
> > > > >
> > > > >
> > > > > ----- Original Message -----
> > > > > From: "Mark Abraham" <mark.j.abraham at gmail.com>
> > > > > To: gmx-users at gromacs.org
> > > > > Sent: Tuesday, February 23, 2016 4:17:17 PM
> > > > > Subject: Re: [gmx-users] Regarding installation problem
> > > > >
> > > > > Hi,
> > > > >
> > > > > Yes, I know. That's its job. The only likely relevant part is very
> > near
> > > > the
> > > > > end. But first I wanted to see the terminal output - what you saw
> on
> > > the
> > > > > screen when you ran cmake.
> > > > >
> > > > > Mark
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
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> > > > > posting!
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> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
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