[gmx-users] Gromacs 2020

[Mark Abraham]

Hi,

The code is tested extensively on a range of compilers, so we believe it is
correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS
tests with 6.4.0, so the issue might have been fixed in the meantime. As
newer versions of gcc and cuda will give better performance, I suggest you
get cuda 10.2 and gcc 8 and try again. Sorry!

Mark

On Mon, 9 Mar 2020 at 10:56, Turega, Simon <S.Turega at shu.ac.uk> wrote:

> Hi all
>
> After attempting to install GROMACS 2020 on new system, I get the error
> below. The system details &  other details are below the error.
>
>  cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020
> -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=gcc -DGMX_GPU=ON -Wno-dev
>
> make
>
> [ 84%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o
> In file included from
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:48:0,
>                  from
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h: In
> instantiation of 'std::unique_ptr<gmx::ISimulator>
> gmx::SimulatorBuilder::build(bool, Args&& ...) [with Args = {_IO_FILE*&,
> t_commrec*&, gmx_multisim_t*&, gmx::MDLogger&, int, const t_filenm*,
> gmx_output_env_t*&, gmx::MdrunOptions&, gmx::StartingBehavior&,
> gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*, gmx::BoxDeformation*,
> gmx::IMDOutputProvider*, const gmx::MdModulesNotifier&, t_inputrec*&,
> gmx::ImdSession*, pull_t*&, t_swap*&, gmx_mtop_t*, t_fcdata*&, t_state*,
> ObservablesHistory*, gmx::MDAtoms*, t_nrnb*, gmx_wallcycle*&, t_forcerec*&,
> gmx_enerdata_t*, gmx_ekindata_t*, gmx::MdrunScheduleWorkload*,
> ReplicaExchangeParameters&, gmx_membed_t*&, gmx_walltime_accounting*&,
> std::unique_ptr<gmx::StopHandlerBuilder,
> std::default_delete<gmx::StopHandlerBuilder> >, const bool&}]':
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:1612:77:
>  required from here
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/legacysimulator.h:94:23:
> error: use of deleted function 'std::unique_ptr<_Tp, _Dp>::unique_ptr(const
> std::unique_ptr<_Tp, _Dp>&) [with _Tp = gmx::StopHandlerBuilder; _Dp =
> std::default_delete<gmx::StopHandlerBuilder>]'
>      using ISimulator::ISimulator;
>                        ^~~~~~~~~~
> In file included from
> /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
>                  from
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.h:48,
>                  from
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:46:
> /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note:
> declared here
>        unique_ptr(const unique_ptr&) = delete;
>        ^~~~~~~~~~
> In file included from
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/runner.cpp:161:0:
> /home/b5018993/src/gromacs-2020/src/gromacs/mdrun/simulatorbuilder.h:123:45:
> note: synthesized method 'gmx::LegacySimulator::LegacySimulator(FILE*,
> t_commrec*, const gmx_multisim_t*, const gmx::MDLogger&, int, const
> t_filenm*, const gmx_output_env_t*, const gmx::MdrunOptions&,
> gmx::StartingBehavior, gmx_vsite_t*, gmx::Constraints*, gmx_enfrot*,
> gmx::BoxDeformation*, gmx::IMDOutputProvider*, const
> gmx::MdModulesNotifier&, t_inputrec*, gmx::ImdSession*, pull_t*, t_swap*,
> gmx_mtop_t*, t_fcdata*, t_state*, ObservablesHistory*, gmx::MDAtoms*,
> t_nrnb*, gmx_wallcycle*, t_forcerec*, gmx_enerdata_t*, gmx_ekindata_t*,
> gmx::MdrunScheduleWorkload*, const ReplicaExchangeParameters&,
> gmx_membed_t*, gmx_walltime_accounting*,
> std::unique_ptr<gmx::StopHandlerBuilder>, bool)' first required here
>      return std::unique_ptr<LegacySimulator>(new
> LegacySimulator(std::forward<Args>(args)...));
>
>  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o]
> Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> System details
>
> Architecture: x86_64
> CPU op modes: 32-bit, 64-bit
>
> OS details
>
> CentOS Linux release 7.3.1611 (Core)
> Linux 3.10.0-327.22.2.el7.x86_64
>
> Compiler/ nvcc details
>
> openmpi/intel-ofed/gcc/64/1.10.4
> Cuda 90 toolkit/9.0.176
> gcc version 6.1.0
>
> Thanks in advance for your help
>
> Simon Turega
> --
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