[gmx-users] [gmx-announce] GROMACS 5.0 official release

Wed Jul 2 11:23:15 CEST 2014

Hi,

Thank you for this new version!

When compiling we've got these warnings:

> attribute warn_unused_result [-Wunused-result]
>      fscanf(in, "%6s", buf);
>                            ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:391:28:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>      fscanf(in, "%15s", buf);
>                             ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:412:36:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>              fscanf(in, "%15s", buf);
>                                     ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:416:40:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>                  fscanf(in, "%15s", buf);
>                                         ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:435:36:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>              fscanf(in, "%15s", buf);
>                                     ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:439:32:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>          fscanf(in, "%15s", buf);
>                                 ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function
> ‘void ReadAccOpen(const char*, FILE*)’:
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:106:27:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>      fscanf(in, "%4s", buf);
>                            ^
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function
> ‘void ReadAccClose(const char*, FILE*)’:
> /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:117:27:
> warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
> declared with attribute warn_unused_result [-Wunused-result]
>      fscanf(in, "%4s", buf);
>                            ^

OS is ubuntu 14.04 64 bit, virtualbox machine:

GROMACS:      gmx, VERSION 5.0
> Executable:   /usr/local/gromacs/bin/gmx
> Library dir:  /usr/local/gromacs/share/gromacs/top
> Command line:
>   gmx -version
> Gromacs version:    VERSION 5.0
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled
> GPU support:        disabled
> invsqrt routine:    gmx_software_invsqrt(x)
> SIMD instructions:  SSE2
> FFT library:        fftw-3.3.3-sse2-avx
> RDTSCP usage:       enabled
> C++11 compilation:  enabled
> TNG support:        enabled
> Tracing support:    disabled
> Built on:           Qua Jul  2 09:54:48 WEST 2014
> Built by:           arh at arh-VirtualBox [CMAKE]
> Build OS/arch:      Linux 3.13.0-24-generic x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:    Intel(R) Xeon(R) CPU           E5530  @ 2.40GHz
> Build CPU family:   6   Model: 26   Stepping: 5
> Build CPU features: apic clfsh cmov cx8 lahf_lm mmx msr pse rdtscp sse2
> sse3 ssse3
> C compiler:         /usr/bin/cc GNU 4.8.2
> C compiler flags:    -msse2   -Wno-maybe-uninitialized -Wextra
> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> -Wno-unused -Wunused-value -Wunused-parameter   -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds  -O3 -DNDEBUG
> C++ compiler:       /usr/bin/c++ GNU 4.8.2
> C++ compiler flags:  -msse2   -std=c++0x -Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
>   -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast
>  -Wno-array-bounds  -O3 -DNDEBUG
> Boost version:      1.55.0 (internal)

On 29 June 2014 21:53, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi GROMACS users,
>
> The official release of GROMACS 5.0 is available!
>
> What new things can you expect?
>
> * GROMACS now uses a combination of *C++98* and C99, so you will need a
> working C++ compiler that is intended to work with your C compiler
>
>
> * Building GROMACS now requires *CMake version 2.8.8*, which will mean
> some of you will need to update your version in order to build GROMACS.
>
> * The native GPU port available in GROMACS 4.6 supports a wider range of
> simulation types, and now requires CUDA 4.0
>
> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
> design principles is that GROMACS will do correct simulations by default,
> and the use of this scheme makes that easy and fast. The group cut-off
> scheme will be removed in a future version, so start planning for that!
>
> * You can now treat *Lennard-Jones interactions with PME*, which is
> expected to provide a much better treatment of spatially heterogeneous
> long-ranged dispersion interactions at cost comparable to that of a cutoff.
> LJPME is supported for both cut-off schemes, and almost all kinds of
> simullations
>
> * GROMACS deploys the Random123 stateless random-number generator
>
> * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga &
> Berendsen
>
> * GROMACS tools are now bundled together into *just two binaries* - mdrun
> and gmx. The latter contains most of the tools familiar to you, perhaps
> with new names, and a couple of new ones. For the time being, the install
> procedure will also create symbolic links so that your old scripts will
> keep working for a time, but these will go away at some future point!
>
> * There is support for the new TNG compressed trajectory format
>
> * GROMACS contains a feature for "computational electrophysiology"
> simulations, to simulate a steady-state ion concentration difference
> between compartments of a double membrane
>
> * GROMACS supports some special interactions for coarse-grained
> interactions with Martini force fields
>
> * GROMACS support for Interactive Molecular Dynamics (IMD)
>
>
> * A handful of the tools have been re-implemented using a *new C++
> analysis framework*, which we hope will provide a better platform for
> maintaining and adding to their functionality in the future.
>
>
> * There is an enhanced testing suite, with *unit tests* for most new C++
> code.
>
> * There is preliminary support for Intel Xeon Phi (only in native mode,
> and performance will only be slightly improved)
>
> * GROMACS has removed support for particle decomposition - the simulation
> types that required it are now limited to a single MPI rank (but perhaps
> multiple OpenMP threads)
>
> Please see the link to the release notes below for more details. All the
> content of GROMACS 4.6.6 (whose release is imminent) is present, apart from
> features that have been removed.
>
> You can find the code, manual, release notes, installation instructions
> and test suite at the links below.
>
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
>
> ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf
>
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0
>
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>
> http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz
>
> Happy simulating!
>
> Mark Abraham
> GROMACS development manager
>
> _______________________________________________
> Announcements from the Gromacs team
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-announce
>