[gmx-users] [gmx-announce] GROMACS 5.0 official release
Mark Abraham
mark.j.abraham at gmail.com
Wed Jul 2 18:59:52 CEST 2014
Hi,
The warnings are not a problem - gmx view does not get as much love as the
rest of the project!
Mark
On Jul 2, 2014 11:23 AM, "Luís Pereira" <luisp2005 at gmail.com> wrote:
> 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
> >
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