Hi,
your not saying what version you are trying to install. Assuming 5.0.5 it
should just work with
cmake -DGMX_BUILD_SHARED_EXE=off ..
Make sure to select GCC or ICC as compiler with a command such as (might be
different on your machine)
module swap PrgEnv-pgi PrgEnv-gnu
If it still doesn't wor
Hi,
yes the variable is ignored. Because with GROMACS 5 large file support is
required. Thus if the variable is set to false it also prints a fatal
error. It was never a variable which was suppose to be set by the user.
Why do you ask? What do you try to achieve?
Roland
On Tue, Jun 23, 2015 at 3
Hi,
please rerun cmake from an empty build directly and post both the full
cmake output and the content of CMakeFiles/CMakeError.log.
Roland
On Thu, May 7, 2015 at 7:38 PM, James Lord wrote:
> Hi Mark,Szilard and Christopher,
> Thanks for the comments,
> apparently gcc 4.8.2 is there. Really c
On Tue, Dec 16, 2014 at 10:09 AM, Mike Hanby wrote:
>
> Howdy,
>
> I'm attempting to build Gromacs 5.0.4 using Intel compilers 13.1.1 for one
> of the users of our HPC fabric and it errors when running test 13 during
> the "make check"
>
There are several known problems with ICC 13. This might be
Hi,
CMakeFiles/CMakeError.log should show why cmake thinks your gcc doesn't
support -mavx2.
Roland
On Mon, Dec 15, 2014 at 9:18 AM, Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:
>
> BS"D
>
> Dear Mark,
>
> Here is where it fails:
>
> -- Try C++ compiler AVX2 flag = [-mavx2]
>
Hi,
Gromacs < 5.0 uses a Mersenne twister. See gmx_random.h. Starting with 5.0
it uses Random123 threefry2x64. Why do you think your results are affected
by the PRNG?
Roland
On Wed, Oct 29, 2014 at 6:23 PM, Johnny Lu wrote:
> Hi.
>
> Before I start to feel optimistic about my alanine tripeptid
Hi,
assuming you want to run on the CPU, nothing special should be required.
Make sure to let support know that they don't have the most recent version
and they should install the most recent version.
Roland
On Wed, Oct 22, 2014 at 5:24 AM, Amrash wrote:
> Dear all,
>
> I was wondering if ther
Hi,
this seems to be the boost bug https://svn.boost.org/trac/boost/ticket/10420
. Please file a Gromacs redmine issue. As a temporary solution use
gcc>=4.7. It should be as fast as ICC at least when used with GPU.
Roland
On Fri, Oct 17, 2014 at 2:23 AM, Éric Germaneau
wrote:
> Dear all,
>
> I
> L1d cache: 32K
> L1i cache: 32K
> L2 cache: 256K
> L3 cache: 20480K
> NUMA node0 CPU(s): 0-7
> NUMA node1 CPU(s): 8-15
>
> I hope this information will help. Thank you.
>
> Yunlong
>
>
>
>
>
>
> On
Hi,
please don't use gmx-developers for user questions. Feel free to use it if
you want to fix the problem, and have questions about implementation
details.
Please provide more details: How large is your system? How much memory does
a node have? On how many nodes do you try to run? How many mpi-r
On Mon, Jul 21, 2014 at 9:48 PM, John Doe wrote:
> Attempting to build the Git clone (git clone
> https://gerrit.gromacs.org/gromacs)
In general if you are a user and not a developer you want to use the latest
release branch (contains only bugfixes relative since the last version) and
not the ma
On Mon, Jul 21, 2014 at 7:17 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 22.07.2014 00:51, John Doe wrote:
> > [ 8%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o
> > /home/User/gromacs/gromacs-5.0/src/gromacs/gmxpreprocess/fflibuti
Hi,
you either need to use this patch: https://gerrit.gromacs.org/#/c/3764, or
the latest release-5-0 branch (which includes the patch), or
add -std=gnu++0x to the CXXFLAGS.
Roland
On Mon, Jul 21, 2014 at 6:51 PM, John Doe wrote:
> Hello,
>
> I'm attempting to install Gromacs-5.0 on Cygwin64.
gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
>
Hi,
GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you building
under Linux? It probably didn't find dlopen support. Look for "Result of
test for dlopen" when you run cmake in a new build folder. You can see in
CMakeFiles/CMakeError.log why the dlopen test fails.
Roland
On Tue,
Hi,
use -quiet (in 5.0) or 2>/dev/null
Roland
On Mon, Jul 7, 2014 at 6:28 PM, Chetan Mahajan wrote:
> Dear All,
>
> I recently made a molecular dynamics run of TiO2-water-sodium-formate
> system of 12740 atoms. Then I extracted dump file from xtc file of
> production run ( NPT, 300 K, 1 bar)
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh
wrote:
> I ran the md5sum but it does not match with any of the hashes.What should I
> do now?
>
Which file from which server (/which URL) did you download? What md5 did
you get?
Roland
>
>
> On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll
> wrot
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
http://fossies.org/linux/privat/gromacs-5.0.tar.gz
If you download from a mirror make sure to check the md5sum.
On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll wrote:
> The link is correct, something m
Hi
we have fixed quite a few installation issues since beta2. Could you try to
download the latest version from git?
git clone git://git.gromacs.org/gromacs.git
Let us know if you still see the issue.
If you don't have git you can download it from:
https://github.com/gromacs/gromacs/archive/mast
Hi,
I uploaded fixes for both issues:
https://gerrit.gromacs.org/#/c/3040/
https://gerrit.gromacs.org/#/c/3041/
Thanks for the feedback.
Roland
On Wed, Jan 29, 2014 at 12:59 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 29.01.2014 15:06, Mirco Wahab wrote:
> > A test run (
Hi,
sorry we had a mixup with the account activation. Your account should be
activated now.
Roland
On Mon, Dec 9, 2013 at 3:35 AM, Patrick Fuchs <
patrick.fu...@univ-paris-diderot.fr> wrote:
> Hi all,
> I tried to make an account on http://redmine.gromacs.org/ by filling the
> online form, but
Hi,
what compiler is used by mpicc? What does "mpicc -showme" and "mpicc
--version" show? Does it help to uncomment the line containing F77_FUNC int
src/config.h.cmakein?
Roland
On Sun, Dec 8, 2013 at 7:44 PM, Michael Shirts wrote:
> So, I'm trying to compile with MPI using mpich3. Previous
Hi,
I haven't tried it but it should work if you set verlet-buffer-drift=-1 and
set rlist manually.
Roland
On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten wrote:
> I am trying to add virtual sites to a simulation with no mass or charge,
> just
> to make tracking the center of mass of groups l
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