[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04

Szilárd Páll pall.szilard at gmail.com
Wed May 24 17:03:07 CEST 2017 

That should not be needed if this is a default Ubnutu 17.04 install that
comes with gcc 6 ootb, I think.

--
Szilárd

On Wed, May 24, 2017 at 2:13 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Using a gcc version also entails linking to the standard library that comes
> along with it, ie libstdc++.so. By default, it will link at run time to the
> version that shipped with the package. For any sufficiently new compiler,
> that won't work (by design) because the library and the compiler evolve
> together. To tell the resulting gromacs which new standard library to link
> to, you need to set the LD_LIBRARY_PATH environment variable, e.g. for bash
> on a 64-bit Linux system (almost all of them these days):
>
> export LD_LIBRARY_PATH=/path/to/your/gcc/lib64:$LD_LIBRARY_PATH
>
> in the shell from which you want to run gmx.
>
> We should probably look into having cmake hack on the RPATH so this can
> work more automagically.
>
> Mark
>
> On Wed, May 24, 2017 at 12:12 PM Steffen Graether <graether at uoguelph.ca>
> wrote:
>
> > Hi Vytautas,
> >
> > I should have mentioned that I had deleted the ‘build’ directory and
> tried
> > the cmake command again, but I received the same error.
> >
> > I had installed a large number of different compilers (clang-3.8,
> > clang-4.0, gcc-5) to get my CUDA installation to work but thought I had
> > removed them all afterwards (just ran apt-get remove again to delete
> > clang-4.0). Still getting the same error.
> >
> > Regards,
> > Steffen
> >
> > Date: Wed, 24 May 2017 08:45:57 +0000 (UTC)
> >
> > > From: Vytautas Rakeviius <vytautas1987 at yahoo.com>
> > > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
> > >       "gromacs.org_gmx-users at maillist.sys.kth.se"
> > >       <gromacs.org_gmx-users at maillist.sys.kth.se>
> > > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> > >       17.04
> > > Message-ID: <743319698.939458.1495615557030 at mail.yahoo.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Ubuntu 17.04 should give you quite up-to date gcc and co.
> > > Make sure you try this on clean folder: remove everything download and
> > try again. Maybe some old files interfering.
> > >
> > >
> > >    On Wednesday, May 24, 2017 4:14 AM, Steffen Graether <
> > graether at uoguelph.ca> wrote:
> > >
> > >
> > > Hi,
> > >
> > > I?ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I?ve checked that
> > gcc-6 and g++6 are installed, but when running cmake? I get the following
> > error:
> > >
> > > -- Performing Test CXX11_STDLIB_PRESENT - Failed
> > > CMake Error at cmake/gmxTestCXX11.cmake:139 (message):
> > > ? This version of GROMACS requires C++11-compatible standard library.?
> > Please
> > > ? use a newer compiler, or a newer standard library, or use the GROMACS
> > 5.1.x
> > > ? release.? See the installation guide for details.
> > > Call Stack (most recent call first):
> > > ? CMakeLists.txt:164 (gmx_test_cxx11)
> > >
> > > Searching for this problem I find a few references to having an up to
> > date gcc, but nothing else. Can anyone point me in the right direction to
> > fix this?
> > >
> > > Thanks,
> > > Steffen
> > >
> > >
> > >
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 4
> > > Date: Wed, 24 May 2017 11:28:55 +0200
> > > From: "Kamps, M." <m.kamps at student.rug.nl>
> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Subject: [gmx-users] Problem with accelerations
> > > Message-ID:
> > >       <
> > CACsKKu3niwEwt7d8O-nTEqmgQ+VwpG0mfmbUD_S-0kcpAOvYkA at mail.gmail.com>
> > > Content-Type: text/plain; charset="UTF-8"
> > >
> > > Mark,
> > >
> > > I'm not really sure what you mean by technique. I assume NEMD stands
> > > for Non-equilibrium MD? That is the case in my simulation..
> > >
> > > About my simulation: I am trying to simulate a fluid flow between
> > > surfaces. Two atomistic surfaces of gold atoms have been created at
> > > Z=0 and Z=z, where z is the top of the box. These surfaces are fixed.
> > > In between is a fluid that should be accelerated in order to create a
> > > flow. This is done by applying a constant acceleration in the X
> > > direction via the commands; 'acc-grps = FLUID' and 'accelerate = 0.05
> > > 0 0'. Is this equal to the bug you referenced to?
> > >
> > > Suppose the command is broken, does this mean that the simulation is
> > > worthless since there are computational errors, or is the applied
> > > velocity buggy but the results still useful? Suppose I can find the
> > > right accelerations, can I still use the results?
> > >
> > > Another question, how can I properly 'reply' to an answer working from
> > > the digest mailing list? If I reply normally (via my mail client) and
> > > delete the other messages, my message will not be displayed as a reply
> > > in online mailing-list viewers such as Narkive etc. Am I replying
> > > correctly?
> > >
> > >
> > > Mark Abraham wrote:
> > >> Hi,
> > >> Which technique are you using for this?
> > >> https://redmine.gromacs.org/issues/1354 speculates that this code is
> > just
> > >> broken, has been so for years, and should be removed given that nobody
> > >> wishes to do the work to fix it ( :-( )
> > >> Mark
> > >> On Tue, May 23, 2017 at 11:13 AM Kamps, M. <m.kamps at student.rug.nl>
> > wrote:
> > >>> Dear GMX users,
> > >>>
> > >>> I have some strange behaviour which I cannot explain.
> > >>>
> > >>> I want to accelerate atoms through my box at a certain velocity.
> Since
> > >>> I can only adjust the acceleration, I have to trial-and-error my way
> > >>> to the right accelerations.
> > >>>
> > >>> To do this, I create a smaller 'testing' simulation, which is
> > >>> continued from an extensive equilibrium. I apply an acceleration of
> > >>> 0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with
> > >>> an gmx select input) says that the velocity is stable at around 0.04
> > >>> nm/ps. throughout the simulation the velocity slightly increases due
> > >>> to the atoms rearranging etc.
> > >>>
> > >>> Now I want to simulate the same behaviour, but for a longer amount of
> > >>> time. I therefore take the exact same MDP file, and change nothing
> > >>> except the time-related parameters. I change the number of total
> steps
> > >>> and the timestep, but leave the acceleration intact. After analysing
> > >>> the data I get a MUCH higher velocity! I can understand this due to
> > >>> rearranging of the atoms on the longer term, but after the same 200ps
> > >>> the velocity is also way higher.
> > >>>
> > >>> So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in
> > >>> this longer run, the velocity is 0.2 nm/ps after the same 200ps. How
> > >>> is this possible? The exact same acceleration is applied.
> > >>>
> > >>> Am I missing something?
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at
> > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>> posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
> > >>> * For (un)subscribe requests visit
> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-request at gromacs.org.
> > >>>
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 5
> > > Date: Wed, 24 May 2017 08:45:57 +0000 (UTC)
> > > From: Vytautas Rakeviius <vytautas1987 at yahoo.com>
> > > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
> > >       "gromacs.org_gmx-users at maillist.sys.kth.se"
> > >       <gromacs.org_gmx-users at maillist.sys.kth.se>
> > > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> > >       17.04
> > > Message-ID: <743319698.939458.1495615557030 at mail.yahoo.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Ubuntu 17.04 should give you quite up-to date gcc and co.
> > > Make sure you try this on clean folder: remove everything download and
> > try again. Maybe some old files interfering.
> > >
> > >
> > >    On Wednesday, May 24, 2017 4:14 AM, Steffen Graether <
> > graether at uoguelph.ca> wrote:
> > >
> > >
> > > Hi,
> > >
> > > I?ve tried installing GROMACS 2016.3 on Ubuntu 17.04. I?ve checked that
> > gcc-6 and g++6 are installed, but when running cmake? I get the following
> > error:
> > >
> > > -- Performing Test CXX11_STDLIB_PRESENT - Failed
> > > CMake Error at cmake/gmxTestCXX11.cmake:139 (message):
> > > ? This version of GROMACS requires C++11-compatible standard library.?
> > Please
> > > ? use a newer compiler, or a newer standard library, or use the GROMACS
> > 5.1.x
> > > ? release.? See the installation guide for details.
> > > Call Stack (most recent call first):
> > > ? CMakeLists.txt:164 (gmx_test_cxx11)
> > >
> > > Searching for this problem I find a few references to having an up to
> > date gcc, but nothing else. Can anyone point me in the right direction to
> > fix this?
> > >
> > > Thanks,
> > > Steffen
> > >
> > >
> > >
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > >
> > >
> > >
> > > ------------------------------
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
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> > send a mail to gmx-users-request at gromacs.org.
> > >
> > > End of gromacs.org_gmx-users Digest, Vol 157, Issue 115
> > > *******************************************************
> >
> > --
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> >
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