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

Wed May 24 14:13:58 CEST 2017

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
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 157, Issue 115
> > *******************************************************
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>
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>
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