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

Wed May 24 12:11:35 CEST 2017

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
> 
> 
> 
> 
> -- 
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> 
> 
> ------------------------------
> 
> 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.
> 
> 
> 
> ------------------------------
> 
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> 
> * 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
> 
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> End of gromacs.org_gmx-users Digest, Vol 157, Issue 115
> *******************************************************