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

[Steffen Graether]

Hi,

Replying to say thanks and add a few details in case anyone comes across this 
thread in a search.

Setting LD_LIBRARY_PATH did the trick. On Ubuntu 17.04 that’s 
/usr/lib/gcc/x86_64-linux-gnu. 

Also, I had to install gcc-5 and g++-5 again because the CUDA 8 toolkit doesn’t 
like version 6, and specify their use with -DCMAKE_C_COMPILER=gcc-5 and 
-DCMAKE_CXX_COMPILER=g++-5

The output from gcc -v (with g++ being identical except for the the first line) 
was:
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 6.3.0-12ubuntu2' 
--with-bugurl=file:///usr/share/doc/gcc-6/README.Bugs 
--enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr 
--program-suffix=-6 --program-prefix=x86_64-linux-gnu- --enable-shared 
--enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext 
--enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ 
--enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes 
--with-default-libstdcxx-abi=new --enable-gnu-unique-object 
--disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie 
--with-system-zlib --disable-browser-plugin --enable-java-awt=gtk 
--enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-6-amd64/jre 
--enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-6-amd64 
--with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-6-amd64 
--with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar 
--with-target-system-zlib --enable-objc-gc=auto --enable-multiarch 
--disable-werror --with-arch-32=i686 --with-abi=m64 
--with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic 
--enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu 
--target=x86_64-linux-gnu
Thread model: posix
gcc version 6.3.0 20170406 (Ubuntu 6.3.0-12ubuntu2) 

So the build was successful and all test passed. Now on to some benchmarking to 
see if I can get CUDA acceleration to work.

—Steffen



> On May 24, 2017, at 8:19 AM, Vytautas Rakeviius <vytautas1...@yahoo.com> 
> wrote:
> 
> 
> Hmm It might be problem that you removed compilers. Wonder what you have 
> now.If you still have problem please post output of:
> g++ -v && gcc -v
> Command. 
> 
>On Wednesday, May 24, 2017 3:14 PM, Mark Abraham 
> <mark.j.abra...@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 <graet...@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 + (UTC)
>> 
>>> From: Vytautas Rakeviius <vytautas1...@yahoo.com>
>>> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
>>>   "gromacs.org_gmx-users@maillist.sys.kth.se"
>>>   <gromacs.org_gmx-users@maillist.sys.kth.se>
>>> Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
>>>   17.04
>>> Message-ID: <743319698.939458.1495615557...@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 <
>> graet...@uoguelph.ca> wrote:
>>> 
>>> 
>>> Hi,
>>> 
>>> I?ve tried 

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

[Szilárd Páll]

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.abra...@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 <graet...@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 + (UTC)
> >
> > > From: Vytautas Rakeviius <vytautas1...@yahoo.com>
> > > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
> > >   "gromacs.org_gmx-users@maillist.sys.kth.se"
> > >   <gromacs.org_gmx-users@maillist.sys.kth.se>
> > > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> > >   17.04
> > > Message-ID: <743319698.939458.1495615557...@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 <
> > graet...@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-requ...@gromacs.org.
> > >
> > >
> > >
> > > --
> > >
> > > Message: 4
> > > Date: Wed, 24 May 2017 11:28:55 +0200
> > > From: "Kamps, M." <m.ka...@student.rug.nl>
> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > > Subject: [gmx-users] Problem with accelerations
> > > Message-ID:
> > >   <
> > cacskku3niwewt7d8o-nteqmgq+vwpg0mfmbud_s-0kcpaov...@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

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

[Vytautas Rakeviius]

Hmm It might be problem that you removed compilers. Wonder what you have now.If 
you still have problem please post output of:
g++ -v && gcc -v
Command. 

On Wednesday, May 24, 2017 3:14 PM, Mark Abraham <mark.j.abra...@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 <graet...@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 + (UTC)
>
> > From: Vytautas Rakeviius <vytautas1...@yahoo.com>
> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
> >      "gromacs.org_gmx-users@maillist.sys.kth.se"
> >      <gromacs.org_gmx-users@maillist.sys.kth.se>
> > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> >      17.04
> > Message-ID: <743319698.939458.1495615557...@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 <
> graet...@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-requ...@gromacs.org.
> >
> >
> >
> > --
> >
> > Message: 4
> > Date: Wed, 24 May 2017 11:28:55 +0200
> > From: "Kamps, M." <m.ka...@student.rug.nl>
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Problem with accelerations
> > Message-ID:
> >      <
> cacskku3niwewt7d8o-nteqmgq+vwpg0mfmbud_s-0kcpaov...@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 com

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

[Mark Abraham]

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 <graet...@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 + (UTC)
>
> > From: Vytautas Rakeviius <vytautas1...@yahoo.com>
> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
> >   "gromacs.org_gmx-users@maillist.sys.kth.se"
> >   <gromacs.org_gmx-users@maillist.sys.kth.se>
> > Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
> >   17.04
> > Message-ID: <743319698.939458.1495615557...@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 <
> graet...@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-requ...@gromacs.org.
> >
> >
> >
> > --
> >
> > Message: 4
> > Date: Wed, 24 May 2017 11:28:55 +0200
> > From: "Kamps, M." <m.ka...@student.rug.nl>
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Problem with accelerations
> > Message-ID:
> >   <
> cacskku3niwewt7d8o-nteqmgq+vwpg0mfmbud_s-0kcpaov...@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, 

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

[Steffen Graether]

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 + (UTC)

> From: Vytautas Rakeviius <vytautas1...@yahoo.com>
> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>,
>   "gromacs.org_gmx-users@maillist.sys.kth.se"
>   <gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] Problems install GROMACS 2016.3 on Ubuntu
>   17.04
> Message-ID: <743319698.939458.1495615557...@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 
> <graet...@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-requ...@gromacs.org.
> 
> 
> 
> --
> 
> Message: 4
> Date: Wed, 24 May 2017 11:28:55 +0200
> From: "Kamps, M." <m.ka...@student.rug.nl>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Problem with accelerations
> Message-ID:
>   <cacskku3niwewt7d8o-nteqmgq+vwpg0mfmbud_s-0kcpaov...@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.ka...@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 creat

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

[Vytautas Rakeviius]

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  
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-requ...@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-requ...@gromacs.org.

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

[Steffen Graether]

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-requ...@gromacs.org.