[gmx-users] Problems install GROMACS 2016.3 on Ubuntu 17.04
Steffen Graether
graether at uoguelph.ca
Thu May 25 01:48:55 CEST 2017
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 <vytautas1987 at 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.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!
>>>
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>> 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!
>>>>>
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>>>>>
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>>>>> 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
>>>
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>>> 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
>>> *******************************************************
>>
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>> Gromacs Users mailing list
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