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 +0000 (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 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-requ...@gromacs.org. >>>>> >>> >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Wed, 24 May 2017 08:45:57 +0000 (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. >>> >>> >>> >>> ------------------------------ >>> >>> -- >>> 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. >>> >>> End of gromacs.org_gmx-users Digest, Vol 157, Issue 115 >>> ******************************************************* >> >> -- >> 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. > > > -- > 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.