[gmx-users] 2016.3 installation

Mark Abraham mark.j.abraham at gmail.com
Tue May 2 14:41:04 CEST 2017 

Hi,

The "virtue" of CentOS is that they ship old versions of software and hope
that this helps the machine to be more "stable." Obviously this gets in
your way as a computational scientist needing access also to more recent
versions of things in order to get work done efficiently. For this reason,
you should install and use the devtoolset packages that are provided for
the purpose, e.g.
https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/. (Which I
just tested on Centos 6.9, and works beautifully.) Or consider alternative
Linux distributions next time.

The rpm for gcc that you've installed does not work *by itself* because the
resulting binaries need updated C++ and C standard libraries, and those you
have not installed. That gives you the symptoms that you see when you run
the binaries. Using a devtoolset takes care of all of that stuff.

And please do yourself a favour and use your root access to your machine
for running yum, make install, and basically nothing else. It's too easy
for someone who is still learning their way around to break things they do
not intend to change.

Mark

On Tue, May 2, 2017 at 11:58 AM RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Dear Mark..
>
> I am on CentOS 6.9 version loaded with GCC version 5.3.
>
> I use the following commands to install Gromacs
>
>
>
>
>
>
>
>
>
> *tar xfz gromacs-2016.3.tar.gzcd gromacs-2016.3mkdir buildcd buildCC=gcc53
> CXX=g++53 cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ONmakemake check*
> *"Here i get errors"*
>
> make install
>
>
> MY GCC details
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[root at mqml Desktop]# rpm -qa gcc53-c++ gcc53-c++-5.3.0-1.el6.x86_64
> [root at mqml Desktop]# which gcc53 /usr/bin/gcc53 [root at mqml Desktop]# which
> g++53 /usr/bin/g++53 [root at mqml Desktop]# gcc53 -v Using built-in specs.
> COLLECT_GCC=gcc53
>
> COLLECT_LTO_WRAPPER=/usr/local/gcc53/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
> Target: x86_64-unknown-linux-gnu Configured with: ../gcc-5.3.0/configure
> --prefix=/usr/local/gcc53 --program-suffix=53 --enable-languages=c,c++
> --with-system-zlib --disable-multilib Thread model: posix gcc version 5.3.0
> (GCC) [root at mqml Desktop]# g++53 -v Using built-in specs.
> COLLECT_GCC=g++53
>
> COLLECT_LTO_WRAPPER=/usr/local/gcc53/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
> Target: x86_64-unknown-linux-gnu Configured with: ../gcc-5.3.0/configure
> --prefix=/usr/local/gcc53 --program-suffix=53 --enable-languages=c,c++
> --with-system-zlib --disable-multilib Thread model: posixgcc version 5.3.0
> (GCC) *
>
>
>
> I couldn't reconize the error. I request your precious guidance
>
>
>
> On Tue, May 2, 2017 at 2:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > That seems like you're now running in a different environment from the
> one
> > in which you compiled. I can't be specific, because I don't know anything
> > about your machine, but you need to load the same compiler module,
> > devtoolset, or something like that.
> >
> > Mark
> >
> > On Tue, May 2, 2017 at 9:43 AM RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Dear Mark,
> > >
> > > I executed the test files from bin and I et the following error
> > >
> > > ./analysisdata-test
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20'
> > > not found (required by ./analysisdata-test)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8'
> > not
> > > found (required by ./analysisdata-test)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.21'
> > > not found (required by ./analysisdata-test)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.15'
> > > not found (required by ./analysisdata-test)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.20'
> > > not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8'
> > not
> > > found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.18'
> > > not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.14'
> > > not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.21'
> > > not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > > ./analysisdata-test: /usr/lib64/libstdc++.so.6: version
> `GLIBCXX_3.4.15'
> > > not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> > >
> > >
> > > Await your precious response
> > >
> > > On Mon, May 1, 2017 at 5:25 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> > > wrote:
> > >
> > > > Dear Mark
> > > >
> > > > First apology that I am unaware how to run the test programs.
> > > >
> > > > Next, I tried to simulate a protein and i get the following error.
> > > >
> > > >
> > > > *[user at mqml rahul]$* source /usr/local/gromacs/bin/GMXRC
> > > > *[user at mqml rahul]$* gmx pdb2gmx -f 99nsInput.pdb -o 99nsInput.gro
> -p
> > > > 99nsInput.top
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found
> > > > (required by gmx)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found
> > > > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found
> > > (required
> > > > by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found
> > > > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found
> > > > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found
> > > > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> > > > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > > > *[user at mqml rahul]$*
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, May 1, 2017 at 12:58 AM, Mark Abraham <
> > mark.j.abraham at gmail.com>
> > > > wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> We can't tell. Run one of the test programs you can see in the
> > > $build/bin
> > > >> did
> > > >>
> > > >> Mark
> > > >>
> > > >> On Sat, 29 Apr 2017 12:40 RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> > > >>
> > > >> > Dear Users
> > > >> >
> > > >> > I am trying to install Gromacs 2016.3
> > > >> >
> > > >> > For make check command I am getting the following errors.
> > > >> >
> > > >> > I need your assistance to overcome this issue.
> > > >> >
> > > >> >
> > > >> > 22% tests passed, 21 tests failed out of 27
> > > >> >
> > > >> > Label Time Summary:
> > > >> > GTest                 =   0.02 sec (18 tests)
> > > >> > IntegrationTest       =   0.00 sec (2 tests)
> > > >> > MpiIntegrationTest    =   0.00 sec (1 test)
> > > >> > UnitTest              =   0.02 sec (18 tests)
> > > >> >
> > > >> > Total Test time (real) =   0.82 sec
> > > >> >
> > > >> > The following tests FAILED:
> > > >> >       1 - TestUtilsUnitTests (Failed)
> > > >> >       2 - MdlibUnitTest (Failed)
> > > >> >       3 - CommandLineUnitTests (Failed)
> > > >> >       4 - FFTUnitTests (Failed)
> > > >> >       5 - HardwareUnitTests (Failed)
> > > >> >       6 - MathUnitTests (Failed)
> > > >> >       7 - OnlineHelpUnitTests (Failed)
> > > >> >       8 - OptionsUnitTests (Failed)
> > > >> >       9 - RandomUnitTests (Failed)
> > > >> >      10 - UtilityUnitTests (Failed)
> > > >> >      11 - FileIOTests (Failed)
> > > >> >      12 - PullTest (Failed)
> > > >> >      13 - SimdUnitTests (Failed)
> > > >> >      14 - LegacyToolsTests (Failed)
> > > >> >      15 - GmxPreprocessTests (Failed)
> > > >> >      16 - CorrelationsTest (Failed)
> > > >> >      17 - AnalysisDataUnitTests (Failed)
> > > >> >      18 - SelectionUnitTests (Failed)
> > > >> >      19 - TrajectoryAnalysisUnitTests (Failed)
> > > >> >      20 - MdrunTests (Failed)
> > > >> >      21 - MdrunMpiTests (Failed)
> > > >> > Errors while running CTest
> > > >> > make[3]: *** [CMakeFiles/run-ctest] Error 8
> > > >> > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
> > > >> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > > >> > make: *** [check] Error 2
> > > >> > [root at mqml build]#
> > > >> >
> > > >> > --
> > > >> > *Regards,*
> > > >> > *Rahul Suresh*
> > > >> > *Research Scholar*
> > > >> > *Bharathiar University*
> > > >> > *Coimbatore*
> > > >> > --
> > > >> > 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.
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > >
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > 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.
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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.
>

More information about the gromacs.org_gmx-users mailing list