[gmx-users] 2016.3 installation

RAHUL SURESH drrahulsuresh at gmail.com
Wed May 3 08:57:02 CEST 2017 

Dear Mark,

To my minimum knowledge I think I have worked the way as you have guided. I
have devtoolset-4.0. I wish to make a note, I make running all my commands
as "ROOT".

I tried reinstalling cleaning my old packages and I receive the same error
i.e same list of errors. 21/27 failed.

On Tue, May 2, 2017 at 6:10 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > > > >> >
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> > > > >> >
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> > > or
> > > > >> > send a mail to gmx-users-request at gromacs.org.
> > > > >> >
> > > > >> --
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> gmx-users
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> > > > >>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> or
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> > > >
> > > --
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> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*

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