[gmx-users] 2016.3 installation
RAHUL SURESH
drrahulsuresh at gmail.com
Tue May 2 11:58:34 CEST 2017
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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> 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
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> > >>
> > >
> > >
> > >
> > > --
> > > *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
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
> --
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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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