[gmx-users] gromacs-5.1.4 installation issue

[Mark Abraham]

Hi,

Yes, those are from the standard system compiler, which obviously doesn't
work. You're not using that compiler, so you need to know how the one you
are using should be used and where its standard library is and why the
clusters are not actually identical because one compiler works and one
doesn't ;-) That means talking to the people who set them up. For example,
you forgot to load the module one time. Or one module sets LD_LIBRARY_PATH
and one does not.

Mark


On Thu, May 25, 2017 at 8:41 AM abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> On Wed, May 24, 2017 at 6:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > You should ask the cluster maintainers how they intend the compiler to be
> > used. You need to find the same infrastructure at run time as you used at
> > compile time, e.g. by loading the same modules.
> >
> > Yes I did check.
> I have 2 cluster with identical configurations. In Cluster_1 it compiled
> well and running nicely.
> But in Cluster_2 it is giving this error.
>
> To check the GLIBCXX version available in both Clusters, we used: strings
> /usr/lib/libstdc++.so.6 | grep GLIBCXX
> Output of BOTH clusters:
> GLIBCXX_3.4
> GLIBCXX_3.4.1
> GLIBCXX_3.4.2
> GLIBCXX_3.4.3
> GLIBCXX_3.4.4
> GLIBCXX_3.4.5
> GLIBCXX_3.4.6
> GLIBCXX_3.4.7
> GLIBCXX_3.4.8
> GLIBCXX_3.4.9
> GLIBCXX_3.4.10
> GLIBCXX_3.4.11
> GLIBCXX_3.4.12
> GLIBCXX_3.4.13
> GLIBCXX_FORCE_NEW
> GLIBCXX_DEBUG_MESSAGE_LENGTH
>
> So, I'm confused regarding both the machine does not have  `GLIBCXX_3.4.15`
> , then why in one machine /gromacs-5.1.4/lib64/libgromacs_mpi.so.1 is
> raising error but not in the other ?
>
> Is there any way to overcome this ? I'm really confused.
>
> Some advice regarding this concern will be highly appreciated.
>
> Thank you.
>
>
>
> > Mark
> >
> > On Wed, May 24, 2017 at 2:13 PM abhisek Mondal <abhisek.mndl at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > >    I have been trying to install latest version of gromacs
> > (Gromacs-5.1.4)
> > > in my cluster.
> > >
> > > Installation went without any error. But whenever I'm giving the
> command:
> > > gmx_mpi
> > > An error report comes:
> > > gmx_mpi: /lib64/libz.so.1: no version information available (required
> by
> > > /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> > > gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> > > (required by /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> > >
> > >
> > > Can you please help me out here, regarding what is going wrong here.
> > >
> > > Thank you.
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
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>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> 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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