Thanks for reply
I have added two lines in bashrc file
export PATH=/home/myname/amber16/fftw-install/
export PATH=/home/myname/amber16/mpich-install/
The error is same
Is there something missing.
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On Thu, Feb 8, 2018 at 8:56 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi
> for MPI support I have installed mpich-3.1.4 and fftw-3.3.7
> > mpicpi-3.14 is installed in /home/myname/amber16/mpich-install
> directory
> > and fftw-3.3.7 is installed in /home/myname/amber16/mpich-install
> > directory
> These are unusual directories to install MPI and FFTW libraries, have you
> made these entries in the bashrc or cshrc?
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Tasneem Kausar <tasneemkausar12.gmail.com>
> Sent: 08 February 2018 08:44
> To: amber.ambermd.org
> Subject: Re: [AMBER] Problem in installing Amber16
>
> I am still waiting for reply.
>
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> On Wed, Feb 7, 2018 at 2:13 PM, Tasneem Kausar <tasneemkausar12.gmail.com>
> wrote:
>
> > Dear all
> >
> > I am trying to install amber16 in my home directory.
> > I am using these steps
> > export AMBERHOME=/home/myname/amber16/
> > cd $ AMBERHOME
> > ./configure gnu
> > make install
> >
> > for MPI support I have installed mpich-3.1.4 and fftw-3.3.7
> > mpicpi-3.14 is installed in /home/myname/amber16/mpich-install
> directory
> > and fftw-3.3.7 is installed in /home/myname/amber16/mpich-install
> > directory
> >
> > then I have run command
> > ./configure -mpi gnu
> >
> > ------------------------------------------------------------
> > --------------------
> > Environment resource files are provided to set the proper environment
> > variables to use AMBER and AmberTools. This is required to run any Python
> > programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
> >
> > If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> > /home/myname//amber.sh file in your shell. Consider adding the line
> > test -f /home/myname/amber16//amber.sh && source
> > /home/myname/amber16//amber.sh
> > to your startup file (e.g., ~/.bashrc)
> >
> > If you use a C shell (e.g., csh, tcsh), source the
> > /home/myname/amber16//amber.csh file in your shell. Consider adding the
> > line
> > test -f /home/myname/amber16//amber.csh && source
> > /home/myname/amber16//amber.csh
> > to your startup file (e.g., ~/.cshrc)
> >
> > NOTE: MacOS users might need to add the content to ~/.bash_profile file
> > (You need to do the above before running 'make install')
> >
> > Warning: No parallel NetCDF specified (--with-pnetcdf <dir>).
> > Parallel NetCDF trajectory output will not be available
> > in cpptraj.MPI.
> >
> > ------------------------------------------------------------
> > --------------------
> >
> > The next step is to source the amber.sh or amber.csh file
> > (if needed, see above), and then to type 'make install'
> >
> > Cleaning the src directories. This may take a few moments.
> > Configure complete.
> >
> > However I ignored the warning and typed
> > make install
> >
> > It gives the error massage as follows
> >
> >
> >
> > /home/apps/ics/impi/4.1.3.049/intel64/lib/libmpigf.so: undefined
> > reference to `MPID_b_use_gettimeofday'
> > collect2: ld returned 1 exit status
> > make[2]: *** [/home/myname/amber16//bin/mdgx.MPI] Error 1
> > make[2]: Leaving directory `/home/myname/amber16/AmberTools/src/mdgx'
> > make[1]: *** [parallel] Error 2
> > make[1]: Leaving directory `/home/myname/amber16/AmberTools/src'
> > make: *** [install] Error 2
> >
> >
> > I don't have access as super user and I am unable to resolve the error.
> > Kindly resolve the issue.
> >
> > Thanks and Regards
> > Tasneem Kausar
> > Research Scholar
> > AMU, Aligarh, India
> >
> >
> >
> >
> >
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Received on Wed Feb 07 2018 - 20:00:01 PST
