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 - 19:30:02 PST
