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 - 01:00:02 PST
