[AMBER] Regarding Amber16 installation

From: <dilrajl.bii.a-star.edu.sg>
Date: Tue, 26 Nov 2019 12:15:09 +0000

Dear Amber users,
                               I am trying to install AMBER16 in a
Redhat enterprise linux server release 6.9. I have followed the
instructions as given and have successfully installed the serial and
parallel version of the program. Here are the output messages I get
after installation.



FOR SERIAL
-----------------------------------------------------------------------------

Installation of AmberTools16 serial is complete at Mon Nov 25 10:12:06
CET 2019.

make[1]: Leaving directory `/home/md/dilrajl/amber16/AmberTools/src'
==============================================================
/home/md/dilrajl/amber16/src/Makefile not found, or -noamber was set.

This is expected if you do not have Amber16.
==============================================================

FOR PARALLEL

"Installation of AmberTools16 MPI is complete at Mon Nov 25 17:18:06 CET 2019.

make[1]: Leaving directory `/home/md/dilrajl/amber16/AmberTools/src'

==============================================================
/home/md/dilrajl/amber16/src/Makefile not found, or -noamber was set.

This is expected if you do not have Amber16.
==============================================================
------------------------------------------------------------------------------



The executables for these versions like "sander" and "sander.MPI" are
successfully created in the bin folder.

Then i tried to install the cuda version of the program.

./configure -cuda gnu


HERE IS PART OF THE OUPUT AFTER THE CONFIGURATION STEP

****************************************************************************************************

The configuration file, config.h, was successfully created.
--------------------------------------------------------------------------------

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/md/dilrajl/amber16/amber.sh file in your shell. Consider adding the line

   test -f /home/md/dilrajl/amber16/amber.sh && source
/home/md/dilrajl/amber16/amber.sh

to your startup file (e.g., ~/.bashrc)

If you use a C shell (e.g., csh, tcsh), source the

/home/md/dilrajl/amber16/amber.csh file in your shell. Consider adding
the line

test -f /home/md/dilrajl/amber16/amber.csh && source
/home/md/dilrajl/amber16/amber.csh

to your startup file (e.g., ~/.cshrc)

(You need to do the above before running 'make install')

If you have not already done so, you may need to add
/home/md/dilrajl/amber16/cuda-8.0/lib

and/or /home/md/dilrajl/amber16/cuda-8.0/lib64 to LD_LIBRARY_PATH
using the command

   export
LD_LIBRARY_PATH="/home/md/dilrajl/amber16/cuda-8.0/lib:${LD_LIBRARY_PATH}"
(bash, sh)

   setenv LD_LIBRARY_PATH
"/home/md/dilrajl/amber16/cuda-8.0/lib:${LD_LIBRARY_PATH}" (tcsh, csh)

--------------------------------------------------------------------------------------------------------

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.


*********************************************************************************************************


So the configuration file was successfully created.

But when I execute the "make install" command, then I only get this output


**********************************************************************************************************
cd AmberTools/src && make install

make[1]: Entering directory `/home/md/dilrajl/amber16/AmberTools/src'

AmberTools16 has no CUDA-enabled components

make[1]: Leaving directory `/home/md/dilrajl/amber16/AmberTools/src'

==============================================================

/home/md/dilrajl/amber16/src/Makefile not found, or -noamber was set.

This is expected if you do not have Amber16.

==============================================================

**********************************************************************************************************

And I don't see any executables that was created.

I will be glad if someone can give me a pointer and suggestions to
address this issue.

Thank you,
Dilraj


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Received on Tue Nov 26 2019 - 04:30:02 PST
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