Re: [AMBER] installing Amber12 in parallel

From: case <>
Date: Fri, 13 Apr 2012 23:01:08 -0400

On Fri, Apr 13, 2012, Marc van der Kamp wrote:
> I have downloaded and installed Amber12. I would like to install parallel
> versions of the executables now (sander.MPI, pmemd.MPI).
> I was hoping to use the easy script
> provided: $AMBERHOME/AmberTools/src/configure_openmpi
> This is what I did:
> cd $AMBERHOME/AmberTools/src
> wget
> tar xvfj openmpi-1.5.4.tar.bz2
> ./configure_openmpi gnu
> I seem to get to the 'make install' stage (final lines of the
> configure_openmpi script), as these are the final lines from running the
> above command:
> rm -f *.o *.obj *.mod pmemd.MPI pmemd pmemd.cuda pmemd.cuda.MPI *.d work.pc*
> `/export/users/chmwvdk/amber12/src/pmemd.amoeba/src'
> rm -f *.o *.obj *.mod pmemd.amoeba.MPI pmemd.amoeba *.d work.pc*
> make[2]: Leaving directory
> `/export/users/chmwvdk/amber12/src/pmemd.amoeba/src'
> make[1]: Leaving directory `/export/users/chmwvdk/amber12/src/pmemd.amoeba'

Looks like something went dreadfully wrong during the configure_openmpi
script. You need to examine everything that happened there: buried in the
voluminous output should be a line "openmpi configure succeeded", and a line
about LD_LIBRARY_PATH. Immediately following this should be a line like
"Making clean in test". Later on you will see hundreds of lines with "CC"
followed by file names. (The "make install" command in the script should
be runnning inside amber12/AmberTools/src/openmpi-1.5.4, and wouldn't be doing
anything with any amber files like pmemd.)

Alternatively, there may be a line saying "openmpi configure failed"; at this
point the script should exit, giving you back a command prompt.

Somehow, the script seems to have been running the "make clean" command
from the amber12 directory. I don't see how this could have happened
based on what you said you did. It looks like you need to re-run the
configure_openmpi script, and follow carefully what happens.

> However, I don't have any .MPI executables in $AMBERHOME/bin/ afterwards.
> AmberTools12.pdf section 1.2 point 7 says: "Follow the instructions of
> these scripts, then return to step 6."
> (But step 6 is "make test")

Should say return to step 7. You have to cd to $AMBERHOME and run configure
from there, followed by "make install".

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Received on Fri Apr 13 2012 - 20:30:03 PDT
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