AMBER Archive (2009)

Subject: Re: [AMBER] amber10 installation problem

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Jul 08 2009 - 06:56:19 CDT

On Wed, Jul 08, 2009, Lan JIN wrote:
>
> I have been trying to install Amber10 and AmberTool
> 1.2 on my Linux (Intel core2, RHEL4, 32 bit) computer. Bugfix files for
> both were downloaded and 'patch' did as well.
>
> My first
> question is if these two packages are totally independent during
> installation or failure of AmberTool installation will affect the
> installation of AMBER10. 

Amber10 relies on AmberTools, so you can't run it if the AmberTools
installation fails.

> I also tried to edit config.h file by changing to FC=ifort from g77

Dont do that! Only g77 or gfortran will work.

>
>
> > ./configure_at gcc
> Setting AMBERHOME to /usr/local/AMBER/amber10
>
> Using Intel MKL libraries in /opt/intel/mkl/10.1.1.019
>
> .............
> .............
> xyzint.o(.text+0x266): In function `xyzint_':
> : undefined reference to `__intel_cpu_indicator'

> make[1]: *** [mopac] error 1
> make[1]: Leaving directory `/usr/local/AMBER/amber10/src/mopac6/src'

This looks(?) like some problem with ifort, which you should not be using
anyway. What was the error when using gfortran or g77? To be safe,
unset your MKL_HOME environment variable, in case there is some conflict
there.

> make: *** [install] error 2
>
>
> 'make -f Makefile_at test' stopped at 

Well, of course...if the installation failed, you can be pretty sure that the
test cases will fail as well.

> ======================for Amber10====================
>
> I continued to install Amber10 assuming the AmberTool would not affect this process.
>
> > ./configure_amber ifort
> > make serial
> > make clean
>
> > make test
>
> .............
> cd bintraj && ./Run.bintraj
> ../../src/netcdf/bin/ncdump: Command not found.
> diffing nc_headers.save with nc_headers
> possible FAILURE:  check nc_headers.dif

OK, it looks like the "make clean" script above removes things that are needed
for the bintraj test. If other things work, you can ignore this problem, or
run "configure_amber" again. (Generally, the idea is to run "make clean"
before a new compilation; it is not needed afterwards. But we should fix this
glitch.)

> cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma
> DFTB SLKO files not found - Skipping Test...

Please see p. 86 of the Users' Manual.

>
> AmberTool
> should be not installed. xleap, ptraj etc do not exist but antechamber
> is there.

This is because your installation of AmberTools stopped in the middle (with
the error in the mopac compilation). So some executables were created and
others were not.

.....dac

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