Re: [AMBER] Amber 11 installation problems

From: Scott Brozell <>
Date: Wed, 17 Nov 2010 22:37:08 -0500


On Wed, Nov 17, 2010 at 01:36:00PM -0500, case wrote:
> On Wed, Nov 17, 2010, Linus Johannissen wrote:
> > /opt/software/gaussian/d02/g03/bsd/install -c -m 644 './netcdf_f90.3' '/home/linusj/amber/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f90.3'
> This is pretty suspicious, but I am just guessing. You are using the Guassian
> "install" program, and the netcdf script is expecting something like
> "/usr/bin/install".

Yes, this is a known bug.

On Wed, Nov 17, 2010 at 06:17:28PM -0500, Jason Swails wrote:
> On Wed, Nov 17, 2010 at 5:34 PM, Linus Johannissen <
>> wrote:
> I'm going to side with Dave Case on this one. What you should do before you
> install Amber is *unload* your Gaussian module, since it's plopping an
> "install" into your path that I'm guessing is mucking up the install
> process. I have never seen an error in the NETCDF build (which is where
> this is occurring) before, and I've installed it on a lot of different
> systems/clusters.

I have seen this error before.
While Jason's advice is correct, it is incomplete:
it may not be a user action or a user script that is altering the PATH
- a system script may be the culprit.
Thus, follow Dave's advice:
modify your PATH variable so that /usr/bin/install becomes the result of
which install.


> As long as you see the "phrase": /opt/software/gaussian/d02/g03/bsd/install
> -c -m 644
> then the compilation process is using the *wrong* install which is likely
> breaking stuff.
> As a note to general users: Do NOT source Gaussian files that set up your
> environment in normal shell environments. ONLY source them in PBS scripts
> that specifically run Gaussian. The reason is that their profile scripts
> that set up environment variables are effectively poison to every other
> package that uses these variables (notably LD_LIBRARY_PATH). These scripts
> set up the environment variables properly for Gaussian, so g03/g09 will run
> properly, but it could easily break other packages (this drove me insane for
> some time before I figured it out). Therefore, source the Gaussian scripts
> and/or load the Gaussian module only in sessions that you are actually
> running a Gaussian job.

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Received on Wed Nov 17 2010 - 20:00:03 PST
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