RE: AMBER: Compiling Amber 7

From: David J. Powers <>
Date: Sat, 10 Feb 2007 10:59:42 -0500

Hi Ross,

Thanks for your help in getting Amber7 to install successfully. I've gone
thru the Test of the Amber
distribution and for the most part everything passes the tests. I've
installed Amber7 as a root user
and ran the Tests also as a root user. When I try to run the Tests or the
programs (i.e., sander)
as a non-root user, I get I/O errors, permission denied, etc. Basically
the problem is that some
input files may restrict access to the owner or group and when creating an
output file the directory
permissions don't allow just any user to write to it. I am familiar with
LINUX and the chmod command.
What I need to know is which input directories/files need to be
changed. Also, what is the default
output directory(s) for programs like sander, gibbs, etc? Once I know
these details I can set the
file permissions appropriately. Currently, MPI is set-up to be run by
non-root users and of course
we need to be able to run Amber7 in a non-root mode.

Thanks in advance for your help.

Dave Powers

At 08:30 AM 2/8/2007 -0800, you wrote:
>Dear David,
> > I set the environment variables, AMBERHOME and MPICH_HOME.
> > During the
> > "make install"
> > I got an error making sander. The errors were specifically:
> > undefined reference to 'pthread_getspecific'
> > and undefined reference to 'pthread_getspecific'
>Try adding -lpthread to the loadlib line. I.e.:
>setenv LOADLIB "-lm -L$MPICH_LIBDIR -l$MPICH_LIB -lpthread"
>The other option, assuming that you have your mpich paths set up correctly
>is to replace g77 with mpif77. This is a wrapper for the compiling mpi
>programs and should append the correct library options automatically.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
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Received on Sun Feb 11 2007 - 06:07:43 PST
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