On Mon, 2013-11-04 at 21:24 +0800, Dhananjay wrote:
> Dear all,
>
> I tried clean installation once again, by taking all the suggestions into
> account that have been given before.
> As previously experienced, I got following error:
>
> use netcdf, only : nf90_double, nf90_float
> 1
> Fatal Error: Wrong module version '0' (expected '9') for file 'netcdf.mod'
> opened at (1)
>
>
> Further, as per Jeson's suggestion "Try deleting the netcdf.mod file and
> then recompiling",
> I did "rm include/netcdf.mod "
>
>
> However, I got following error:
>
> gfortran -DBINTRAJ -c -O3 -mtune=native -ffree-form
> -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm
> -I../../AmberTools/src/rism -I../../include -I/opt/amber12/include
> -I/opt/amber12/include -o ncsu-umbrella.o ncsu-umbrella.F90
> ncsu-umbrella.F90:9.4:
>
> use netcdf, only : nf90_double, nf90_float
> 1
> Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No
> such file or directory
>
>
> I just gave a try as follows:
>
> *cp /opt/amber12/AmberTools/include/netcdf.mod /opt/amber12/include/*
Now this is very weird. I amber12/AmberTools/include and
amber12/include should _definitely_ be simlinked. The fact that it's not
suggests to me that your filesystem does not properly support simlinks
or that there is some other strange condition causing new directories to
be created instead of simlinks.
I think we need to know a bit more about your setup. Are you running
Debian 7 in a virtual machine (and if so, what is the host OS)? What
filesystems are you using (ext4, ext3, reiserfs, etc.)? Do you have any
additional information that could help us reproduce these strange
issues? I'll try to set up a Debian 7 VM on my Linux box, but any
information you can give that will let us reproduce your setup will
help.
> This made my installation complete:
> Installation of Amber12 (serial) is complete at Mon Nov 4 07:05:07 EST
> 2013.
>
> make[1]: Leaving directory `/opt/amber12/src'
>
>
> Finally, I ran "make test" which seem successful:
>
> Finished serial test suite for Amber 12 at Mon Nov 4 08:16:21 EST 2013.
>
> make[2]: Leaving directory `/opt/amber12/test'
> 529 file comparisons passed
> 9 file comparisons failed
> 0 tests experienced errors
> Test log file saved as
> /opt/amber12/logs/test_amber_serial/2013-11-04_07-34-24.log
> Test diffs file saved as
> /opt/amber12/logs/test_amber_serial/2013-11-04_07-34-24.diff
> make[1]: Leaving directory `/opt/amber12/test'
>
> Summary of AmberTools serial tests:
>
> 555 file comparisons passed
> 0 file comparisons failed
> 1 tests experienced errors
> Test log file saved as
> /opt/amber12/logs/test_at_serial/2013-11-04_07-07-14.log
> No test diffs to save!
It looks like most of your tests appear to pass. What are the failures
and errors, though?
> I am not sure whether there is problem with my installation OR a common
> issue with Debian 7.
I am equally stumped at this point.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 04 2013 - 06:30:04 PST
