No virtual machine. I am using 64 bit Debian OS on Supermicro workstation
with following details:
Distributor ID: Debian
Description: Debian GNU/Linux 7.2 (wheezy)
Release: 7.2
Codename: wheezy
The only error message I got in amber12 "make test" is as follows:
==============================================================
Cleaning temporary files and quitting.
make[3]: Leaving directory `/opt/amber12/AmberTools/test/mmpbsa_py'
cd parmed/normal_prmtop && ./Run.parmed
./Run.parmed: Program error
make[2]: *** [test.parmed] Error 1
cd ambpdb && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/04 Time = 15:33:29
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/04 Time = 15:33:29
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/04 Time = 15:33:29
diffing restrt.pdb.save with restrt.pdb
PASSED
==============================================================
Well, in order to find out the source of problem, I rebooted the machine.
Then used Amber12.tar.bz2 and AmberTools13.tar.bz2 to re-installed from the
step 1.
Ah...., this time I did not get any error ! This is surprising to me !!!!
This concludes that something was really wrong with my original amber12
files/folder or with my newly installed OS Debian 7. I guess, some of the
updates/upgrades strictly need reboot.
Anyways, I tried the installation at different locations such as
"/home/amber12" and "/opt/amber12".
Both installations are successful and there is no error messages in "make
test".
Thank you.
Best,
-- Joshi
On Mon, Nov 4, 2013 at 10:14 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
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Received on Tue Nov 05 2013 - 21:00:02 PST
