Dear Daniel and Jason,
I realized my mistake of not recognizing the correct patches.
After I have downloaded the correct patches, it seems that things have
worked fine. As suggested on the site I have run the command
(./patch_amber.py) twice. At present I'm running the "make install" command.
Regarding the proxy setting I did not really understand the discussion as
I'm not a networking expert.
But I'm happy that the other way round seems to have worked. (With amber
there is something new to learn everyday).
Thanks all for your time and suggestions.
---------
linux-rfml:/usr/local/amber12 # ./patch_amber.py --update-tree
Determining patches to download for AmberTools12
AmberTools12 is up to date. Nothing to download
Determining patches to download for Amber12
Downloading bugfix.1
Downloading bugfix.2
Downloading bugfix.3
Downloading bugfix.4
Downloading bugfix.5
Downloading bugfix.6
Downloading bugfix.7
Downloading bugfix.8
Applying AmberTools12 patches
Applying Amber12 patches
Moving bugfix.1 to Amber_Applied_Patches
Moving bugfix.2 to Amber_Applied_Patches
Moving bugfix.3 to Amber_Applied_Patches
Creating file
/usr/local/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/Run.aladip.hf_sto-3g.MechEm
Creating file
/usr/local/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/aladip.hf_sto-3g.MechEm.mdout.save
Creating file
/usr/local/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/aladip.hf_sto-3g.MechEm.restrt.save
Creating file
/usr/local/amber12/test/qmmm_EXTERN/QMMM_MD_TeraChem/Run.aladip.hf_sto-3g.MechEm
Moving bugfix.4 to Amber_Applied_Patches
Moving bugfix.5 to Amber_Applied_Patches
Moving bugfix.6 to Amber_Applied_Patches
Moving bugfix.7 to Amber_Applied_Patches
Moving bugfix.8 to Amber_Applied_Patches
inux-rfml:/usr/local/amber12 # ./patch_amber.py --update-tree
Determining patches to download for AmberTools12
AmberTools12 is up to date. Nothing to download
Determining patches to download for Amber12
Amber12 is up to date. Nothing to download
linux-rfml:/usr/local/amber12 # ./configure gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.6.2
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the gfortran compiler:
gfortran -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
test_pointer_size.c
Detected 32 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
Configuring XBLAS (may be time-consuming)...
XBLAS configure succeeded.
Configuring MTK++ (may be time-consuming)...
MTK++-0.2.0 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
linux-rfml:/usr/local/amber12 # make install
On Wed, Jan 30, 2013 at 6:24 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> Jason,
> Just to clarify, I think the problem is "authenticated" proxies. I also
> have had
> no problem with my proxy setting the http_proxy environmental variable
> but it seems Vaibhav's proxy requires username/password.
> According to his e-mail he had the un/pwd set already.
> >From what I gather in the docs urllib2 does support authenticated proxies.
>
>
>
>
>
> On Wed, Jan 30, 2013 at 9:27 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Wed, Jan 30, 2013 at 12:27 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> > >wrote:
> >
> > > Dear Daniel,
> > > I have followed your suggestions and after making changes it is giving
> > this
> > > message below.
> > > Did it apply patches correctly? I did not really understand the meaning
> > of
> > > the warning given below. It seems to have skipped some of the patchs,
> did
> > > it? I have attached the patch_amber.py file, if check if it is
> according
> > to
> > > your expectation.
> > >
> >
> > This is not right. Amber12 only has 14 patches. AmberTools 12 has 34.
> > Therefore, it appears like you loaded /home/gm/bugfixes/12.0 with all of
> > the AmberTools bug fixes. You need to be careful about putting the
> correct
> > bug fixes in the correct directory. The error messages that appeared are
> > fine -- it means that some patches were already applied (which makes
> sense,
> > since AmberTools12 now ships with bug fixes 1-13). When you get your
> > directories filled with the correct bug fixes, unpack a fresh version of
> > Amber 12 and AmberTools 12 and try over (but make sure you keep your
> > modified patch_amber.py).
> >
> > Also, while Dan said that the API documentation of urllib.urlopen does
> not
> > technically support proxies, I've never had a problem connecting through
> a
> > proxy by setting the http_proxy environment variable. If wget works,
> > patch_amber.py should work, too. Perhaps a local sysadmin can help.
> > Hopefully the next iteration of the updater will have better proxy
> > support.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> sindhikara.gmail.com <http://www.dansindhikara.com>
> --
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Jan 30 2013 - 05:30:03 PST
