Dear Dr. Jason and Amber people,
Thanks a lot for helping me figure about that small (silly) directory name
error. After fixing that it seems to have worked fine as shown below and
patch level is also 35 and 14 for AmberTools and Amber respectively now. I
hope whatever files patch_amber.py has moved, is what was expected, please
suggest if you find something wrong there.
About setting mirrors: As we had discussed earlier
here<
http://archive.ambermd.org/201301/0451.html>,
I tried many ways but my proxy settings won't let me go online while using
patch_amber.py and gives error "No internet access!". Thus I have to follow
this path.
The make install & make test steps gave a few warnings, but have completed
successfully as seen in the bottom of this message.
Out of curiosity: whenever a new patch becomes available for AmberTools, is
it necessary for us to reconfigure/recompile Amber along with AmberTools
and vise-versa?
Thanks a lot.
linux-rfml:/usr/local/newamber/amber12 # vim patch_amber.py
linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree
Determining patches to download for AmberTools12
Downloading bugfix.14
Downloading bugfix.15
Downloading bugfix.16
Downloading bugfix.17
Downloading bugfix.18
Downloading bugfix.19
Downloading bugfix.20
Downloading bugfix.21
Downloading bugfix.22
Downloading bugfix.23
Downloading bugfix.24
Downloading bugfix.25
Downloading bugfix.26
Downloading bugfix.27
Downloading bugfix.28
Downloading bugfix.29
Downloading bugfix.30
Downloading bugfix.31
Downloading bugfix.32
Downloading bugfix.33
Downloading bugfix.34
Downloading bugfix.35
Determining patches to download for Amber12
Amber12 is up to date. Nothing to download
Applying AmberTools12 patches
Moving bugfix.14 to AmberTools_Applied_Patches
Moving bugfix.15 to AmberTools_Applied_Patches
Creating file
/usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
Creating file
/usr/local/newamber/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.h
Moving bugfix.16 to AmberTools_Applied_Patches
Moving bugfix.17 to AmberTools_Applied_Patches
Moving bugfix.18 to AmberTools_Applied_Patches
Moving bugfix.19 to AmberTools_Applied_Patches
Moving bugfix.20 to AmberTools_Applied_Patches
Moving bugfix.21 to AmberTools_Applied_Patches
This patch patches patch_amber.py. I will quit after this patch so the rest
may be applied with the updated version.
Moving bugfix.22 to AmberTools_Applied_Patches
linux-rfml:/usr/local/newamber/amber12 # ./patch_amber.py --update-tree
Determining patches to download for AmberTools12
Downloading bugfix.23
Downloading bugfix.24
Downloading bugfix.25
Downloading bugfix.26
Downloading bugfix.27
Downloading bugfix.28
Downloading bugfix.29
Downloading bugfix.30
Downloading bugfix.31
Downloading bugfix.32
Downloading bugfix.33
Downloading bugfix.34
Downloading bugfix.35
Determining patches to download for Amber12
Downloading bugfix.9.bz2_
Decompressing .patches/Amber_Unapplied_Patches/bugfix.9.bz2 with
/usr/bin/bunzip2
Downloading bugfix.10
Downloading bugfix.11
Downloading bugfix.12
Downloading bugfix.13
Downloading bugfix.14
Applying AmberTools12 patches
Moving bugfix.23 to AmberTools_Applied_Patches
Moving bugfix.24 to AmberTools_Applied_Patches
Moving bugfix.25 to AmberTools_Applied_Patches
Moving bugfix.26 to AmberTools_Applied_Patches
Moving bugfix.27 to AmberTools_Applied_Patches
Moving bugfix.28 to AmberTools_Applied_Patches
Moving bugfix.29 to AmberTools_Applied_Patches
Moving bugfix.30 to AmberTools_Applied_Patches
Moving bugfix.31 to AmberTools_Applied_Patches
Moving bugfix.32 to AmberTools_Applied_Patches
Moving bugfix.33 to AmberTools_Applied_Patches
Moving bugfix.34 to AmberTools_Applied_Patches
Moving bugfix.35 to AmberTools_Applied_Patches
Applying Amber12 patches
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Moving bugfix.9 to Amber_Applied_Patches
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Moving bugfix.11 to Amber_Applied_Patches
Moving bugfix.12 to Amber_Applied_Patches
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Moving bugfix.14 to Amber_Applied_Patches
linux-rfml:/usr/local/newamber/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/newamber/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/newamber/amber12 # ./patch_amber.py --patch-level
Latest patch applied to AmberTools12: 35
Latest patch applied to Amber12: 14
linux-rfml:/usr/local/newamber/amber12 # make install
make[3]: Leaving directory
`/usr/local/newamber/amber12/src/pmemd.amoeba/src'
Installation of pmemd.amoeba complete
make[2]: Leaving directory `/usr/local/newamber/amber12/src/pmemd.amoeba'
Installation of Amber12 (serial) is complete at Mon Mar 25 15:29:40 IST
2013.
make[1]: Leaving directory `/usr/local/newamber/amber12/src'
linux-rfml:/usr/local/newamber/amber12 # make test
........
make[2]: Leaving directory `/usr/local/newamber/amber12/test'
524 file comparisons passed
36 file comparisons failed
26 tests experienced errors
Test log file saved as
/usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.log
Test diffs file saved as
/usr/local/newamber/amber12/logs/test_amber_serial/2013-03-25_15-59-30.diff
make[1]: Leaving directory `/usr/local/newamber/amber12/test'
Summary of AmberTools serial tests:
604 file comparisons passed
6 file comparisons failed
0 tests experienced errors
Test log file saved as
/usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.log
Test diffs file saved as
/usr/local/newamber/amber12/logs/test_at_serial/2013-03-25_15-32-02.diff
On Mon, Mar 25, 2013 at 5:49 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Please disregard my last suggestion. I found your problem.
>
> On Sun, Mar 24, 2013 at 8:17 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> >
> > linux-rfml:/usr/local/newamber/amber12 # ls
> > ../../bugfixes/AmberTools12/12.0/
> >
>
> You are storing the bug fixes for AmberTools 12 in
> /usr/local/bugfixes/AmberTools12/12.0/ but you are looking for them in
> /usr/local/bugfixes/AmberTools/12.0/ (notice the extra 12 in the first
> version). Therefore, patch_amber.py finds no patches for AmberTools 12 and
> patches nothing. And bugfixes for Amber 9 and above cannot be
> applied/found until bugfix.22 from AmberTools has been applied.
>
> So change the directory name from AmberTools12 to AmberTools and everything
> should work.
>
> The question remains though, why set up mirrors instead of allowing
> patch_amber.py to download the files directly?
>
> All the best,
> 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
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 24 2013 - 23:00:02 PDT
