On Sun, Mar 24, 2013 at 8:17 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>wrote:
> Dear Amber users,
> I earlier had problem patching amber due to proxy server problem. So I
> downloaded all bugfixes, made the suggested changes in patch_amber.py and
> installed amber.
> patch_amber.py --update-tree showed nothing to download, but as Jason had
> suspected here <http://archive.ambermd.org/201301/0453.html>, not all
> bugfixes are applied and I find that "patch_amber.py --patch-level" shows
> only 8 and 13 patches applied to Amber12 and AmberTools12 respectively. I
> have reproduced the same issue in another directory below.
>
> Please suggest why all updates are not being applied and how I can solve
> this problem to make use of the latest versions of Amber12 and
> AmberTools12.
>
> Following are the command line details which confirm that I have followed
> the prescribed procedure, all bugfixes are located in the appropriate
> location and Amber paths have been set properly. My patch_amber.py file is
> attached for your suggestions.
>
> Thanks in advance.
>
> linux-rfml:/usr/local/newamber/amber12 # cd $AMBERHOME
> linux-rfml:/usr/local/newamber/amber12 #
>
> 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: 13
> No patches have been applied to Amber12 yet.
> 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
> 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/newamber/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/Run.aladip.hf_sto-3g.MechEm
> Creating file
>
> /usr/local/newamber/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/aladip.hf_sto-3g.MechEm.mdout.save
> Creating file
>
> /usr/local/newamber/amber12/test/qmmm_EXTERN/QMMM_MD_Orca/aladip.hf_sto-3g.MechEm.restrt.save
> Creating file
>
> /usr/local/newamber/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
> 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 # ./patch_amber.py --patch-level
> Latest patch applied to AmberTools12: 13
> Latest patch applied to Amber12: 8
> linux-rfml:/usr/local/newamber/amber12 #
>
> Bugfixes saved:
> linux-rfml:/usr/local/newamber/amber12 # ls ../../bugfixes/12.0/
> total 16020
> -rw-r--r-- 1 root root 57524 Mar 24 22:35 bugfix.13
> -rw-r--r-- 1 root root 25943 Mar 24 22:35 bugfix.11
> -rw-r--r-- 1 root root 1339854 Mar 24 22:35 bugfix.10
> -rw-r--r-- 1 root root 34423 Mar 24 22:35 bugfix.4
> -rw-r--r-- 1 root root 2388 Mar 24 22:35 bugfix.3
> -rw-r--r-- 1 root root 574862 Mar 24 22:35 bugfix.2
> -rwxr-xr-x 1 root root 664 Mar 24 22:35 patch_amber.sh~
> -rw-r--r-- 1 root root 4500 Mar 24 22:35 bugfix.7
> -rw-r--r-- 1 root root 1138 Mar 24 22:35 bugfix.8
> -rw-r--r-- 1 root root 13439214 Mar 24 22:35 bugfix.9.bz2_
> -rw-r--r-- 1 root root 1912 Mar 24 22:35 bugfix.5
> -rw-r--r-- 1 root root 944 Mar 24 22:35 bugfix.6
> -rw-r--r-- 1 root root 863526 Mar 24 22:35 bugfix.14
> -rwxr-xr-x 1 root root 669 Mar 24 22:35 patch_amber.sh
> -rw-r--r-- 1 root root 1257 Mar 24 22:35 bugfix.12
> -rw-r--r-- 1 root root 1940 Mar 24 22:35 bugfix.1
> drwxr-xr-x 2 root root 4096 Mar 24 22:35 .
> drwxr-xr-x 4 root root 4096 Mar 24 22:35 ..
> linux-rfml:/usr/local/newamber/amber12 # ls
> ../../bugfixes/AmberTools12/12.0/
> total 832
> drwxr-xr-x 3 root root 4096 Mar 24 22:35 ..
> -rw-r--r-- 1 root root 8290 Mar 24 22:35 bugfix.22
> -rw-r--r-- 1 root root 1632 Mar 24 22:35 bugfix.13
> -rw-r--r-- 1 root root 29408 Mar 24 22:35 bugfix.23
> -rw-r--r-- 1 root root 2333 Mar 24 22:35 bugfix.11
> -rw-r--r-- 1 root root 30425 Mar 24 22:35 bugfix.9
> -rw-r--r-- 1 root root 3343 Mar 24 22:35 bugfix.10
> -rw-r--r-- 1 root root 129142 Mar 24 22:35 bugfix.4
> -rw-r--r-- 1 root root 2632 Mar 24 22:35 bugfix.33
> -rw-r--r-- 1 root root 5067 Mar 24 22:35 bugfix.25
> -rw-r--r-- 1 root root 8040 Mar 24 22:35 bugfix.27
> -rw-r--r-- 1 root root 1914 Mar 24 22:35 bugfix.17
> -rw-r--r-- 1 root root 870 Mar 24 22:35 bugfix.3
> -rw-r--r-- 1 root root 3668 Mar 24 22:35 bugfix.26
> -rw-r--r-- 1 root root 1939 Mar 24 22:35 patch_amber.sh~
-rw-r--r-- 1 root root 5577 Mar 24 22:35 bugfix.29
> -rw-r--r-- 1 root root 740 Mar 24 22:35 bugfix.28
> -rw-r--r-- 1 root root 4913 Mar 24 22:35 bugfix.2
> -rw-r--r-- 1 root root 1331 Mar 24 22:35 bugfix.7
> -rw-r--r-- 1 root root 2453 Mar 24 22:35 bugfix.8
> -rw-r--r-- 1 root root 4564 Mar 24 22:35 bugfix.5
> -rw-r--r-- 1 root root 1123 Mar 24 22:35 bugfix.34
> -rw-r--r-- 1 root root 5211 Mar 24 22:35 bugfix.32
> -rw-r--r-- 1 root root 25928 Mar 24 22:35 bugfix.14
> -rw-r--r-- 1 root root 42598 Mar 24 22:35 bugfix.6
> -rw-r--r-- 1 root root 4529 Mar 24 22:35 bugfix.19
> -rw-r--r-- 1 root root 44085 Mar 24 22:35 bugfix.16
> -rw-r--r-- 1 root root 1312 Mar 24 22:35 bugfix.15
> -rw-r--r-- 1 root root 15702 Mar 24 22:35 bugfix.1
> -r-xr-xr-x 1 root root 1939 Mar 24 22:35 patch.sh
> -rw-r--r-- 1 root root 9864 Mar 24 22:35 bugfix.35
> -rw-r--r-- 1 root root 1601 Mar 24 22:35 bugfix.30
> -rw-r--r-- 1 root root 4608 Mar 24 22:35 bugfix.21
> -rw-r--r-- 1 root root 2477 Mar 24 22:35 bugfix.18
> -rw-r--r-- 1 root root 2682 Mar 24 22:35 bugfix.12
> -rw-r--r-- 1 root root 14923 Mar 24 22:35 bugfix.31
> -rw-r--r-- 1 root root 5292 Mar 24 22:35 bugfix.24
> drwxr-xr-x 2 root root 4096 Mar 24 22:35 .
> -rw-r--r-- 1 root root 324369 Mar 24 22:35 bugfix.20
> linux-rfml:/usr/local/newamber/amber12 #
>
Try getting rid of all files that are _not_ bug fixes (i.e. the *.sh
files). I've set up mirrors like this myself and it has always worked fine
for me.
Out of curiosity, why are you setting up mirrors in the first place? Why
not just download them directly from Amber's website?
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Mar 24 2013 - 17:30:02 PDT
