[AMBER] patching unsuccessful even after modifying patch_amber.py

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Sun, 24 Mar 2013 17:47:50 +0530

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 #




-- 
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 Sun Mar 24 2013 - 05:30:04 PDT
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