Dear all,
I am trying to install Amber12 and AmberTools12 software in opensuse linux.
when i run ./configure gnu i got the below output. from this it seems that
configuration is ok.
But no update of patch is done for both Amber12 and AmberTools12.
I also tried the options provided in AmberTools 12 manual in Chapter 1
Section 5. But still the patch remains unupdated.
I have provided the outputs from the commands below.
amber.linux-t1qy:~> export AMBERHOME=/home/amber/amber12
amber.linux-t1qy:~> cd $AMBERHOME
amber.linux-t1qy:~/amber12> ./configure gnu
Checking for updates...
AmberTools12 has 16 unapplied patches: 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29
Amber12 has 8 unapplied patches: 1, 2, 3, 4, 5, 6, 7, 8
There are patches available. Do you want to apply them now? [y/n]
(Recommended Y)
NOT updating your tree and continuing anyway.
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.7.1
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.
amber.linux-t1qy:~/amber12> $AMBERHOME/patch_amber.py --check-updates
AmberTools12 has 16 unapplied patches: 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, 27, 28, 29
Amber12 has 8 unapplied patches: 1, 2, 3, 4, 5, 6, 7, 8
amber.linux-t1qy:~/amber12> $AMBERHOME/patch_amber.py --patch-level
Latest patch applied to AmberTools12: 13
No patches have been applied to Amber12 yet.
amber.linux-t1qy:~/amber12> $AMBERHOME/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
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
Fatal Error: Cannot find the patch program.
amber.linux-t1qy:~/amber12>
Thanks in advance
M.Prabu
--
M. Prabu
Research Scholar (CSIR-SRF)
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Received on Thu Dec 20 2012 - 03:30:03 PST
