Greetings to all,
Thanks to all who develop and help to improve ambertools.
Below I paste what I have done, before the error occurred, and how I
solved it.
I don't know whether "Run this script again to get all updates." in
./configure
is a demand or a statement. However I get the same error if I run it
one or two
times.
Hope this helps
Matthias
System: OpenSuse 11.4
bohner.linux34:~>tar -xjvf AmberTools13.tar.bz2
[...]
[no errors]
[...]
bohner.linux34:~>cd amber12
bohner.linux34:~/amber12> export AMBERHOME=`pwd`
bohner.linux34:~/amber12> ./configure gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
update.1 (modifies cpptraj)
update.2 (modifies MMPBSA.py, and, ParmEd)
update.3 (modifies cpptraj, ParmEd, calcpka)
update.4 (modifies pbsa)
update.5 (modifies cpptraj, MMPBSA.py, ParmEd)
update.6 (modifies configure2)
update.7 (modifies update_amber)
update.8 (modifies configure)
update.9 (modifies MMPBSA.py)
update.10 (modifies cpptraj)
There are patches available. Do you want to apply them now? [y/n]
(Recommended Y)
Y
Preparing to apply updates... please wait.
Downloading updates for AmberTools 13
Downloading AmberTools 13/update.1 (14.25 KB)
Applying AmberTools 13/update.1
Downloading AmberTools 13/update.2 (1.99 KB)
Applying AmberTools 13/update.2
Downloading AmberTools 13/update.3 (39.60 KB)
Applying AmberTools 13/update.3
Downloading AmberTools 13/update.4 (602.14 KB)
Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0%
Done.
Applying AmberTools 13/update.4
Downloading AmberTools 13/update.5 (35.79 KB)
Applying AmberTools 13/update.5
Downloading AmberTools 13/update.6 (4.83 KB)
Applying AmberTools 13/update.6
Downloading AmberTools 13/update.7 (949 Bytes)
Applying AmberTools 13/update.7
updater.py has found a patch to itself... I am quitting now so
future updates will apply with the fixed script.
Run this script again to get all updates.
Preparing to apply updates... please wait.
Downloading updates for AmberTools 13
Downloading AmberTools 13/update.8 (1.15 KB)
Applying AmberTools 13/update.8
Downloading AmberTools 13/update.9 (968 Bytes)
Applying AmberTools 13/update.9
Downloading AmberTools 13/update.10 (77.46 KB)
Applying AmberTools 13/update.10
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.5.1
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 64 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.
bohner.linux34:~/amber12> ./configure gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
No patches available
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.5.1
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 64 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.
bohner.linux34:~/amber12>make install
cd AmberTools/src && make install
make[1]: Entering directory `/home/linux34_i1/bohner/amber12/AmberTools/src'
cd netcdf/src && make && make -j 1 install
make[2]: Entering directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src'
make all-recursive
make[3]: Entering directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src'
Making all in f90
make[4]: Entering directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src/f90'
/bin/sh ../libtool --mode=compile gfortran -I../libsrc -I. -O3
-mtune=native -c -o typeSizes.lo typeSizes.f90
libtool: compile: unable to infer tagged configuration
libtool: compile: specify a tag with `--tag'
make[4]: *** [typeSizes.lo] Error 1
make[4]: Leaving directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src/f90'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory
`/home/linux34_i1/bohner/amber12/AmberTools/src/netcdf/src'
make[1]: *** [/home/linux34_i1/bohner/amber12/include/netcdf.mod] Error 2
make[1]: Leaving directory `/home/linux34_i1/bohner/amber12/AmberTools/src'
make: *** [install] Error 2
A small change of the following Makefile solves the problem for me
diff $AMBERHOME/AmberTools/src/netcdf/src/f90/Makefile
$AMBERHOME/AmberTools/src/netcdf/src/f90/Makefile.orig
175c175
< LIBTOOL = $(SHELL) $(top_builddir)/libtool --tag=gfortran
---
> LIBTOOL = $(SHELL) $(top_builddir)/libtool
-------- Original Message --------
Subject: Re: Is it a buck? Ambertools
Date: Mon, 24 Jun 2013 11:46:10 -0400
From: David A Case <amber-admin.biomaps.rutgers.edu>
To: Matthias Bohner <bohner.theochem.uni-stuttgart.de>
CC: jason.biomaps.rutgers.edu, daniel.r.roe.gmail.com
On Mon, Jun 24, 2013, Matthias Bohner wrote:
> Dear Sir or Madam,
Please send amber-related questions to the mail reflector, amber.ambermd.org,
and not to amber-admin. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.
>
> After executing downloading and extracting ambertools and running
> ./configure gnu
> I had to change line 175 in /amber12/src/netcdf/src/f90/Makefile to
>
> LIBTOOL = $(SHELL) $(top_builddir)/libtool --tag=gfortan
Could you report the result of "gfortran --version"? What was the error
message? As far as I know, no one has ever reported a problem like this
before...
...thanks...dac
--
David A. Case
For the Amber Development Team
email: amber-admin.biomaps.rutgers.edu
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Received on Tue Jun 25 2013 - 01:00:02 PDT
