I think make is giving you a clue!
make[2]: yacc: Command not found
So, `sudo apt-get install bison`, or something similar.
HTH,
--asn
2009/4/1 Francesco Pietra <chiendarret.gmail.com>:
> Hi:
> On a multisocket uma-type board with dual-opterons, following failure
> of one disk of raid1, I have changed both with larger disks and
> installed from scratch debian linux amd64 lenny raid1, intel compilers
> 10.1.015 and mkl lib.
>
> As I want to install a modified version of amber9, I took from
> previous working disk the ifort-gcc-mkl install of amber9, replaced
> modified files in sander, recompiled, ending in failure.
>
> In the remote hypothesis that previous installation was not fully
> patched, I started from scratch, i.e.amber9 source. Patched with the
> complete bugfix.all. To simplify, "chown -R francesco
> /usr/local/amber9". First I tried to compile the standard
> fully-patched version, ending in failure again:
>
> $ ./configure ifort_x86_64
>
> $ make clean 2>&1 | tee make.clean.out
>
> $ make 2>&1 | tee make.out
>
>
>
> make.clean.out reported what I guess are irrelevant errors. Last part reads:
>
> rules.make:142: warning: ignoring old commands for target `/man3f90'
> make[1]: *** No rule to make target `macros.make'. Stop.
> make[1]: Leaving directory `/usr/local/amber9/src/netcdf/src'
> make: [clean] Error 2 (ignored)
> cd netcdf/lib && rm -f libnetcdf.a
> /bin/sh: line 0: cd: netcdf/lib: No such file or directory
> make: [clean] Error 1 (ignored)
> cd netcdf/include && rm -f *.mod
> /bin/sh: line 0: cd: netcdf/include: No such file or directory
> make: [clean] Error 1 (ignored)
>
>
> make.out ended in serious errors. Last part reads (attached please
> find the whole out file):
>
> build.c: In function ‘BuildInternalsForSimpleRings’:
> build.c:2185: warning: passing argument 1 of
> ‘GraphUtilFindAllSmallestRingsAndRingGroups’ from incompatible pointer
> type
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o elements.o elements.c
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o library.o library.c
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o chirality.o chirality.c
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o minimizer.o minimizer.c
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o model.o model.c
> model.c: In function ‘zModelOrderAtoms’:
> model.c:497: warning: passing argument 1 of ‘Sift’ from incompatible
> pointer type
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o parmLib.o parmLib.c
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o pdbFile.o pdbFile.c
> pdbFile.c: In function ‘zPdbBuildCoordinatesForContainer’:
> pdbFile.c:1088: warning: passing argument 1 of ‘BuildFixInternals’
> from incompatible pointer type
> pdbFile.c: In function ‘zPdbAddAtom’:
> pdbFile.c:1207: warning: passing argument 1 of
> ‘BuildInternalsForContainer’ from incompatible pointer type
> pdbFile.c: In function ‘writeTER’:
> pdbFile.c:1761: warning: initialization from incompatible pointer type
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o tools.o tools.c
> tools.c: In function ‘iToolDistanceSearch’:
> tools.c:1643: warning: passing argument 1 of ‘SortByDouble’ from
> incompatible pointer type
> tools.c:1643: warning: passing argument 4 of ‘SortByDouble’ from
> incompatible pointer type
> tools.c: In function ‘ToolOrientPrincipleAxisAlongCoordinateAxis’:
> tools.c:1714: warning: passing argument 2 of ‘MathOpDiagonalize’ from
> incompatible pointer type
> gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -m64 -O2 -o variables.o variables.c
> yacc parser.y
> make[2]: yacc: Command not found
> make[2]: *** [parser.c] Error 127
> make[2]: Leaving directory `/usr/local/amber9/src/leap/src/leap'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory `/usr/local/amber9/src/leap'
> make: *** [serial] Error 2
>
> As far as I understand, the errors are related to X. A frequent "ifort
> command line option -tp not supported" is probably irrelevant)
>
> What I checked: startx provides the X server and a minimal window
> (enough for xleap in my experience). Package "xorg-dev" and the
> environment for compilation, package "build-essential" are installed
> correctly.
>
> gcc -v 4.3.2
>
> make -v 3.81
>
> Curiously, I had no problems with previous identical installation on
> debian amd64 etch, which passed without any need of recompiling to
> debian amd64 lenny. Unfortunately I did not save the output of make of
> the original successful installation.
>
> thanks for help
>
> francesco pietra
>
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>
>
--
[ ]s
--alessandro
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Received on Fri Apr 03 2009 - 01:07:53 PDT
