AMBER Archive (2009)

Subject: [AMBER] Failure to compile amber9 serial ifort gcc

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 01 2009 - 06:04:18 CDT

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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