ok, thanks you all.... I'm not a great shell user i know ... that's why I
need your kind help.
so..
I separated the two directories amber7 and amber11 (they're now in
usr/local/bin)
I set AMBERHOME with this string in a [t]csh shell
setenv AMBERHOME /usr/local/bin/amber11
I set the path as follows:
set path = ( $path $AMBERHOME/bin\:/usr/local/bin/amber7/exe )
I run xleap and this time it didn't start at all (before these changes it
started, but when I typed edit pep2 this was the error message : segmentation
falut (core dumped) and the Universe Editor crashed)
However, this time the Universe Editor didn't started, this was the Error:
-I: Adding /usr/local/bin/amber11/dat/leap/prep to search path.
-I: Adding /usr/local/bin/amber11/dat/leap/lib to search path.
-I: Adding /usr/local/bin/amber11/dat/leap/parm to search path.
-I: Adding /usr/local/bin/amber11/dat/leap/cmd to search path.
Wcl Error: WcWidgetCreation(xaLeap) - Failed
Problem: No children could be created from Xrm database.
Possible: Resource file not found
user environment:
XENVIRONMENT is not set,
XAPPLRESDIR not terminated with '/'
user environment or installation:
$XENVIRONMENT/XaLeap does not exist.
Possible: top level widget in resource file not named 'xaLeap'
Error: Shell widget xaLeap has zero width and/or height
I think I'm wrong again with these environments...
However, I tried to complete the installation of AmberTool, as written in
the .pdf in amber11/doc so, after setting the path, it was written to type
cd amber11/AmberTools/src
./configure gnu
make
but this was the result
cd netcdf/src && make install
make[1]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
Making install in f90
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f90.3'
'/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f90.3'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/include" || mkdir -p
-- "/usr/local/bin/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'typesizes.mod'
'/usr/local/bin/amber11/AmberTools/src/netcdf/include/typesizes.mod'
/usr/bin/install -c -m 644 'netcdf.mod'
'/usr/local/bin/amber11/AmberTools/src/netcdf/include/netcdf.mod'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/f90'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/f90'
Making install in fortran
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-attio.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-attio.lo fort-attio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-attio.lo -MD -MP -MF
.deps/fort-attio.Tpo -c fort-attio.c -o fort-attio.o
depbase=`echo fort-control.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-control.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-control.lo fort-control.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-control.lo -MD -MP -MF
.deps/fort-control.Tpo -c fort-control.c -o fort-control.o
depbase=`echo fort-dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-dim.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-dim.lo fort-dim.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-dim.lo -MD -MP -MF
.deps/fort-dim.Tpo -c fort-dim.c -o fort-dim.o
depbase=`echo fort-genatt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-genatt.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-genatt.lo fort-genatt.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-genatt.lo -MD -MP -MF
.deps/fort-genatt.Tpo -c fort-genatt.c -o fort-genatt.o
depbase=`echo fort-geninq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-geninq.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-geninq.lo fort-geninq.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-geninq.lo -MD -MP -MF
.deps/fort-geninq.Tpo -c fort-geninq.c -o fort-geninq.o
depbase=`echo fort-genvar.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-genvar.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-genvar.lo fort-genvar.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-genvar.lo -MD -MP -MF
.deps/fort-genvar.Tpo -c fort-genvar.c -o fort-genvar.o
depbase=`echo fort-lib.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-lib.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-lib.lo fort-lib.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-lib.lo -MD -MP -MF
.deps/fort-lib.Tpo -c fort-lib.c -o fort-lib.o
depbase=`echo fort-misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-misc.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-misc.lo fort-misc.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-misc.lo -MD -MP -MF
.deps/fort-misc.Tpo -c fort-misc.c -o fort-misc.o
depbase=`echo fort-v2compat.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-v2compat.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-v2compat.lo fort-v2compat.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-v2compat.lo -MD -MP -MF
.deps/fort-v2compat.Tpo -c fort-v2compat.c -o fort-v2compat.o
depbase=`echo fort-vario.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-vario.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-vario.lo fort-vario.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-vario.lo -MD -MP -MF
.deps/fort-vario.Tpo -c fort-vario.c -o fort-vario.o
depbase=`echo fort-var1io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-var1io.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-var1io.lo fort-var1io.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-var1io.lo -MD -MP -MF
.deps/fort-var1io.Tpo -c fort-var1io.c -o fort-var1io.o
depbase=`echo fort-varaio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varaio.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-varaio.lo fort-varaio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-varaio.lo -MD -MP -MF
.deps/fort-varaio.Tpo -c fort-varaio.c -o fort-varaio.o
depbase=`echo fort-varmio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varmio.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-varmio.lo fort-varmio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-varmio.lo -MD -MP -MF
.deps/fort-varmio.Tpo -c fort-varmio.c -o fort-varmio.o
depbase=`echo fort-varsio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.
-I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varsio.lo -MD -MP -MF "$depbase.Tpo" -c -o
fort-varsio.lo fort-varsio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1;
fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT fort-varsio.lo -MD -MP -MF
.deps/fort-varsio.Tpo -c fort-varsio.c -o fort-varsio.o
/bin/sh ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o libnetcdff.la fort-attio.lo fort-control.lo
fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo fort-lib.lo
fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo fort-varaio.lo
fort-varmio.lo fort-varsio.lo ../f90/libnetcdff90.la
rm -fr .libs/libnetcdff.a .libs/libnetcdff.la
rm -fr .libs/libnetcdff.lax
mkdir .libs/libnetcdff.lax
rm -fr .libs/libnetcdff.lax/libnetcdff90.a
mkdir .libs/libnetcdff.lax/libnetcdff90.a
(cd .libs/libnetcdff.lax/libnetcdff90.a && ar x
/usr/local/bin/amber11/AmberTools/src/netcdf/src/fortran/../f90/.libs/libnetcdff90.a)
ar cru .libs/libnetcdff.a fort-attio.o fort-control.o fort-dim.o
fort-genatt.o fort-geninq.o fort-genvar.o fort-lib.o fort-misc.o
fort-v2compat.o fort-vario.o fort-var1io.o fort-varaio.o fort-varmio.o
fort-varsio.o .libs/libnetcdff.lax/libnetcdff90.a/netcdf.o
.libs/libnetcdff.lax/libnetcdff90.a/typeSizes.o
ranlib .libs/libnetcdff.a
rm -fr .libs/libnetcdff.lax
creating libnetcdff.la
(cd .libs && rm -f libnetcdff.la && ln -s ../libnetcdff.la libnetcdff.la)
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/fortran'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/lib" || mkdir -p --
"/usr/local/bin/amber11/AmberTools/src/netcdf/lib"
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/include" || mkdir -p
-- "/usr/local/bin/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.inc'
'/usr/local/bin/amber11/AmberTools/src/netcdf/include/netcdf.inc'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f77.3'
'/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f77.3'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/fortran'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/fortran'
Making install in libsrc
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc'
/bin/sh ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o libnetcdf.la -rpath
/usr/local/bin/amber11/AmberTools/src/netcdf/lib -version-info 4:0:0
-no-undefined attr.lo ncx.lo putget.lo dim.lo error.lo libvers.lo nc.lo
string.lo v1hpg.lo var.lo posixio.lo libnetcdf2.la ../fortran/libnetcdff.la
rm -fr .libs/libnetcdf.a .libs/libnetcdf.la .libs/libnetcdf.lai
rm -fr .libs/libnetcdf.lax
mkdir .libs/libnetcdf.lax
rm -fr .libs/libnetcdf.lax/libnetcdf2.a
mkdir .libs/libnetcdf.lax/libnetcdf2.a
(cd .libs/libnetcdf.lax/libnetcdf2.a && ar x
/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc/./.libs/libnetcdf2.a)
rm -fr .libs/libnetcdf.lax/libnetcdff.a
mkdir .libs/libnetcdf.lax/libnetcdff.a
(cd .libs/libnetcdf.lax/libnetcdff.a && ar x
/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc/../fortran/.libs/libnetcdff.a)
ar cru .libs/libnetcdf.a attr.o ncx.o putget.o dim.o error.o libvers.o nc.o
string.o v1hpg.o var.o posixio.o .libs/libnetcdf.lax/libnetcdf2.a/v2i.o
.libs/libnetcdf.lax/libnetcdff.a/netcdf.o
.libs/libnetcdf.lax/libnetcdff.a/fort-misc.o
.libs/libnetcdf.lax/libnetcdff.a/fort-var1io.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varaio.o
.libs/libnetcdf.lax/libnetcdff.a/typeSizes.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varmio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-lib.o
.libs/libnetcdf.lax/libnetcdff.a/fort-v2compat.o
.libs/libnetcdf.lax/libnetcdff.a/fort-control.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varsio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-genvar.o
.libs/libnetcdf.lax/libnetcdff.a/fort-genatt.o
.libs/libnetcdf.lax/libnetcdff.a/fort-geninq.o
.libs/libnetcdf.lax/libnetcdff.a/fort-attio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-dim.o
.libs/libnetcdf.lax/libnetcdff.a/fort-vario.o
ranlib .libs/libnetcdf.a
rm -fr .libs/libnetcdf.lax
creating libnetcdf.la
(cd .libs && rm -f libnetcdf.la && ln -s ../libnetcdf.la libnetcdf.la)
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/lib" || mkdir -p --
"/usr/local/bin/amber11/AmberTools/src/netcdf/lib"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'libnetcdf.la'
'/usr/local/bin/amber11/AmberTools/src/netcdf/lib/libnetcdf.la'
/usr/bin/install -c .libs/libnetcdf.lai
/usr/local/bin/amber11/AmberTools/src/netcdf/lib/libnetcdf.la
/usr/bin/install -c .libs/libnetcdf.a
/usr/local/bin/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
chmod 644 /usr/local/bin/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
ranlib /usr/local/bin/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
PATH="$PATH:/sbin" ldconfig -n
/usr/local/bin/amber11/AmberTools/src/netcdf/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/bin/amber11/AmberTools/src/netcdf/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,--rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/include" || mkdir -p
-- "/usr/local/bin/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.h'
'/usr/local/bin/amber11/AmberTools/src/netcdf/include/netcdf.h'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf.3'
'/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man3/netcdf.3'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/libsrc'
Making install in nctest
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nctest'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nctest'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nctest'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nctest'
Making install in ncgen
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncgen'
/bin/sh ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o ncgen main.o load.o ncgentab.o escapes.o getfill.o
init.o genlib.o ../libsrc/libnetcdf.la
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ncgen main.o load.o
ncgentab.o escapes.o getfill.o init.o genlib.o ../libsrc/.libs/libnetcdf.a
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncgen'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/bin" || mkdir -p --
"/usr/local/bin/amber11/AmberTools/src/netcdf/bin"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'ncgen'
'/usr/local/bin/amber11/AmberTools/src/netcdf/bin/ncgen'
/usr/bin/install -c ncgen
/usr/local/bin/amber11/AmberTools/src/netcdf/bin/ncgentest -z
"/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1" || mkdir -p --
"/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncgen.1'
'/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1/ncgen.1'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncgen'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncgen'
Making install in ncdump
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncdump'
/bin/sh ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o ncdump ncdump.o vardata.o dumplib.o -lm
../libsrc/libnetcdf.la
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o ncdump ncdump.o vardata.o
dumplib.o -lm ../libsrc/.libs/libnetcdf.a
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncdump'
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/bin" || mkdir -p --
"/usr/local/bin/amber11/AmberTools/src/netcdf/bin"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'ncdump'
'/usr/local/bin/amber11/AmberTools/src/netcdf/bin/ncdump'
/usr/bin/install -c ncdump
/usr/local/bin/amber11/AmberTools/src/netcdf/bin/ncdump
test -z "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1" ||
mkdir -p -- "/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncdump.1'
'/usr/local/bin/amber11/AmberTools/src/netcdf/share/man/man1/ncdump.1'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncdump'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/ncdump'
Making install in nf_test
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nf_test'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nf_test'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nf_test'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nf_test'
Making install in nc_test
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nc_test'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nc_test'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nc_test'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/nc_test'
Making install in examples
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
Making install in C
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/C'
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/C'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/C'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/C'
Making install in CDL
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/CDL'
Making install in F77
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F77'
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F77'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F77'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F77'
Making install in F90
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make install-am
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make[5]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make[5]: Nothing to be done for `install-exec-am'.
make[5]: Nothing to be done for `install-data-am'.
make[5]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples/F90'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src/examples'
make[2]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
make[3]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
make[3]: Nothing to be done for `install-exec-am'.
make install-data-hook
make[4]: Entering directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
+-------------------------------------------------------------+
| CAUTION: |
| |
| If you have not already run "make check", then we strongly |
| recommend you do so. It does not take very long. |
| |
| Before using netCDF to store important data, test your |
| build with "make check". |
| |
| NetCDF is tested nightly on many platforms at Unidata |
| but your platform is probably different in some ways. |
| |
| If any tests fail, please see the netCDF web site: |
|
http://www.unidata.ucar.edu/software/netcdf/ |
| |
| NetCDF is developed and maintained at the Unidata Program |
| Center. Unidata provides a broad array of data and software |
| tools for use in geoscience education and research. |
|
http://www.unidata.ucar.edu |
+-------------------------------------------------------------+
make[4]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
make[3]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
make[2]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
make[1]: Leaving directory
`/usr/local/bin/amber11/AmberTools/src/netcdf/src'
Starting installation of AmberTools, version 1.4 serial at Wed Sep 8
16:45:07 CEST 2010.
(cd ucpp-1.3 && make install )
make[1]: Entering directory `/usr/local/bin/amber11/AmberTools/src/ucpp-1.3'
gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
mv ucpp /usr/local/bin/amber11/bin
make[1]: Leaving directory `/usr/local/bin/amber11/AmberTools/src/ucpp-1.3'
(cd byacc && make install )
make[1]: Entering directory `/usr/local/bin/amber11/AmberTools/src/byacc'
main.o(.text+0x65b): In function `create_file_names':
main.c: warning: the use of `mktemp' is dangerous, better use `mkstemp'
mv yacc /usr/local/bin/amber11/bin
make[1]: Leaving directory `/usr/local/bin/amber11/AmberTools/src/byacc'
(cd arpack && make install );
make[1]: Entering directory `/usr/local/bin/amber11/AmberTools/src/arpack'
gfortran -c -O3 -o dsarpack.o dsarpack.f
In file dsarpack.f:424
12 go to 11
1
In file dsarpack.f:199
go to (12,18) label
2
Error: Label at (1) is not in the same block as the GOTO statement at (2)
In file dsarpack.f:545
18 go to 17
1
In file dsarpack.f:199
go to (12,18) label
2
Error: Label at (1) is not in the same block as the GOTO statement at (2)
make[1]: *** [dsarpack.o] Error 1
make[1]: Leaving directory `/usr/local/bin/amber11/AmberTools/src/arpack'
make: *** [serial] Error 2
What do you think I should do now? (give up???)
0/9/8, Jason Swails <jason.swails.gmail.com>:
> On Wed, Sep 8, 2010 at 9:45 AM, Frank Thommen <
> structures-it.embl-heidelberg.de> wrote:
>
> > > Also, set path = ( $path $AMBERHOME/exe ) won't work, because you need
> to
> > > set it as an environment variable. Also, PATH is all uppercase, and
> many
> > > unices are case-sensitive so you have to make sure they're all
> uppercase.
> > > Furthermore, PATH should be colon-delimited, not space-delimited I
> > believe.
> > > Google how to set up environment variables with whatever shell you're
> > using
> > > and follow those instructions for PATH and AMBERHOME.
> >
> > 'set path = ( $path $AMBERHOME/exe )' is syntactically correct and does
> > the same as 'setenv PATH=${PATH}:$AMBERHOME/exe'. [t]csh automatically
> > converts $path into $PATH and the other way round, as soon as you modify
> > either variable.
> >
>
>
> Ah, so it becomes evident that bash is my shell of choice :). Thanks for
> the clarification.
>
>
> --Jason
>
>
>
> >
> > But for everything else I agree.
> >
> > frank
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
> --
>
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
>
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Sep 08 2010 - 08:00:03 PDT
