Compiling AmberTools1.4 and amber11 on an AMD-64 4-core cpu under Ubuntu
Linux 10.04 (after running bugfix.all, Apr. 12, 2011), with a GeForce
GTX 275 card and with the latest cuda toolkit installed
(cudatoolkit_3.2.16_linux_64_ubuntu10.04.run):
The output from `configure` and `make` (copied below) seem to document
the following successes and failures:
1) configuring for -cuda and gnu successfully generate a config.h file
2) cd'ing to the .../amber11/src dir and typing 'make cuda' initiates a
lot of compilation work, apparently successful.
3) Until it get to make in dir
/usr/local/lib/amber11/src/pmemd/src/cuda, where fatal erros are reported.
4) The errors seem to stem from the absence of radixsort.h, which is
indeed not to be found in my $CUDA_HOME directory tree.
Can anyone bail me out of the problem?
Thanks, Bob Wohlhueter
*******************************************************************************************************************************
root.winter-linux: ...AmberTools/src (4%)# ./configure -cuda gnu
./configure -cuda gnu
Your AMBERHOME environment variable should be set to /usr/local/lib/amber11
Obtaining the gnu suite version:
gcc -v
The version is 4.4.3Compiling AmberTools1.4 and amber11 on an AMD-64
4-core cpu under Ubuntu Linux 10.04 (after running bugfix.all, Apr. 7,
2011), with a GeForce GTX 275 card and NVIDIA driver version 260.19.36:
The excerpts below seem to document the following successes and failures:
1) configuring for -cuda and gnu successfully generate a config.h file
2) cd'ing to the .../amber11/src dir and typing 'make cuda' initiates a
lot of compilation work, apparently successful.
3) Until I get to make in dir /usr/local/lib/amber11/src/pmemd/src/cuda,
culminating a several errors.
4) Most of the errors refer to .h files in /usr/include/bits and in
/usr/local/cuda/bin/../include
Can anyone give me an explanation of what has gone wrong?
Thanks, Bob Wohlhueter
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Validating the C++ compiler version:
g++ -v
The version is 4.4.3
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 -o testp testp.c.o testp.f.o -lgfortran
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.
Configuring fftw-2.1.5; (may be time-consuming)
fftw-2.1.5 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to cd to ../../src and type 'make cuda'
root.winter-linux: ...AmberTools/src (5%)# cd ../../src
cd ../../src
root.winter-linux: ...amber11/src (6%)# make cuda
make cuda
cd netcdf/src && make install
make[1]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
Making install in f90
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
/bin/bash ../libtool --mode=compile gfortran -I../libsrc -I. -O3
-mtune=generic -c -o typeSizes.lo typeSizes.f90
gfortran -I../libsrc -I. -O3 -mtune=generic -c typeSizes.f90 -o
typeSizes.o
/bin/bash ../libtool --mode=compile gfortran -I../libsrc -I. -O3
-mtune=generic -c -o netcdf.lo netcdf.f90
gfortran -I../libsrc -I. -O3 -mtune=generic -c netcdf.f90 -o netcdf.o
/bin/bash ../libtool --mode=link gfortran -I../libsrc -I. -O3
-mtune=generic -o libnetcdff90.la typeSizes.lo netcdf.lo
mkdir .libs
ar cru .libs/libnetcdff90.a typeSizes.o netcdf.o
ranlib .libs/libnetcdff90.a
creating libnetcdff90.la
(cd .libs && rm -f libnetcdff90.la && ln -s ../libnetcdff90.la
libnetcdff90.la)
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f90.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f90.3'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'typesizes.mod'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/typesizes.mod'
/usr/bin/install -c -m 644 'netcdf.mod'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.mod'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
Making install in fortran
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-attio.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-control.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-dim.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-genatt.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-geninq.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-genvar.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-lib.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-misc.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-v2compat.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-vario.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-var1io.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varaio.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varmio.lo -MD -MP -MF "$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$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT fort-varsio.lo -MD -MP -MF "$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/bash ../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
mkdir .libs
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/lib/amber11/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/typeSizes.o
.libs/libnetcdff.lax/libnetcdff90.a/netcdf.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/lib/amber11/AmberTools/src/netcdf/src/fortran'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/lib" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/lib"
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.inc'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.inc'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f77.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f77.3'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
Making install in libsrc
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
depbase=`echo attr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT attr.lo -MD -MP -MF "$depbase.Tpo" -c -o attr.lo
attr.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT attr.lo -MD -MP -MF
.deps/attr.Tpo -c attr.c -o attr.o
depbase=`echo ncx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT ncx.lo -MD -MP -MF "$depbase.Tpo" -c -o ncx.lo
ncx.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT ncx.lo -MD -MP -MF
.deps/ncx.Tpo -c ncx.c -o ncx.o
depbase=`echo putget.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT putget.lo -MD -MP -MF "$depbase.Tpo" -c -o
putget.lo putget.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT putget.lo -MD -MP -MF
.deps/putget.Tpo -c putget.c -o putget.o
depbase=`echo dim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT dim.lo -MD -MP -MF "$depbase.Tpo" -c -o dim.lo
dim.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT dim.lo -MD -MP -MF
.deps/dim.Tpo -c dim.c -o dim.o
depbase=`echo error.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT error.lo -MD -MP -MF "$depbase.Tpo" -c -o
error.lo error.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT error.lo -MD -MP -MF
.deps/error.Tpo -c error.c -o error.o
depbase=`echo libvers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT libvers.lo -MD -MP -MF "$depbase.Tpo" -c -o
libvers.lo libvers.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT libvers.lo -MD -MP -MF
.deps/libvers.Tpo -c libvers.c -o libvers.o
depbase=`echo nc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT nc.lo -MD -MP -MF "$depbase.Tpo" -c -o nc.lo nc.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT nc.lo -MD -MP -MF
.deps/nc.Tpo -c nc.c -o nc.o
depbase=`echo string.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT string.lo -MD -MP -MF "$depbase.Tpo" -c -o
string.lo string.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT string.lo -MD -MP -MF
.deps/string.Tpo -c string.c -o string.o
depbase=`echo v1hpg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT v1hpg.lo -MD -MP -MF "$depbase.Tpo" -c -o
v1hpg.lo v1hpg.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT v1hpg.lo -MD -MP -MF
.deps/v1hpg.Tpo -c v1hpg.c -o v1hpg.o
depbase=`echo var.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT var.lo -MD -MP -MF "$depbase.Tpo" -c -o var.lo
var.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT var.lo -MD -MP -MF
.deps/var.Tpo -c var.c -o var.o
depbase=`echo posixio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT posixio.lo -MD -MP -MF "$depbase.Tpo" -c -o
posixio.lo posixio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT posixio.lo -MD -MP -MF
.deps/posixio.Tpo -c posixio.c -o posixio.o
depbase=`echo v2i.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H
-I. -I. -I.. -I../fortran -DNDEBUG -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -MT v2i.lo -MD -MP -MF "$depbase.Tpo" -c -o v2i.lo
v2i.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f
"$depbase.Tpo"; exit 1; fi
gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -DNDEBUG
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT v2i.lo -MD -MP -MF
.deps/v2i.Tpo -c v2i.c -o v2i.o
/bin/bash ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o libnetcdf2.la v2i.lo
mkdir .libs
ar cru .libs/libnetcdf2.a v2i.o
ranlib .libs/libnetcdf2.a
creating libnetcdf2.la
(cd .libs && rm -f libnetcdf2.la && ln -s ../libnetcdf2.la libnetcdf2.la)
/bin/bash ../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -o libnetcdf.la -rpath
/usr/local/lib/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.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/lib/amber11/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/lib/amber11/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/fort-dim.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varaio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varsio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-lib.o
.libs/libnetcdf.lax/libnetcdff.a/fort-attio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-misc.o
.libs/libnetcdf.lax/libnetcdff.a/fort-genatt.o
.libs/libnetcdf.lax/libnetcdff.a/typeSizes.o
.libs/libnetcdf.lax/libnetcdff.a/fort-vario.o
.libs/libnetcdf.lax/libnetcdff.a/fort-control.o
.libs/libnetcdf.lax/libnetcdff.a/fort-varmio.o
.libs/libnetcdf.lax/libnetcdff.a/fort-geninq.o
.libs/libnetcdf.lax/libnetcdff.a/netcdf.o
.libs/libnetcdf.lax/libnetcdff.a/fort-v2compat.o
.libs/libnetcdf.lax/libnetcdff.a/fort-genvar.o
.libs/libnetcdf.lax/libnetcdff.a/fort-var1io.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/lib/amber11/AmberTools/src/netcdf/src/libsrc'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/lib" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/lib"
/bin/bash ../libtool --mode=install /usr/bin/install -c
'libnetcdf.la'
'/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.la'
/usr/bin/install -c .libs/libnetcdf.lai
/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.la
/usr/bin/install -c .libs/libnetcdf.a
/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
chmod 644 /usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
ranlib /usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
PATH="$PATH:/sbin" ldconfig -n
/usr/local/lib/amber11/AmberTools/src/netcdf/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.h'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.h'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf.3'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
Making install in nctest
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nctest'
make[3]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/nctest'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nctest'
Making install in ncgen
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
main.o -MD -MP -MF "$depbase.Tpo" -c -o main.o main.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo load.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
load.o -MD -MP -MF "$depbase.Tpo" -c -o load.o load.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo ncgentab.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
ncgentab.o -MD -MP -MF "$depbase.Tpo" -c -o ncgentab.o ncgentab.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo escapes.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
escapes.o -MD -MP -MF "$depbase.Tpo" -c -o escapes.o escapes.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo getfill.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
getfill.o -MD -MP -MF "$depbase.Tpo" -c -o getfill.o getfill.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo init.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
init.o -MD -MP -MF "$depbase.Tpo" -c -o init.o init.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo genlib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I.. -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
genlib.o -MD -MP -MF "$depbase.Tpo" -c -o genlib.o genlib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
/bin/bash ../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
mkdir .libs
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/lib/amber11/AmberTools/src/netcdf/src/ncgen'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/bin" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/bin"
/bin/bash ../libtool --mode=install /usr/bin/install -c 'ncgen'
'/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncgen'
/usr/bin/install -c ncgen
/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncgen
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncgen.1'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1/ncgen.1'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
Making install in ncdump
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
depbase=`echo ncdump.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
ncdump.o -MD -MP -MF "$depbase.Tpo" -c -o ncdump.o ncdump.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
depbase=`echo vardata.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
vardata.o -MD -MP -MF "$depbase.Tpo" -c -o vardata.o vardata.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
vardata.c: In function ‘pr_bvals’:
vardata.c:491: warning: format not a string literal and no format arguments
vardata.c:501: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_svals’:
vardata.c:539: warning: format not a string literal and no format arguments
vardata.c:549: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_ivals’:
vardata.c:589: warning: format not a string literal and no format arguments
vardata.c:599: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_fvals’:
vardata.c:637: warning: format not a string literal and no format arguments
vardata.c:647: warning: format not a string literal and no format arguments
vardata.c: In function ‘pr_dvals’:
vardata.c:685: warning: format not a string literal and no format arguments
vardata.c:695: warning: format not a string literal and no format arguments
depbase=`echo dumplib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc
-I../libsrc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -MT
dumplib.o -MD -MP -MF "$depbase.Tpo" -c -o dumplib.o dumplib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo";
exit 1; fi
/bin/bash ../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
mkdir .libs
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/lib/amber11/AmberTools/src/netcdf/src/ncdump'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/bin" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/bin"
/bin/bash ../libtool --mode=install /usr/bin/install -c 'ncdump'
'/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncdump'
/usr/bin/install -c ncdump
/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncdump
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncdump.1'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1/ncdump.1'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
Making install in nf_test
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nf_test'
make[3]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/nf_test'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nf_test'
Making install in nc_test
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nc_test'
make[3]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/nc_test'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nc_test'
Making install in examples
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
Making install in C
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/C'
make[4]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/examples/C'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/C'
Making install in CDL
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[4]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
Making install in F77
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
make[4]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
Making install in F90
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make install-am
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[5]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[4]: Entering directory
`/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/src/examples'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[3]: Entering directory
`/usr/local/lib/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/lib/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/lib/amber11/AmberTools/src/netcdf/src'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[1]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
Starting installation of Amber11 (cuda) at Tue Apr 12 11:48:09 EDT 2011.
cd pmemd && make cuda
make[1]: Entering directory `/usr/local/lib/amber11/src/pmemd'
make -C ../netcdf/src install
make[2]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
Making install in f90
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
make[4]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f90.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f90.3'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'typesizes.mod'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/typesizes.mod'
/usr/bin/install -c -m 644 'netcdf.mod'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.mod'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/f90'
Making install in fortran
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/lib" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/lib"
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.inc'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.inc'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf_f77.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf_f77.3'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/fortran'
Making install in libsrc
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/lib" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/lib"
/bin/bash ../libtool --mode=install /usr/bin/install -c
'libnetcdf.la'
'/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.la'
/usr/bin/install -c .libs/libnetcdf.lai
/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.la
/usr/bin/install -c .libs/libnetcdf.a
/usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
chmod 644 /usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
ranlib /usr/local/lib/amber11/AmberTools/src/netcdf/lib/libnetcdf.a
PATH="$PATH:/sbin" ldconfig -n
/usr/local/lib/amber11/AmberTools/src/netcdf/lib
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib/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/lib/amber11/AmberTools/src/netcdf/include" || mkdir
-p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/include"
/usr/bin/install -c -m 644 'netcdf.h'
'/usr/local/lib/amber11/AmberTools/src/netcdf/include/netcdf.h'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3"
/usr/bin/install -c -m 644 './netcdf.3'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man3/netcdf.3'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/libsrc'
Making install in nctest
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nctest'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nctest'
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/lib/amber11/AmberTools/src/netcdf/src/nctest'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nctest'
Making install in ncgen
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/bin" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/bin"
/bin/bash ../libtool --mode=install /usr/bin/install -c 'ncgen'
'/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncgen'
/usr/bin/install -c ncgen
/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncgen
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncgen.1'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1/ncgen.1'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncgen'
Making install in ncdump
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/bin" || mkdir -p
-- "/usr/local/lib/amber11/AmberTools/src/netcdf/bin"
/bin/bash ../libtool --mode=install /usr/bin/install -c 'ncdump'
'/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncdump'
/usr/bin/install -c ncdump
/usr/local/lib/amber11/AmberTools/src/netcdf/bin/ncdump
test -z "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1" ||
mkdir -p -- "/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1"
/usr/bin/install -c -m 644 './ncdump.1'
'/usr/local/lib/amber11/AmberTools/src/netcdf/share/man/man1/ncdump.1'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/ncdump'
Making install in nf_test
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nf_test'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nf_test'
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/lib/amber11/AmberTools/src/netcdf/src/nf_test'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nf_test'
Making install in nc_test
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nc_test'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nc_test'
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/lib/amber11/AmberTools/src/netcdf/src/nc_test'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/nc_test'
Making install in examples
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
Making install in C
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/C'
make[5]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/C'
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/lib/amber11/AmberTools/src/netcdf/src/examples/C'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/C'
Making install in CDL
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[5]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
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/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/CDL'
Making install in F77
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
make[5]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
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/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F77'
Making install in F90
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make install-am
make[5]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[6]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[6]: Nothing to be done for `install-exec-am'.
make[6]: Nothing to be done for `install-data-am'.
make[6]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[5]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples/F90'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[5]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
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/lib/amber11/AmberTools/src/netcdf/src/examples'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src/examples'
make[3]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[4]: Entering directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[4]: Nothing to be done for `install-exec-am'.
make install-data-hook
make[5]: Entering directory
`/usr/local/lib/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[5]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[4]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[3]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
make[2]: Leaving directory
`/usr/local/lib/amber11/AmberTools/src/netcdf/src'
cp ../netcdf/include/*.mod ./src
make -C src/ cuda
make[2]: Entering directory `/usr/local/lib/amber11/src/pmemd/src'
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gbl_constants.fpp
gbl_constants.f90
gfortran -O3 -mtune=generic -DCUDA -c gbl_constants.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gbl_datatypes.fpp
gbl_datatypes.f90
gfortran -O3 -mtune=generic -DCUDA -c gbl_datatypes.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA state_info.fpp
state_info.f90
gfortran -O3 -mtune=generic -DCUDA -c state_info.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA file_io_dat.fpp
file_io_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c file_io_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pmemd_lib.fpp
pmemd_lib.f90
gfortran -O3 -mtune=generic -DCUDA -c pmemd_lib.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA parallel_dat.fpp
parallel_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c parallel_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA file_io.fpp file_io.f90
gfortran -O3 -mtune=generic -DCUDA -c file_io.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA mdin_ctrl_dat.fpp
mdin_ctrl_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c mdin_ctrl_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA axis_optimize.fpp
axis_optimize.f90
gfortran -O3 -mtune=generic -DCUDA -c axis_optimize.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA fft1d.fpp fft1d.f90
gfortran -O3 -mtune=generic -DCUDA -c fft1d.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA charmm.fpp charmm.f90
gfortran -O3 -mtune=generic -DCUDA -c charmm.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA nextprmtop_section.fpp
nextprmtop_section.f90
gfortran -O3 -mtune=generic -DCUDA -c nextprmtop_section.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA prmtop_dat.fpp
prmtop_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c prmtop_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA mdin_ewald_dat.fpp
mdin_ewald_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c mdin_ewald_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA mdin_debugf_dat.fpp
mdin_debugf_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c mdin_debugf_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA inpcrd_dat.fpp
inpcrd_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c inpcrd_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA mol_list.fpp mol_list.f90
gfortran -O3 -mtune=generic -DCUDA -c mol_list.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA extra_pnts_nb14.fpp
extra_pnts_nb14.f90
gfortran -O3 -mtune=generic -DCUDA -c extra_pnts_nb14.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA prfs.fpp prfs.f90
gfortran -O3 -mtune=generic -DCUDA -c prfs.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA dynamics_dat.fpp
dynamics_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c dynamics_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA random.fpp random.f90
gfortran -O3 -mtune=generic -DCUDA -c random.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA dynamics.fpp dynamics.f90
gfortran -O3 -mtune=generic -DCUDA -c dynamics.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pbc.fpp pbc.f90
gfortran -O3 -mtune=generic -DCUDA -c pbc.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA img.fpp img.f90
gfortran -O3 -mtune=generic -DCUDA -c img.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA timers.fpp timers.f90
gfortran -O3 -mtune=generic -DCUDA -c timers.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA bspline.fpp bspline.f90
gfortran -O3 -mtune=generic -DCUDA -c bspline.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_recip_dat.fpp
pme_recip_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_recip_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_fft_dat.fpp
pme_fft_dat.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_fft_dat.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_blk_fft.fpp
pme_blk_fft.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_blk_fft.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_slab_fft.fpp
pme_slab_fft.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_slab_fft.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA constraints.fpp
constraints.f90
gfortran -O3 -mtune=generic -DCUDA -c constraints.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA shake.fpp shake.f90
gfortran -O3 -mtune=generic -DCUDA -c shake.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA nmr_lib.fpp nmr_lib.f90
gfortran -O3 -mtune=generic -DCUDA -c nmr_lib.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA nmr_calls.fpp
nmr_calls.f90
gfortran -O3 -mtune=generic -DCUDA -c nmr_calls.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA angles.fpp angles.f90
gfortran -O3 -mtune=generic -DCUDA -c angles.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA angles_ub.fpp
angles_ub.f90
gfortran -O3 -mtune=generic -DCUDA -c angles_ub.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA cmap.fpp cmap.f90
gfortran -O3 -mtune=generic -DCUDA -c cmap.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA bonds.fpp bonds.f90
gfortran -O3 -mtune=generic -DCUDA -c bonds.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA cit.fpp cit.f90
gfortran -O3 -mtune=generic -DCUDA -c cit.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA dihedrals.fpp
dihedrals.f90
gfortran -O3 -mtune=generic -DCUDA -c dihedrals.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA dihedrals_imp.fpp
dihedrals_imp.f90
gfortran -O3 -mtune=generic -DCUDA -c dihedrals_imp.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA nb_exclusions.fpp
nb_exclusions.f90
gfortran -O3 -mtune=generic -DCUDA -c nb_exclusions.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA parallel.fpp parallel.f90
gfortran -O3 -mtune=generic -DCUDA -c parallel.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gb_parallel.fpp
gb_parallel.f90
gfortran -O3 -mtune=generic -DCUDA -c gb_parallel.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA nb_pairlist.fpp
nb_pairlist.f90
gfortran -O3 -mtune=generic -DCUDA -c nb_pairlist.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA loadbal.fpp loadbal.f90
gfortran -O3 -mtune=generic -DCUDA -c loadbal.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_blk_recip.fpp
pme_blk_recip.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_blk_recip.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_slab_recip.fpp
pme_slab_recip.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_slab_recip.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA ene_frc_splines.fpp
ene_frc_splines.f90
gfortran -O3 -mtune=generic -DCUDA -c ene_frc_splines.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_direct.fpp
pme_direct.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_direct.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA bintraj.fpp bintraj.f90
gfortran -O3 -mtune=generic -DCUDA -c bintraj.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA runfiles.fpp runfiles.f90
gfortran -O3 -mtune=generic -DCUDA -c runfiles.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_force.fpp
pme_force.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_force.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA degcnt.fpp degcnt.f90
gfortran -O3 -mtune=generic -DCUDA -c degcnt.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gb_ene.fpp gb_ene.f90
gfortran -O3 -mtune=generic -DCUDA -c gb_ene.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gb_force.fpp gb_force.f90
gfortran -O3 -mtune=generic -DCUDA -c gb_force.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA runmd.fpp runmd.f90
gfortran -O3 -mtune=generic -DCUDA -c runmd.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA runmin.fpp runmin.f90
gfortran -O3 -mtune=generic -DCUDA -c runmin.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA veclib.fpp veclib.f90
gfortran -O3 -mtune=generic -DCUDA -c veclib.f90
gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DCUDA -c pmemd_clib.c
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA gb_alltasks_setup.fpp
gb_alltasks_setup.f90
gfortran -O3 -mtune=generic -DCUDA -c gb_alltasks_setup.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_alltasks_setup.fpp
pme_alltasks_setup.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_alltasks_setup.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pme_setup.fpp
pme_setup.f90
gfortran -O3 -mtune=generic -DCUDA -c pme_setup.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA get_cmdline.fpp
get_cmdline.f90
gfortran -O3 -mtune=generic -DCUDA -c get_cmdline.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA master_setup.fpp
master_setup.f90
gfortran -O3 -mtune=generic -DCUDA -c master_setup.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA pmemd.fpp pmemd.f90
gfortran -O3 -mtune=generic -DCUDA -c pmemd.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA erfcfun.fpp erfcfun.f90
gfortran -O3 -mtune=generic -DCUDA -c erfcfun.f90
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA charmm_gold.fpp
charmm_gold.f90
gfortran -O3 -mtune=generic -DCUDA -c charmm_gold.f90
make -C ./cuda
make[3]: Entering directory `/usr/local/lib/amber11/src/pmemd/src/cuda'
cpp -traditional -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA cuda_info.fpp
cuda_info.f90
gfortran -O3 -mtune=generic -DCUDA -I/usr/local/cuda/include -c
cuda_info.f90
gcc -O3 -mtune=generic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DCUDA -I/usr/local/cuda/include -c gpu.cpp
In file included from gpu.cpp:21:
gputypes.h:22:23: error: radixsort.h: No such file or directory
In file included from gpu.cpp:21:
gputypes.h:952: error: ‘nvRadixSort’ has not been declared
gputypes.h:952: error: ISO C++ forbids declaration of ‘RadixSort’ with
no type
gputypes.h:952: error: expected ‘;’ before ‘*’ token
gpu.cpp: In function ‘void gpu_neighbor_list_setup_(int*, int*, double*,
double*)’:
gpu.cpp:1974: error: ‘struct _gpuContext’ has no member named ‘pRadixSort’
gpu.cpp:2096: error: ‘struct _gpuContext’ has no member named ‘pRadixSort’
gpu.cpp:2096: error: expected type-specifier before ‘nvRadixSort’
gpu.cpp:2096: error: expected ‘;’ before ‘nvRadixSort’
gpu.cpp: In function ‘void gpu_build_neighbor_list_()’:
gpu.cpp:2871: error: ‘struct _gpuContext’ has no member named ‘pRadixSort’
make[3]: *** [gpu.o] Error 1
make[3]: Leaving directory `/usr/local/lib/amber11/src/pmemd/src/cuda'
make[2]: *** [-L/usr/local/cuda/lib64] Error 2
make[2]: Leaving directory `/usr/local/lib/amber11/src/pmemd/src'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/usr/local/lib/amber11/src/pmemd'
make: *** [cuda] Error 2
root.winter-linux: ...amber11/src (7%)#
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Received on Tue Apr 12 2011 - 09:30:05 PDT
