Re: [AMBER] errors compiling amber11 for cuda from Ross Walker on 2011-04-12 (Amber Archive Apr 2011)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 12 Apr 2011 15:27:34 -0700

Hi Robert,

The Radix sort header file was removed by the latest patch however the problem you are seeing look suspiciously to me like the bugfixes were only partially applied. One possibility is that the patching was run with an AMBERHOME environment variable pointing to the wrong place.

I suggest (for sanity) going back to the original tar files for Amber 11 and AmberTools 1.4 and then patching and building cleanly from there. An example would be:

------------------------------------------

cd $AMBERHOME
cd ..
rm -rf $AMBERHOME

(Copy the original tar files here)

tar xvjf AmberTools-1.4.tar.bz2
tar xvjf Amber11.tar.bz2

cd $AMBERHOME

wget http://ambermd.org/bugfixes/AmberTools/1.4/bugfix.all
patch -p0 <bugfix.all
rm -f bugfix.all

wget http://ambermd.org/bugfixes/11.0/bugfix.all
wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x

./apply_bugfix.x bugfix.all

cd $AMBERHOME/AmberTools/src

./configure -cuda gnu

cd ../../src
make cuda

cd ../test
make test.cuda

------------------------------------------

Good luck,

Ross

> -----Original Message-----
> From: Robert Wohlhueter [mailto:bobwohlhueter.earthlink.net]
> Sent: Tuesday, April 12, 2011 9:19 AM
> To: amber.ambermd.org
> Subject: [AMBER] errors compiling amber11 for cuda
>
> 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/libnetcdf
> f.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 - 15:30:03 PDT