Building protomol-2.0.3_9.txz (origin /buildshare/ports/355755/biology/protomol) for powerpc-10-0 on XXX Pre-existing file system for this slot! slot1: removed slot1: created x distfiles/ x distfiles/protomol-2.0.3-tar.gz x packages/ x packages/xproto-7.0.25.txz x packages/glproto-1.4.17.txz x packages/libpthread-stubs-0.3_4.txz x packages/makedepend-1.0.5,1.txz x packages/libgpg-error-1.13.txz x packages/tiff-4.0.3_2.txz x packages/xorg-macros-1.19.0.txz x packages/pkg-1.2.7_2.txz x packages/py27-setuptools27-2.0.1.txz x packages/randrproto-1.4.0.txz x packages/libdrm-2.4.17_1.txz x packages/libX11-1.6.2_2,1.txz x packages/pciids-20140526.txz x packages/xf86bigfontproto-1.2.0.txz x packages/renderproto-0.11.1.txz x packages/bigreqsproto-1.1.2.txz x packages/libGLU-9.0.0.txz x packages/libcheck-0.9.12.txz x packages/kbproto-1.0.6.txz x packages/libXmu-1.1.2_2,1.txz x packages/libXext-1.3.2_2,1.txz x packages/libxcb-1.10_2.txz x packages/libXrandr-1.4.2_2.txz x packages/libtool-2.4.2_3.txz x packages/xcb-proto-1.10_1.txz x packages/freeglut-2.8.1_2.txz x packages/libXrender-0.9.8_2.txz x packages/libxml2-2.9.1_1.txz x packages/libpciaccess-0.13.2_2.txz x packages/expat-2.1.0.txz x packages/gmake-3.82_1.txz x packages/perl5-5.16.3_10.txz x packages/libXxf86vm-1.1.3_2.txz x packages/py27-libxml2-2.9.1.txz x packages/jpeg-8_5.txz x packages/damageproto-1.2.1.txz x packages/libSM-1.2.2_2,1.txz x packages/python2-2_2.txz x packages/xcmiscproto-1.2.2.txz x packages/libXdmcp-1.1.1_2.txz x packages/inputproto-2.3.txz x packages/libgcrypt-1.5.3_2.txz x packages/png-1.5.18.txz x packages/libGL-7.6.1_4.txz x packages/dri2proto-2.8.txz x packages/libXdamage-1.1.4_2.txz x packages/libxslt-1.1.28_3.txz x packages/cmake-modules-2.8.12.1_1.txz x packages/cmake-2.8.12.1_4.txz x packages/libXfixes-5.0.1_2.txz x packages/gettext-0.18.3.1_1.txz x packages/libXau-1.0.8_2.txz x packages/python27-2.7.6_4.txz x packages/xf86vidmodeproto-2.3.1.txz x packages/jbigkit-1.6.txz x packages/xextproto-7.3.0.txz x packages/bison-2.7.1,1.txz x packages/m4-1.4.17_1,1.txz x packages/xtrans-1.3.4_1.txz x packages/fixesproto-5.0.txz x packages/libICE-1.0.8_2,1.txz x packages/libXi-1.7.2_2,1.txz x packages/libXt-1.1.4_2,1.txz x packages/pkgconf-0.9.5.txz ELF ldconfig path: /lib /usr/lib /usr/lib/compat Make depends ===> protomol-2.0.3_9 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg ===> Installing existing package /packages/pkg-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on shared library: libpng15.so - not found ===> Verifying for libpng15.so in /buildshare/ports/355755/graphics/png ===> Installing existing package /packages/png-1.5.18.txz Installing png-1.5.18... done ===> Returning to build of protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on shared library: libjpeg.so - not found ===> Verifying for libjpeg.so in /buildshare/ports/355755/graphics/jpeg ===> Installing existing package /packages/jpeg-8_5.txz Installing jpeg-8_5... done ===> Returning to build of protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on shared library: libtiff.so - not found ===> Verifying for libtiff.so in /buildshare/ports/355755/graphics/tiff ===> Installing existing package /packages/tiff-4.0.3_2.txz Installing tiff-4.0.3_2...Installing freeglut-2.8.1_2...Installing libGLU-9.0.0...Installing libGL-7.6.1_4...Installing dri2proto-2.8... done Installing expat-2.1.0... done Installing libX11-1.6.2_2,1...Installing kbproto-1.0.6... done Installing libXau-1.0.8_2...Installing xproto-7.0.25... done done Installing libXdmcp-1.1.1_2... done Installing libxcb-1.10_2...Installing libpthread-stubs-0.3_4... done Installing libxml2-2.9.1_1... done done done Installing libXdamage-1.1.4_2...Installing damageproto-1.2.1... done Installing libXfixes-5.0.1_2...Installing fixesproto-5.0... done done done Installing libXext-1.3.2_2,1...Installing xextproto-7.3.0... done done Installing libXxf86vm-1.1.3_2...Installing xf86vidmodeproto-2.3.1... done done Installing libdrm-2.4.17_1...Installing libpciaccess-0.13.2_2...Installing pciids-20140526... done done done done done Installing libICE-1.0.8_2,1... done Installing libXi-1.7.2_2,1...Installing inputproto-2.3... done done Installing libXrandr-1.4.2_2...Installing libXrender-0.9.8_2...Installing renderproto-0.11.1... done done Installing randrproto-1.4.0... done done done Installing jbigkit-1.6... done Installing libSM-1.2.2_2,1... done Installing libXmu-1.1.2_2,1...Installing libXt-1.1.4_2,1... done done done Since FreeBSD has new USB stack, freeglut normally doesn't build on FreeBSD 8 (yet). To workaround this a small patch adds one include file and comments out content of one function (only leaves return NULL). This might cause side effects. Joysticks do not work, and there might be ports that do not compile or applications that crash because of this. Do not hesitate to contact x11@FreeBSD.org if there are any issues and side effects because of this. ===> Returning to build of protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so.3.9.0) ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found Make install ===> protomol-2.0.3_9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by protomol-2.0.3_9 for building ===> Extracting for protomol-2.0.3_9 => SHA256 Checksum OK for protomol-2.0.3-tar.gz. ===> Patching for protomol-2.0.3_9 ===> Applying FreeBSD patches for protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> protomol-2.0.3_9 depends on shared library: libpng15.so - found (/usr/local/lib/libpng15.so.15) ===> protomol-2.0.3_9 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so.11) ===> protomol-2.0.3_9 depends on shared library: libtiff.so - found (/usr/local/lib/libtiff.so.4) ===> protomol-2.0.3_9 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so.3.9.0) ===> Configuring for protomol-2.0.3_9 ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/protomol/work/protomol/aclocal.m4 ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/protomol/work/protomol/configure configure: loading site script /buildshare/ports/355755/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel checking whether build environment is sane... yes checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking major version... 2 checking minor version... 0 checking patchlevel... 3 checking for C++ compiler default output... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of c++... none checking preset g++ for SUN with optimization flags ... no checking preset CC fro IRIX with MPI and optimization flags ... no checking preset CC for IRIX with MPI and debugging flags ... no checking preset CC for IRIX with optimization flags ... no checking preset CC for IRIX with debugging flags ... no checking preset icc for generic with optimization flags ... no checking preset icc for generic with debugging flags ... no checking preset icc for generic with MPICH flags ... no checking preset icc for generic with MPICH and optimization flags ... no checking preset icc for generic with MPICH and debugging flags ... no checking preset g++ for generic with MPICH flags ... no checking preset g++ for generic with MPICH XEON flags ... no checking preset g++ for generic with MPICH debug flags ... no checking preset g++ for generic with optimization flags ... no checking preset g++ for generic with debugging flags ... no checking preset g++ for generic with debugging and gdb flags ... no checking preset xlC for PPC with optimization flags ... no checking preset xlC for PPC with debugging flags ... no checking preset xlC for AIX with optimization flags ... no checking preset xlC for AIX with debugging flags ... no checking preset xlC for AIX with MPI and optimization flags ... no checking preset xlC for AIX with MPI and debugging flags ... no checking preset aCC for HPUX with optimization flags ... no checking preset aCC for HPUX with debugging flags ... no checking preset aCC for HPUX with MPI and optimization flags ... no checking preset aCC for HPUX with MPI and debugging flags ... no CC : cc CFLAGS : -O2 -pipe -fno-strict-aliasing CXXFLAGS : -O2 -pipe -fno-strict-aliasing -L/usr/local/lib CXX : c++ CXXCPP : LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking dependency style of c++... (cached) none checking how to run the C++ preprocessor... c++ -E checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking dependency style of cc... none checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel checking for ranlib... ranlib checking using MPI... no checking for X... libraries /usr/local/lib, headers /usr/local/include checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for limits ... yes checking for sstream ... yes checking for partial template specialization... yes checking for socket in -lsocket... no checking for egrep... grep -E checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/socket.h... (cached) yes checking for socketlen type... socklen_t checking for char... (cached) yes checking size of char... 1 checking for short... (cached) yes checking size of short... 2 checking for int... (cached) yes checking size of int... 4 checking for long... (cached) yes checking size of long... 4 checking for size_t... (cached) yes checking size of size_t... 4 checking for void*... yes checking size of void*... 4 checking for 32-bit int... int checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... (cached) yes checking c_asm.h usability... no checking c_asm.h presence... no checking for c_asm.h... no checking intrinsics.h usability... no checking intrinsics.h presence... no checking for intrinsics.h... no checking for hrtime_t... no checking for gethrtime... no checking for clock_gettime... (cached) yes checking for read_real_time... no checking for time_base_to_time... no checking for _rtc intrinsic... no checking for zfftm1di in -lcomplib.sgimath... no checking for zfftm1d in -lcomplib.sgimath... no checking for zfft2di in -lcomplib.sgimath... no checking for zfft2d in -lcomplib.sgimath... no checking for zfft3di in -lcomplib.sgimath... no checking for zfft3d in -lcomplib.sgimath... no checking fft.h usability... no checking fft.h presence... no checking for fft.h... no checking for dcft in -lessl... no checking essl.h usability... no checking essl.h presence... no checking for essl.h... no checking for fftw3d_mpi_create_plan in -lfftw_mpi... no checking for fftw3d_create_plan in -lfftw... no checking fftw_mpi.h usability... no checking fftw_mpi.h presence... no checking for fftw_mpi.h... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking for fftw_plan_dft_3d in -lfftw3... no checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no checking for fftw3d_create_plan in -lfftw... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking FFT SGI complib.sgimath... no checking FFT ESSL... no checking FFT FFTW3... no checking FFT FFTW2... no checking FFT FFTW2 MPI... no using FFT ZFFT checking for compress in -lz... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for png_create_write_struct in -lpng... yes using PNG... yes checking for pthread_cancel in -lpthread... yes checking for dlopen in -ldl... no checking for XmuAllStandardColormaps in -lXmu... yes checking for XtAppInitialize in -lXt... yes checking for SmcOpenConnection in -lSM... yes checking for IceAcceptConnection in -lICE... yes checking for XextCreateExtension in -lXext... yes checking for XOpenDisplay in -lX11... yes checking for XOpenDevice in -lXi... yes checking for pthread_cancel in -lpthread... (cached) yes checking for dlopen in -ldl... (cached) no checking for glClear in -lGL... yes checking for gluLookAt in -lGLU... yes checking for glutMainLoop in -lglut... yes checking GL/glut.h usability... yes checking GL/glut.h presence... yes checking for GL/glut.h... yes checking for jpeg_CreateDecompress in -ljpeg... yes checking for TIFFSetErrorHandler in -ltiff... yes checking found GLUT... yes using GLUT... yes ./configure: perl: not found configure: creating ./config.status config.status: creating Makefile config.status: creating framework/Makefile config.status: creating framework/base/Makefile config.status: creating framework/io/Makefile config.status: creating framework/parallel/Makefile config.status: creating framework/topology/Makefile config.status: creating framework/forces/Makefile config.status: creating framework/imd/Makefile config.status: creating framework/integrators/Makefile config.status: creating framework/frontend/Makefile config.status: creating framework/factories/Makefile config.status: creating applications/Makefile config.status: creating applications/protomol-app/Makefile config.status: creating applications/coulomb-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/factories/Makefile config.status: creating applications/iSGProtomol-app/integrators/Makefile config.status: creating applications/coords2coords-app/Makefile config.status: creating applications/xyzviz-app/Makefile config.status: creating protomol_config.h config.status: executing depfiles commands CC : cc CFLAGS : -O2 -pipe -fno-strict-aliasing CXXFLAGS : -O2 -pipe -fno-strict-aliasing -L/usr/local/lib CXX : c++ CXXCPP : c++ -E LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include make clean; make ===> Building for protomol-2.0.3_9 /usr/bin/make all-recursive Making all in framework Making all in base c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o BSpline.o `test -f 'BSpline.cpp' || echo './'`BSpline.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o BSplineType.o `test -f 'BSplineType.cpp' || echo './'`BSplineType.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Configuration.o `test -f 'Configuration.cpp' || echo './'`Configuration.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ConstraintValueType.o `test -f 'ConstraintValueType.cpp' || echo './'`ConstraintValueType.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o FFTComplex.o `test -f 'FFTComplex.cpp' || echo './'`FFTComplex.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Lagrange.o `test -f 'Lagrange.cpp' || echo './'`Lagrange.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Makeable.o `test -f 'Makeable.cpp' || echo './'`Makeable.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Matrix3by3.o `test -f 'Matrix3by3.cpp' || echo './'`Matrix3by3.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGPAR.o `test -f 'iSGPAR.cpp' || echo './'`iSGPAR.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PAR.o `test -f 'PAR.cpp' || echo './'`PAR.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PDB.o `test -f 'PDB.cpp' || echo './'`PDB.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PPM.o `test -f 'PPM.cpp' || echo './'`PPM.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PGM.o `test -f 'PGM.cpp' || echo './'`PGM.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PSF.o `test -f 'PSF.cpp' || echo './'`PSF.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Parameter.o `test -f 'Parameter.cpp' || echo './'`Parameter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ReducedHessAngle.o `test -f 'ReducedHessAngle.cpp' || echo './'`ReducedHessAngle.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o reducedHessBond.o `test -f 'reducedHessBond.cpp' || echo './'`reducedHessBond.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Report.o `test -f 'Report.cpp' || echo './'`Report.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ScalarStructure.o `test -f 'ScalarStructure.cpp' || echo './'`ScalarStructure.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o TimerStatistic.o `test -f 'TimerStatistic.cpp' || echo './'`TimerStatistic.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Value.o `test -f 'Value.cpp' || echo './'`Value.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ValueType.o `test -f 'ValueType.cpp' || echo './'`ValueType.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Vector3DBlock.o `test -f 'Vector3DBlock.cpp' || echo './'`Vector3DBlock.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZ.o `test -f 'XYZ.cpp' || echo './'`XYZ.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o pmconstants.o `test -f 'pmconstants.cpp' || echo './'`pmconstants.cpp cc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -c `test -f 'fft.c' || echo './'`fft.c c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o mathutilities.o `test -f 'mathutilities.cpp' || echo './'`mathutilities.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o stringutilities.o `test -f 'stringutilities.cpp' || echo './'`stringutilities.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o systemutilities.o `test -f 'systemutilities.cpp' || echo './'`systemutilities.cpp rm -f libbase.a ar cru libbase.a BSpline.o BSplineType.o Configuration.o ConstraintValueType.o FFTComplex.o Lagrange.o Makeable.o Matrix3by3.o iSGPAR.o PAR.o PDB.o PPM.o PGM.o PSF.o Parameter.o ReducedHessAngle.o reducedHessBond.o Report.o ScalarStructure.o Timer.o TimerStatistic.o Value.o ValueType.o Vector3DBlock.o XYZ.o pmconstants.o fft.o mathutilities.o stringutilities.o systemutilities.o ranlib libbase.a Making all in io c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ConfigurationReader.o `test -f 'ConfigurationReader.cpp' || echo './'`ConfigurationReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DCDTrajectoryReader.o `test -f 'DCDTrajectoryReader.cpp' || echo './'`DCDTrajectoryReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DCDTrajectoryWriter.o `test -f 'DCDTrajectoryWriter.cpp' || echo './'`DCDTrajectoryWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o File.o `test -f 'File.cpp' || echo './'`File.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PARReader.o `test -f 'PARReader.cpp' || echo './'`PARReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PARWriter.o `test -f 'PARWriter.cpp' || echo './'`PARWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PDBReader.o `test -f 'PDBReader.cpp' || echo './'`PDBReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PDBWriter.o `test -f 'PDBWriter.cpp' || echo './'`PDBWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PNGWriter.o `test -f 'PNGWriter.cpp' || echo './'`PNGWriter.cpp PNGWriter.cpp: In member function 'bool ProtoMol::PNGWriter::write(const ProtoMol::PPM&)': PNGWriter.cpp:118: warning: deprecated conversion from string constant to 'char*' PNGWriter.cpp:119: warning: deprecated conversion from string constant to 'char*' PNGWriter.cpp:125: warning: deprecated conversion from string constant to 'char*' PNGWriter.cpp:126: warning: deprecated conversion from string constant to 'char*' c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PPMReader.o `test -f 'PPMReader.cpp' || echo './'`PPMReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PPMWriter.o `test -f 'PPMWriter.cpp' || echo './'`PPMWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PGMReader.o `test -f 'PGMReader.cpp' || echo './'`PGMReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PGMWriter.o `test -f 'PGMWriter.cpp' || echo './'`PGMWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PSFReader.o `test -f 'PSFReader.cpp' || echo './'`PSFReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PSFWriter.o `test -f 'PSFWriter.cpp' || echo './'`PSFWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Reader.o `test -f 'Reader.cpp' || echo './'`Reader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Writer.o `test -f 'Writer.cpp' || echo './'`Writer.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XFigWriter.o `test -f 'XFigWriter.cpp' || echo './'`XFigWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZBinReader.o `test -f 'XYZBinReader.cpp' || echo './'`XYZBinReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZBinWriter.o `test -f 'XYZBinWriter.cpp' || echo './'`XYZBinWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZReader.o `test -f 'XYZReader.cpp' || echo './'`XYZReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZTrajectoryReader.o `test -f 'XYZTrajectoryReader.cpp' || echo './'`XYZTrajectoryReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZTrajectoryWriter.o `test -f 'XYZTrajectoryWriter.cpp' || echo './'`XYZTrajectoryWriter.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XYZWriter.o `test -f 'XYZWriter.cpp' || echo './'`XYZWriter.cpp rm -f libio.a ar cru libio.a ConfigurationReader.o DCDTrajectoryReader.o DCDTrajectoryWriter.o File.o PARReader.o PARWriter.o PDBReader.o PDBWriter.o PNGWriter.o PPMReader.o PPMWriter.o PGMReader.o PGMWriter.o PSFReader.o PSFWriter.o Reader.o Writer.o XFigWriter.o XYZBinReader.o XYZBinWriter.o XYZReader.o XYZTrajectoryReader.o XYZTrajectoryWriter.o XYZWriter.o ranlib libio.a Making all in parallel c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Parallel.o `test -f 'Parallel.cpp' || echo './'`Parallel.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ParallelType.o `test -f 'ParallelType.cpp' || echo './'`ParallelType.cpp rm -f libparallel.a ar cru libparallel.a Parallel.o ParallelType.o ranlib libparallel.a Making all in topology c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ArrayCellListStructure.o `test -f 'ArrayCellListStructure.cpp' || echo './'`ArrayCellListStructure.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o C1SwitchingFunctionBase.o `test -f 'C1SwitchingFunctionBase.cpp' || echo './'`C1SwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o C1SwitchingFunction.o `test -f 'C1SwitchingFunction.cpp' || echo './'`C1SwitchingFunction.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o C2SwitchingFunctionBase.o `test -f 'C2SwitchingFunctionBase.cpp' || echo './'`C2SwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o C2SwitchingFunction.o `test -f 'C2SwitchingFunction.cpp' || echo './'`C2SwitchingFunction.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o buildCellLists.o `test -f 'buildCellLists.cpp' || echo './'`buildCellLists.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ComplementSwitchingFunctionBase.o `test -f 'ComplementSwitchingFunctionBase.cpp' || echo './'`ComplementSwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CubicCellManager.o `test -f 'CubicCellManager.cpp' || echo './'`CubicCellManager.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CutoffSwitchingFunctionBase.o `test -f 'CutoffSwitchingFunctionBase.cpp' || echo './'`CutoffSwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CutoffSwitchingFunction.o `test -f 'CutoffSwitchingFunction.cpp' || echo './'`CutoffSwitchingFunction.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExclusionTable.o `test -f 'ExclusionTable.cpp' || echo './'`ExclusionTable.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExclusionType.o `test -f 'ExclusionType.cpp' || echo './'`ExclusionType.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o GenericTopology.o `test -f 'GenericTopology.cpp' || echo './'`GenericTopology.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o LennardJonesParameterTable.o `test -f 'LennardJonesParameterTable.cpp' || echo './'`LennardJonesParameterTable.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PeriodicBoundaryConditions.o `test -f 'PeriodicBoundaryConditions.cpp' || echo './'`PeriodicBoundaryConditions.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o RangeSwitchingFunctionBase.o `test -f 'RangeSwitchingFunctionBase.cpp' || echo './'`RangeSwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ShiftSwitchingFunctionBase.o `test -f 'ShiftSwitchingFunctionBase.cpp' || echo './'`ShiftSwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ShiftSwitchingFunction.o `test -f 'ShiftSwitchingFunction.cpp' || echo './'`ShiftSwitchingFunction.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o topologyutilities.o `test -f 'topologyutilities.cpp' || echo './'`topologyutilities.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o UniversalSwitchingFunctionBase.o `test -f 'UniversalSwitchingFunctionBase.cpp' || echo './'`UniversalSwitchingFunctionBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o VacuumBoundaryConditions.o `test -f 'VacuumBoundaryConditions.cpp' || echo './'`VacuumBoundaryConditions.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o AngleInfo.o `test -f 'AngleInfo.cpp' || echo './'`AngleInfo.cpp rm -f libtopology.a ar cru libtopology.a ArrayCellListStructure.o C1SwitchingFunctionBase.o C1SwitchingFunction.o C2SwitchingFunctionBase.o C2SwitchingFunction.o buildCellLists.o ComplementSwitchingFunctionBase.o CubicCellManager.o CutoffSwitchingFunctionBase.o CutoffSwitchingFunction.o ExclusionTable.o ExclusionType.o GenericTopology.o LennardJonesParameterTable.o PeriodicBoundaryConditions.o RangeSwitchingFunctionBase.o ShiftSwitchingFunctionBase.o ShiftSwitchingFunction.o topologyutilities.o UniversalSwitchingFunctionBase.o VacuumBoundaryConditions.o AngleInfo.o ranlib libtopology.a Making all in forces c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o AngleSystemForceBase.o `test -f 'AngleSystemForceBase.cpp' || echo './'`AngleSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o BondSystemForceBase.o `test -f 'BondSystemForceBase.cpp' || echo './'`BondSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CompareForce.o `test -f 'CompareForce.cpp' || echo './'`CompareForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CoulombEwaldRealForce.o `test -f 'CoulombEwaldRealForce.cpp' || echo './'`CoulombEwaldRealForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CoulombEwaldRealTableForce.o `test -f 'CoulombEwaldRealTableForce.cpp' || echo './'`CoulombEwaldRealTableForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CoulombForce.o `test -f 'CoulombForce.cpp' || echo './'`CoulombForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CoulombMultiGridDirectForceBase.o `test -f 'CoulombMultiGridDirectForceBase.cpp' || echo './'`CoulombMultiGridDirectForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o CoulombMultiGridDirectTableForceBase.o `test -f 'CoulombMultiGridDirectTableForceBase.cpp' || echo './'`CoulombMultiGridDirectTableForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DihedralSystemForceBase.o `test -f 'DihedralSystemForceBase.cpp' || echo './'`DihedralSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o HarmDihedralSystemForceBase.o `test -f 'HarmDihedralSystemForceBase.cpp' || echo './'`HarmDihedralSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ElectricFieldSystemForceBase.o `test -f 'ElectricFieldSystemForceBase.cpp' || echo './'`ElectricFieldSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExternalGravitationSystemForce.o `test -f 'ExternalGravitationSystemForce.cpp' || echo './'`ExternalGravitationSystemForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExternalMagneticFieldExtendedForce.o `test -f 'ExternalMagneticFieldExtendedForce.cpp' || echo './'`ExternalMagneticFieldExtendedForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExtendedCompareForce.o `test -f 'ExtendedCompareForce.cpp' || echo './'`ExtendedCompareForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExtendedForce.o `test -f 'ExtendedForce.cpp' || echo './'`ExtendedForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ExtendedTimeForce.o `test -f 'ExtendedTimeForce.cpp' || echo './'`ExtendedTimeForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Force.o `test -f 'Force.cpp' || echo './'`Force.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ForceGroup.o `test -f 'ForceGroup.cpp' || echo './'`ForceGroup.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o FrictionExtendedForce.o `test -f 'FrictionExtendedForce.cpp' || echo './'`FrictionExtendedForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o GravitationForce.o `test -f 'GravitationForce.cpp' || echo './'`GravitationForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Hermite.o `test -f 'Hermite.cpp' || echo './'`Hermite.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ImproperSystemForceBase.o `test -f 'ImproperSystemForceBase.cpp' || echo './'`ImproperSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o LennardJonesForce.o `test -f 'LennardJonesForce.cpp' || echo './'`LennardJonesForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o LennardJonesTableForce.o `test -f 'LennardJonesTableForce.cpp' || echo './'`LennardJonesTableForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MagneticDipoleForce.o `test -f 'MagneticDipoleForce.cpp' || echo './'`MagneticDipoleForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MagneticDipoleMirrorSystemForceBase.o `test -f 'MagneticDipoleMirrorSystemForceBase.cpp' || echo './'`MagneticDipoleMirrorSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MetaForce.o `test -f 'MetaForce.cpp' || echo './'`MetaForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MollyForce.o `test -f 'MollyForce.cpp' || echo './'`MollyForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedCutoffForceBase.o `test -f 'NonbondedCutoffForceBase.cpp' || echo './'`NonbondedCutoffForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedFullEwaldSystemForceBase.o `test -f 'NonbondedFullEwaldSystemForceBase.cpp' || echo './'`NonbondedFullEwaldSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedFullSystemForceBase.o `test -f 'NonbondedFullSystemForceBase.cpp' || echo './'`NonbondedFullSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedMultiGridSystemForceBase.o `test -f 'NonbondedMultiGridSystemForceBase.cpp' || echo './'`NonbondedMultiGridSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedPMEwaldSystemForceBase.o `test -f 'NonbondedPMEwaldSystemForceBase.cpp' || echo './'`NonbondedPMEwaldSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NonbondedSimpleFullSystemForceBase.o `test -f 'NonbondedSimpleFullSystemForceBase.cpp' || echo './'`NonbondedSimpleFullSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PaulTrapExtendedForceBase.o `test -f 'PaulTrapExtendedForceBase.cpp' || echo './'`PaulTrapExtendedForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ReducedHessCoulomb.o `test -f 'ReducedHessCoulomb.cpp' || echo './'`ReducedHessCoulomb.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ReducedHessLennardJones.o `test -f 'ReducedHessLennardJones.cpp' || echo './'`ReducedHessLennardJones.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o SphericalSystemForce.o `test -f 'SphericalSystemForce.cpp' || echo './'`SphericalSystemForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o SystemCompareForce.o `test -f 'SystemCompareForce.cpp' || echo './'`SystemCompareForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o SystemForce.o `test -f 'SystemForce.cpp' || echo './'`SystemForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o SystemTimeForce.o `test -f 'SystemTimeForce.cpp' || echo './'`SystemTimeForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o TimeForce.o `test -f 'TimeForce.cpp' || echo './'`TimeForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o WrapperMetaForce.o `test -f 'WrapperMetaForce.cpp' || echo './'`WrapperMetaForce.cpp rm -f libforces.a ar cru libforces.a AngleSystemForceBase.o BondSystemForceBase.o CompareForce.o CoulombEwaldRealForce.o CoulombEwaldRealTableForce.o CoulombForce.o CoulombMultiGridDirectForceBase.o CoulombMultiGridDirectTableForceBase.o DihedralSystemForceBase.o HarmDihedralSystemForceBase.o ElectricFieldSystemForceBase.o ExternalGravitationSystemForce.o ExternalMagneticFieldExtendedForce.o ExtendedCompareForce.o ExtendedForce.o ExtendedTimeForce.o Force.o ForceGroup.o FrictionExtendedForce.o GravitationForce.o Hermite.o ImproperSystemForceBase.o LennardJonesForce.o LennardJonesTableForce.o MagneticDipoleForce.o MagneticDipoleMirrorSystemForceBase.o MetaForce.o MollyForce.o NonbondedCutoffForceBase.o NonbondedFullEwaldSystemForceBase.o NonbondedFullSystemForceBase.o NonbondedMultiGridSystemForceBase.o NonbondedPMEwaldSystemForceBase.o NonbondedSimpleFullSystemForceBase.o PaulTrapExtendedForceBase.o ReducedHessCoulomb.o ReducedHessLennardJones.o SphericalSystemForce.o SystemCompareForce.o SystemForce.o SystemTimeForce.o TimeForce.o WrapperMetaForce.o ranlib libforces.a Making all in imd c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o IMDElf.o `test -f 'IMDElf.cpp' || echo './'`IMDElf.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o imd.o `test -f 'imd.cpp' || echo './'`imd.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o vmdsock.o `test -f 'vmdsock.cpp' || echo './'`vmdsock.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o HapticSystemForce.o `test -f 'HapticSystemForce.cpp' || echo './'`HapticSystemForce.cpp rm -f libimd.a ar cru libimd.a IMDElf.o imd.o vmdsock.o HapticSystemForce.o ranlib libimd.a Making all in integrators c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierMetaShake.o `test -f 'ModifierMetaShake.cpp' || echo './'`ModifierMetaShake.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierMetaRattle.o `test -f 'ModifierMetaRattle.cpp' || echo './'`ModifierMetaRattle.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierMetaRattleShake.o `test -f 'ModifierMetaRattleShake.cpp' || echo './'`ModifierMetaRattleShake.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NPTVerletIntegrator.o `test -f 'NPTVerletIntegrator.cpp' || echo './'`NPTVerletIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NVTVerletIntegrator.o `test -f 'NVTVerletIntegrator.cpp' || echo './'`NVTVerletIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o BSplineMOLLYIntegrator.o `test -f 'BSplineMOLLYIntegrator.cpp' || echo './'`BSplineMOLLYIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o EquilibriumMOLLYIntegrator.o `test -f 'EquilibriumMOLLYIntegrator.cpp' || echo './'`EquilibriumMOLLYIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DihedralHMCIntegrator.o `test -f 'DihedralHMCIntegrator.cpp' || echo './'`DihedralHMCIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DLMCIntegrator.o `test -f 'DLMCIntegrator.cpp' || echo './'`DLMCIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ShadowHMCIntegrator.o `test -f 'ShadowHMCIntegrator.cpp' || echo './'`ShadowHMCIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o HMCIntegrator.o `test -f 'HMCIntegrator.cpp' || echo './'`HMCIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MCIntegrator.o `test -f 'MCIntegrator.cpp' || echo './'`MCIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ImpulseIntegrator.o `test -f 'ImpulseIntegrator.cpp' || echo './'`ImpulseIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Integrator.o `test -f 'Integrator.cpp' || echo './'`Integrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o IntegratorDefinition.o `test -f 'IntegratorDefinition.cpp' || echo './'`IntegratorDefinition.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o LeapfrogIntegrator.o `test -f 'LeapfrogIntegrator.cpp' || echo './'`LeapfrogIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o DMDLeapfrogIntegrator.o `test -f 'DMDLeapfrogIntegrator.cpp' || echo './'`DMDLeapfrogIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o BBKIntegrator.o `test -f 'BBKIntegrator.cpp' || echo './'`BBKIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierShake.o `test -f 'ModifierShake.cpp' || echo './'`ModifierShake.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierRattle.o `test -f 'ModifierRattle.cpp' || echo './'`ModifierRattle.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierNPTShake.o `test -f 'ModifierNPTShake.cpp' || echo './'`ModifierNPTShake.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierNPTRattle.o `test -f 'ModifierNPTRattle.cpp' || echo './'`ModifierNPTRattle.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierNVTShake.o `test -f 'ModifierNVTShake.cpp' || echo './'`ModifierNVTShake.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierNVTRattle.o `test -f 'ModifierNVTRattle.cpp' || echo './'`ModifierNVTRattle.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PLeapfrogIntegrator.o `test -f 'PLeapfrogIntegrator.cpp' || echo './'`PLeapfrogIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MOLLYIntegrator.o `test -f 'MOLLYIntegrator.cpp' || echo './'`MOLLYIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o UmbrellaIntegrator.o `test -f 'UmbrellaIntegrator.cpp' || echo './'`UmbrellaIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o MTSIntegrator.o `test -f 'MTSIntegrator.cpp' || echo './'`MTSIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o NoseNVTLeapfrogIntegrator.o `test -f 'NoseNVTLeapfrogIntegrator.cpp' || echo './'`NoseNVTLeapfrogIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o PaulTrapIntegrator.o `test -f 'PaulTrapIntegrator.cpp' || echo './'`PaulTrapIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o LangevinImpulseIntegrator.o `test -f 'LangevinImpulseIntegrator.cpp' || echo './'`LangevinImpulseIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o StandardIntegrator.o `test -f 'StandardIntegrator.cpp' || echo './'`StandardIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o STSIntegrator.o `test -f 'STSIntegrator.cpp' || echo './'`STSIntegrator.cpp rm -f libintegrators.a ar cru libintegrators.a ModifierMetaShake.o ModifierMetaRattle.o ModifierMetaRattleShake.o NPTVerletIntegrator.o NVTVerletIntegrator.o BSplineMOLLYIntegrator.o EquilibriumMOLLYIntegrator.o DihedralHMCIntegrator.o DLMCIntegrator.o ShadowHMCIntegrator.o HMCIntegrator.o MCIntegrator.o ImpulseIntegrator.o Integrator.o IntegratorDefinition.o LeapfrogIntegrator.o DMDLeapfrogIntegrator.o BBKIntegrator.o ModifierShake.o ModifierRattle.o ModifierNPTShake.o ModifierNPTRattle.o ModifierNVTShake.o ModifierNVTRattle.o PLeapfrogIntegrator.o MOLLYIntegrator.o UmbrellaIntegrator.o MTSIntegrator.o NoseNVTLeapfrogIntegrator.o PaulTrapIntegrator.o LangevinImpulseIntegrator.o StandardIntegrator.o STSIntegrator.o NPTVerletIntegrator.o NVTVerletIntegrator.o ranlib libintegrators.a Making all in frontend c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o HelpTextFactory.o `test -f 'HelpTextFactory.cpp' || echo './'`HelpTextFactory.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ForceFactoryDetails.o `test -f 'ForceFactoryDetails.cpp' || echo './'`ForceFactoryDetails.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o InputPosVel.o `test -f 'InputPosVel.cpp' || echo './'`InputPosVel.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o InputPosVelType.o `test -f 'InputPosVelType.cpp' || echo './'`InputPosVelType.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o IntegratorFactoryDetails.o `test -f 'IntegratorFactoryDetails.cpp' || echo './'`IntegratorFactoryDetails.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o Output.o `test -f 'Output.cpp' || echo './'`Output.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputCache.o `test -f 'OutputCache.cpp' || echo './'`OutputCache.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputCollection.o `test -f 'OutputCollection.cpp' || echo './'`OutputCollection.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputDCDTrajectory.o `test -f 'OutputDCDTrajectory.cpp' || echo './'`OutputDCDTrajectory.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputDiffusion.o `test -f 'OutputDiffusion.cpp' || echo './'`OutputDiffusion.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputDihedrals.o `test -f 'OutputDihedrals.cpp' || echo './'`OutputDihedrals.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputEnergies.o `test -f 'OutputEnergies.cpp' || echo './'`OutputEnergies.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFactoryDetails.o `test -f 'OutputFactoryDetails.cpp' || echo './'`OutputFactoryDetails.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFile.o `test -f 'OutputFile.cpp' || echo './'`OutputFile.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalXYZBinPos.o `test -f 'OutputFinalXYZBinPos.cpp' || echo './'`OutputFinalXYZBinPos.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalXYZBinVel.o `test -f 'OutputFinalXYZBinVel.cpp' || echo './'`OutputFinalXYZBinVel.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalXYZPos.o `test -f 'OutputFinalXYZPos.cpp' || echo './'`OutputFinalXYZPos.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalPDBPos.o `test -f 'OutputFinalPDBPos.cpp' || echo './'`OutputFinalPDBPos.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalXYZVel.o `test -f 'OutputFinalXYZVel.cpp' || echo './'`OutputFinalXYZVel.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputMomentum.o `test -f 'OutputMomentum.cpp' || echo './'`OutputMomentum.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputPaulTrap.o `test -f 'OutputPaulTrap.cpp' || echo './'`OutputPaulTrap.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputPDBFramePos.o `test -f 'OutputPDBFramePos.cpp' || echo './'`OutputPDBFramePos.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputScreen.o `test -f 'OutputScreen.cpp' || echo './'`OutputScreen.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputTemperatures.o `test -f 'OutputTemperatures.cpp' || echo './'`OutputTemperatures.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputXYZTrajectoryForce.o `test -f 'OutputXYZTrajectoryForce.cpp' || echo './'`OutputXYZTrajectoryForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputXYZTrajectoryPos.o `test -f 'OutputXYZTrajectoryPos.cpp' || echo './'`OutputXYZTrajectoryPos.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputXYZTrajectoryVel.o `test -f 'OutputXYZTrajectoryVel.cpp' || echo './'`OutputXYZTrajectoryVel.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o TopologyFactoryDetails.o `test -f 'TopologyFactoryDetails.cpp' || echo './'`TopologyFactoryDetails.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o buildTopology.o `test -f 'buildTopology.cpp' || echo './'`buildTopology.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o inputValueDefinitions.o `test -f 'inputValueDefinitions.cpp' || echo './'`inputValueDefinitions.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o parseCommandLine.o `test -f 'parseCommandLine.cpp' || echo './'`parseCommandLine.cpp rm -f libfrontend.a ar cru libfrontend.a HelpTextFactory.o ForceFactoryDetails.o InputPosVel.o InputPosVelType.o IntegratorFactoryDetails.o Output.o OutputCache.o OutputCollection.o OutputDCDTrajectory.o OutputDiffusion.o OutputDihedrals.o OutputEnergies.o OutputFactoryDetails.o OutputFile.o OutputFinalXYZBinPos.o OutputFinalXYZBinVel.o OutputFinalXYZPos.o OutputFinalPDBPos.o OutputFinalXYZVel.o OutputMomentum.o OutputPaulTrap.o OutputPDBFramePos.o OutputScreen.o OutputTemperatures.o OutputXYZTrajectoryForce.o OutputXYZTrajectoryPos.o OutputXYZTrajectoryVel.o TopologyFactoryDetails.o buildTopology.o inputValueDefinitions.o parseCommandLine.o ranlib libfrontend.a Making all in factories c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsBonded.o `test -f 'registerForceExemplarsBonded.cpp' || echo './'`registerForceExemplarsBonded.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsCutoff.o `test -f 'registerForceExemplarsCutoff.cpp' || echo './'`registerForceExemplarsCutoff.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsFastElectrostatic.o `test -f 'registerForceExemplarsFastElectrostatic.cpp' || echo './'`registerForceExemplarsFastElectrostatic.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsFull.o `test -f 'registerForceExemplarsFull.cpp' || echo './'`registerForceExemplarsFull.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsOther.o `test -f 'registerForceExemplarsOther.cpp' || echo './'`registerForceExemplarsOther.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplarsSimpleFull.o `test -f 'registerForceExemplarsSimpleFull.cpp' || echo './'`registerForceExemplarsSimpleFull.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp rm -f libfactories.a ar cru libfactories.a registerForceExemplars.o registerForceExemplarsBonded.o registerForceExemplarsCutoff.o registerForceExemplarsFastElectrostatic.o registerForceExemplarsFull.o registerForceExemplarsOther.o registerForceExemplarsSimpleFull.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o ranlib libfactories.a Making all in applications Making all in protomol-app c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o protomol.o `test -f 'protomol.cpp' || echo './'`protomol.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o protomol protomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../framework/factories -lfactories -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng Making all in coulomb-app cd ../.. && /bin/sh /obj/buildshare/ports/355755/biology/protomol/work/protomol/missing --run automake-1.6 --foreign applications/coulomb-app/Makefile /obj/buildshare/ports/355755/biology/protomol/work/protomol/missing: automake-1.6: not found WARNING: `automake-1.6' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.in'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. cd ../.. && /bin/sh ./config.status applications/coulomb-app/Makefile config.status: creating applications/coulomb-app/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o coulomb.o `test -f 'coulomb.cpp' || echo './'`coulomb.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o coulomb coulomb.o registerForceExemplars.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/integrators -L../../framework/frontend -lfrontend -lintegrators -lforces -ltopology -lparallel -lio -lbase Making all in dcd2dcd-app cd ../.. && /bin/sh ./config.status applications/dcd2dcd-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o dcd2dcd.o `test -f 'dcd2dcd.cpp' || echo './'`dcd2dcd.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o dcd2dcd dcd2dcd.o -L../../framework/base -L../../framework/io -lio -lbase Making all in coords2coords-app cd ../.. && /bin/sh ./config.status applications/coords2coords-app/Makefile config.status: creating applications/coords2coords-app/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o coords2coords.o `test -f 'coords2coords.cpp' || echo './'`coords2coords.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o coords2coords coords2coords.o -L../../framework/base -L../../framework/io -lio -lbase Making all in xyzviz-app cd ../.. && /bin/sh ./config.status applications/xyzviz-app/Makefile config.status: creating applications/xyzviz-app/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o openglutilities.o `test -f 'openglutilities.cpp' || echo './'`openglutilities.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o xyzviz.o `test -f 'xyzviz.cpp' || echo './'`xyzviz.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o xyzviz openglutilities.o xyzviz.o -L../../framework/base -L../../framework/io -lz -L/usr/local/lib -lglut -lGLU -lGL -lXmu -lXt -lSM -lICE -lXext -lX11 -lXi -lXext -lX11 -lpthread -ljpeg -ltiff -lio -lbase Making all in iSGProtomol-app Making all in base cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XSC.o `test -f 'XSC.cpp' || echo './'`XSC.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o TRANS.o `test -f 'TRANS.cpp' || echo './'`TRANS.cpp rm -f libISGbase.a ar cru libISGbase.a XSC.o TRANS.o ranlib libISGbase.a Making all in io cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGPARReader.o `test -f 'iSGPARReader.cpp' || echo './'`iSGPARReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o TRANSReader.o `test -f 'TRANSReader.cpp' || echo './'`TRANSReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XSCReader.o `test -f 'XSCReader.cpp' || echo './'`XSCReader.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o XSCWriter.o `test -f 'XSCWriter.cpp' || echo './'`XSCWriter.cpp rm -f libISGio.a ar cru libISGio.a iSGPARReader.o TRANSReader.o XSCReader.o XSCWriter.o ranlib libISGio.a Making all in forces cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGAngleSystemForceBase.o `test -f 'iSGAngleSystemForceBase.cpp' || echo './'`iSGAngleSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGBondSystemForceBase.o `test -f 'iSGBondSystemForceBase.cpp' || echo './'`iSGBondSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGDihedralSystemForceBase.o `test -f 'iSGDihedralSystemForceBase.cpp' || echo './'`iSGDihedralSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGImproperSystemForceBase.o `test -f 'iSGImproperSystemForceBase.cpp' || echo './'`iSGImproperSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGLennardJonesForce.o `test -f 'iSGLennardJonesForce.cpp' || echo './'`iSGLennardJonesForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGCoulombForce.o `test -f 'iSGCoulombForce.cpp' || echo './'`iSGCoulombForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGNonbondedFullEwaldSystemForceBase.o `test -f 'iSGNonbondedFullEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedFullEwaldSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGNonbondedPMEwaldSystemForceBase.o `test -f 'iSGNonbondedPMEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedPMEwaldSystemForceBase.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGIdealGasCoulombForce.o `test -f 'iSGIdealGasCoulombForce.cpp' || echo './'`iSGIdealGasCoulombForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGIdealGasLennardJonesForce.o `test -f 'iSGIdealGasLennardJonesForce.cpp' || echo './'`iSGIdealGasLennardJonesForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGLennardJonesTableForce.o `test -f 'iSGLennardJonesTableForce.cpp' || echo './'`iSGLennardJonesTableForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGCoulombEwaldRealForce.o `test -f 'iSGCoulombEwaldRealForce.cpp' || echo './'`iSGCoulombEwaldRealForce.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGCoulombEwaldRealTableForce.o `test -f 'iSGCoulombEwaldRealTableForce.cpp' || echo './'`iSGCoulombEwaldRealTableForce.cpp rm -f libISGforces.a ar cru libISGforces.a iSGAngleSystemForceBase.o iSGBondSystemForceBase.o iSGDihedralSystemForceBase.o iSGImproperSystemForceBase.o iSGLennardJonesForce.o iSGCoulombForce.o iSGNonbondedFullEwaldSystemForceBase.o iSGNonbondedPMEwaldSystemForceBase.o iSGIdealGasCoulombForce.o iSGIdealGasLennardJonesForce.o iSGLennardJonesTableForce.o iSGCoulombEwaldRealForce.o iSGCoulombEwaldRealTableForce.o ranlib libISGforces.a Making all in frontend cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalXSC.o `test -f 'OutputFinalXSC.cpp' || echo './'`OutputFinalXSC.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputISGProperties.o `test -f 'OutputISGProperties.cpp' || echo './'`OutputISGProperties.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o OutputFinalPSF.o `test -f 'OutputFinalPSF.cpp' || echo './'`OutputFinalPSF.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o buildISGTopology.o `test -f 'buildISGTopology.cpp' || echo './'`buildISGTopology.cpp rm -f libISGfrontend.a ar cru libISGfrontend.a OutputFinalXSC.o OutputISGProperties.o OutputFinalPSF.o buildISGTopology.o ranlib libISGfrontend.a Making all in factories cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/factories/Makefile config.status: creating applications/iSGProtomol-app/factories/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterOutputExemplars.o `test -f 'iSGregisterOutputExemplars.cpp' || echo './'`iSGregisterOutputExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterIntegratorExemplars.o `test -f 'iSGregisterIntegratorExemplars.cpp' || echo './'`iSGregisterIntegratorExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplars.o `test -f 'iSGregisterForceExemplars.cpp' || echo './'`iSGregisterForceExemplars.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsBonded.o `test -f 'iSGregisterForceExemplarsBonded.cpp' || echo './'`iSGregisterForceExemplarsBonded.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsCutoff.o `test -f 'iSGregisterForceExemplarsCutoff.cpp' || echo './'`iSGregisterForceExemplarsCutoff.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsFull.o `test -f 'iSGregisterForceExemplarsFull.cpp' || echo './'`iSGregisterForceExemplarsFull.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsSimpleFull.o `test -f 'iSGregisterForceExemplarsSimpleFull.cpp' || echo './'`iSGregisterForceExemplarsSimpleFull.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsFastElectrostatic.o `test -f 'iSGregisterForceExemplarsFastElectrostatic.cpp' || echo './'`iSGregisterForceExemplarsFastElectrostatic.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGregisterForceExemplarsIdealGas.o `test -f 'iSGregisterForceExemplarsIdealGas.cpp' || echo './'`iSGregisterForceExemplarsIdealGas.cpp rm -f libISGfactories.a ar cru libISGfactories.a iSGregisterOutputExemplars.o iSGregisterIntegratorExemplars.o iSGregisterForceExemplars.o iSGregisterForceExemplarsBonded.o iSGregisterForceExemplarsCutoff.o iSGregisterForceExemplarsFull.o iSGregisterForceExemplarsSimpleFull.o iSGregisterForceExemplarsFastElectrostatic.o iSGregisterForceExemplarsIdealGas.o ranlib libISGfactories.a Making all in integrators cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/integrators/Makefile config.status: creating applications/iSGProtomol-app/integrators/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGIntegrator.o `test -f 'iSGIntegrator.cpp' || echo './'`iSGIntegrator.cpp c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o ModifierISG.o `test -f 'ModifierISG.cpp' || echo './'`ModifierISG.cpp rm -f libISGintegrators.a ar cru libISGintegrators.a iSGIntegrator.o ModifierISG.o ranlib libISGintegrators.a cd ../.. && /bin/sh ./config.status applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I../../applications/iSGProtomol-app/base -I../../applications/iSGProtomol-app/io -I../../applications/iSGProtomol-app/forces -I../../applications/iSGProtomol-app/frontend -I../../applications/iSGProtomol-app/factories -I../../applications/iSGProtomol-app/integrators -I/usr/local/include -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -c -o iSGProtomol.o `test -f 'iSGProtomol.cpp' || echo './'`iSGProtomol.cpp c++ -O2 -pipe -fno-strict-aliasing -L/usr/local/lib -o iSGProtomol iSGProtomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../applications/iSGProtomol-app/base -L../../applications/iSGProtomol-app/io -L../../applications/iSGProtomol-app/forces -L../../applications/iSGProtomol-app/frontend -L../../applications/iSGProtomol-app/factories -L../../applications/iSGProtomol-app/integrators -lISGintegrators -lISGfactories -lISGfrontend -lISGforces -lISGio -lISGbase ../../framework/factories/registerTopologyExemplars.o -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng cd .. && /bin/sh ./config.status applications/Makefile config.status: creating applications/Makefile cd . && /bin/sh ./config.status Makefile config.status: creating Makefile ===> Installing for protomol-2.0.3_9 ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_9 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> Generating temporary packing list ===> Checking if biology/protomol already installed Making install in framework Making install in base cd ../.. && /bin/sh ./config.status framework/base/Makefile config.status: creating framework/base/Makefile Making install in io cd ../.. && /bin/sh ./config.status framework/io/Makefile config.status: creating framework/io/Makefile Making install in parallel cd ../.. && /bin/sh ./config.status framework/parallel/Makefile config.status: creating framework/parallel/Makefile Making install in topology cd ../.. && /bin/sh ./config.status framework/topology/Makefile config.status: creating framework/topology/Makefile Making install in forces cd ../.. && /bin/sh ./config.status framework/forces/Makefile config.status: creating framework/forces/Makefile Making install in imd cd ../.. && /bin/sh ./config.status framework/imd/Makefile config.status: creating framework/imd/Makefile Making install in integrators cd ../.. && /bin/sh ./config.status framework/integrators/Makefile config.status: creating framework/integrators/Makefile Making install in frontend cd ../.. && /bin/sh ./config.status framework/frontend/Makefile config.status: creating framework/frontend/Makefile Making install in factories cd ../.. && /bin/sh ./config.status framework/factories/Makefile config.status: creating framework/factories/Makefile cd .. && /bin/sh ./config.status framework/Makefile config.status: creating framework/Makefile Making install in applications Making install in protomol-app cd ../.. && /bin/sh ./config.status applications/protomol-app/Makefile config.status: creating applications/protomol-app/Makefile /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 protomol /usr/local/bin/protomol Making install in coulomb-app /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 coulomb /usr/local/bin/coulomb Making install in dcd2dcd-app /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 dcd2dcd /usr/local/bin/dcd2dcd Making install in coords2coords-app /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 coords2coords /usr/local/bin/coords2coords Making install in xyzviz-app /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 xyzviz /usr/local/bin/xyzviz Making install in iSGProtomol-app Making install in base Making install in io Making install in forces Making install in frontend Making install in factories Making install in integrators /bin/sh ../../mkinstalldirs /usr/local/bin install -s -o root -g wheel -m 555 iSGProtomol /usr/local/bin/iSGProtomol cd /obj/buildshare/ports/355755/biology/protomol/work/protomol/examples && /usr/bin/find . | /usr/bin/egrep -v '\.cvsignore' | /usr/bin/cpio -pdmu -R root:wheel /usr/local/share/examples/protomol 10283 blocks ===> Registering installation for protomol-2.0.3_9 Installing protomol-2.0.3_9... done ===> SECURITY REPORT: This port has installed the following files which may act as network servers and may therefore pose a remote security risk to the system. /usr/local/bin/protomol If there are vulnerabilities in these programs there may be a security risk to the system. FreeBSD makes no guarantee about the security of ports included in the Ports Collection. Please type 'make deinstall' to deinstall the port if this is a concern. For more information, and contact details about the security status of this software, see the following webpage: http://protomol.sourceforge.net/ Make package ===> Building package for protomol-2.0.3_9 Creating package for protomol-2.0.3_9 slot1: removed