Log file for computer gs61a-petrov ---------------------------------- 1) 2017.11.01 Installed atlas 3.10.3 http://www.netlib.org/lapack/lapack-3.7.1.tgz mkdir build_64 cd build_64 Rebooted with these options: ro i915.modeset=0 intel_pstate=disable intel_idle.max_cstate=0 processor.max_cstate=1 idle=poll /etc/rc.local /usr/lib/linux-tools/4.4.0-97-generic/cpupower frequency-set -g performance ../configure \ --prefix=/opt64 \ --shared \ --with-netlib-lapack-tarfile=/incoming/lapack-3.7.1.tgz \ -Si latune 1 \ -D c -DL2SIZE=2097152 \ -m 1500 \ -t 0 \ -b 64 \ -Fa alg -fPIC \ -F xc "-DNoChange -march=nehalem" \ -F ic "-DNoChange -march=nehalem" \ -F sk "-DNoChange -march=nehalem" \ -F dk "-DNoChange -march=nehalem" \ -F sm "-DNoChange -march=nehalem" \ -F dm "-DNoChange -march=nehalem" \ -F al "-DNoChange -march=nehalem" \ -F ac "-DNoChange -march=nehalem" \ -C xc /usr/bin/gcc \ -C ic /usr/bin/gcc \ -C sk /usr/bin/gcc \ -C dk /usr/bin/gcc \ -C sm /usr/bin/gcc \ -C dm /usr/bin/gcc \ -C al /usr/bin/gcc \ -C ac /usr/bin/gcc \ -C if /usr/bin/gfortran \ -F if "-ffixed-form -fno-underscoring -fPIC -O3" \ -v 2 \ >& configure.log sed -i 's@soname $(LIBINSTdir)/@soname @g' lib/Makefile date > make_log.txt; make >>& make_log.txt; date >> make_log.txt date > check_log.txt; make check >>& check_log.txt; date >> check_log.txt date > time_log.txt; make time >>& time_log.txt; date >> time_log.txt cd lib make shared >>& ../make_log.txt cd ../ make install >& install.log rm /tmp/file* 2) 2017.11.08 Installed fftw-3.3.6-pl2 http://www.fftw.org/fftw-3.3.6-pl2.tar.gz # make distclean ./configure --prefix=/opt64 \ --enable-sse2 \ --enable-openmp \ --enable-shared \ CC="/usr/bin/gcc" \ CFLAGS="-m64 -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -fno-stack-protector -march=native" \ F77="/usr/bin/gfortran" \ FFLAGS="-m64 -fno-underscoring -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -fno-stack-protector -march=native" # for double precision make -j 4 make install make distclean ./configure --prefix=/opt64 \ --enable-single \ --enable-sse2 \ --enable-sse \ --enable-openmp \ --enable-shared \ CC="/usr/bin/gcc" \ CFLAGS="-m64 -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -fno-stack-protector -march=native" \ F77="/usr/bin/gfortran" \ FFLAGS="-m64 -fno-underscoring -O3 -fomit-frame-pointer -malign-double -fstrict-aliasing -ffast-math -fno-stack-protector -march=native" # for single precision make -j 4 make install # /dist/fftw-3.3.6-pl2/tests/bench -owisdom -onthreads=1 cif1024x1024 3) 2017.11.08 Installed zlib-1.2.11 cd /incoming wget https://zlib.net/zlib-1.2.11.tar.gz cd /dist tar -zxvf /incoming/zlib-1.2.11.tar.gz cd zlib-1.2.11 ./configure --prefix=/opt64 make -j 4 make install 4) 2017.11.08 Installed readline-7.0 cd /incoming https://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz cd /dist tar -zxvf /incoming/readline-7.0.tar.gz cd readline-7.0 ./configure --prefix=/opt64 make -j 4 make install 5) 2017.11.08 Installed petools-20171027 http://astrogeo.org/petools/petools-20171027.tar.bz2 ./configure --prefix=/opt64 \ --with-blas="-L/opt64/lib -lsatlas" \ --bits=64 FC=/usr/bin/gfortran \ --with-zlib=/opt64 \ --with-readline=/opt64 make make install 6) 2017.11.08 Installed ners-20170512 http://earthrotation.net/ners/ners-20170512.tar.bz2 ./configure --prefix=/opt64 \ --with-petools=/opt64 make make install 7) 2017.11.08 Installed cfitsio-3.37 ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3370.tar.gz http://astrogeo.org/pet_inc/cfitsio-3.26.patch mv cfitsio cfitsio-3.37 cd cfitsio-3.37 patch -Np0 -i /incoming/cfitsio-3.26.patch ./configure --prefix=/opt64 \ --enable-reentrant \ --enable-ssse3 \ CC=/usr/bin/gcc \ FC=/usr/bin/gfortran \ CFORTRANFLAGS="-fno-underscoring" \ CFLAGS="-DNoUnderscoreAppend -DGNU -m64" make -j 4 make install gcc -shared -Wl,--whole-archive -Wl,-soname,libcfitsio.so.1 -o /opt64/lib/libcfitsio.so.1.0 /opt64/lib/libcfitsio.a -Wl,-no-whole-archive rm /opt64/lib/libcfitsio.so ln -sf /opt64/lib/libcfitsio.so.1.0 /opt64/lib/libcfitsio.so.1 ln -sf /opt64/lib/libcfitsio.so.1.0 /opt64/lib/libcfitsio.so 8) 2017.11.08 Installed spd_client_20171027 http://astrogeo.org/spd/spd_client-20160727_example.tar.bz2 http://astrogeo.org/spd/spd_client-20160727.tar.bz2 ./configure --prefix=/opt64 \ --with-petools=/opt64 make make install 9) 2017.11.08 Installed vtd_20171017 http://astrogeo.org/vtd/vtd-20171017.tar.bz2 ./configure --prefix=/opt64 \ --data=/home/lpetrov/vtd_data \ --with-petools=/opt64 \ --with-spd_client=/opt64 \ --with-ners=/opt64 \ --with-cfitsio=/opt64 10) 2017.11.08 Installed fourpack_20160428 ./configure --prefix=/opt64 \ --with-petools=/opt64 \ --with-fftw=/opt64 make make install 11) 2017.11.08 Installed gvh_20171027 ./configure --prefix=/opt64 \ --with-petools=/opt64 \ --with-vtd=/opt64 make make install 12) 2017.11.08 Installed bizon-3.0 https://ftp.gnu.org/gnu/bison/bison-3.0.tar.xz ./configure --prefix=/opt64 make -j 5 make install 13) 2017.11.08 Installed autoconf-2.69 https://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.xz ./configure --prefix=/opt64 make -j 5 make install 14) 2017.11.08 Installed unrar-5.2.3 https://www.rarlab.com/rar/rarlinux-x64-5.5.0.tar.gz mv rar rar-5.5.0 cp rar unrar /opt64/bin/ 15) 2017.11.08 Installed ghostview-1.5.0 xmkmf chmod -R u+w ./ Commented out lines in misc.c and SelFile.c extern char *sys_errlist[]; make *make install 16) 2017.11.08 Installed xv-3.10a Edited config.h Commented out line 119 in xv.h Edited Make file: Added at line 17 -I/usr/X11R6/include Ucommented line 105 Added at line 191 -L/usr/X11R6/lib make mkdir /opt64/man mkdir /opt64/man/mat1 make install 17) 2017.11.08 Installed bzip2-1.0.6 http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz sed -i "s@PREFIX=/usr/local@PREFIX=/opt64@g" Makefile make make install 18) 2017.11.08 Installed pbzip2-1.1.13 https://launchpad.net/pbzip2/1.1/1.1.13/+download/pbzip2-1.1.13.tar.gz sed -i "s@CXXFLAGS = -O2@CXXFLAGS = -O2 -I /opt64/include@g" Makefile sed -i "s@PREFIX = /usr@PREFIX = /opt64@g" Makefile sed -i "s@LDFLAGS =@LDFLAGS = -L /opt64/lib@g" Makefile make clean make make install 19) 2017.11.08 Install lbzip2-2.5 http://archive.lbzip2.org/lbzip2-2.5.tar.gz ./configure --prefix=/opt64 make 4 make install 17) 2017.11.08 Installed xz-5.2.3.tar.gz https://github.com/xz-mirror/xz/releases/download/v5.2.3/xz-5.2.3.tar.xz ./configure --prefix=/opt64 LDFLAGS="-L/opt64/lib -lz" make -j 4 make install 18) 2017.10.26 Installed pxz http://jnovy.fedorapeople.org/pxz/pxz-4.999.9beta.20091201git.tar.xz sed -i "s@CFLAGS+=-O3 -march=corei7-avx -fopenmp@CFLAGS+=-O3 -fopenmp -I /opt64/include@g" Makefile make cp pxz /opt64/bin/ 19) 2017.10.26 Installed hexedit-0.9.7 http://www.rogoyski.com/adam/programs/hexedit/hexedit-0.9.7.tar.gz ./configure --prefix=/opt64 make -j 4 make install 20) 2017.11.08 Installed uudeview-0.5.20 http://www.fpx.de/fp/Software/UUDeview/download/uudeview-0.5.20.tar.gz ./configure --prefix=/opt64 make make install 21) 2017.11.08 Installed parallel of 2017.10.22 ftp://ftp.gnu.org/gnu/parallel/parallel-20171022.tar.bz2 ./configure --prefix=/opt64 make make install 22) 2014.12.26 Installed fv-5.3 http://heasarc.gsfc.nasa.gov/FTP/software/lheasoft/fv/fv53_src.tar.gz cd BUILD_DIR ./configure --prefix=/opt64 \ --with-copt="-fPIC" \ --with-cxxopt="-fPIC" make -j 1 make install cp /opt64/x86_64-unknown-linux-gnu-libc2.23-0/bin/fv /opt64/bin/fv sed -i 's@(if [ "x$FV" = x ] ; then@FTOOLS=/opt64/x86_64-unknown-linux-gnu-libc2.20\n(if [ "x$FV" = x ] ; then@' /opt64/bin/fv Edited file /opt64/x86_64-unknown-linux-gnu-libc2.20/lib/fv/class/fvApp.tcl for updating font size 23) 2017.11.09 Installed fastjar-0.94.tar.gz http://www.mirrorservice.org/sites/distfiles.macports.org/fastjar/fastjar-0.94.tar.gz ./configure --prefix=/opt64 LDFLAGS="-L/opt64/lib -lz" sed -i 's@INCLUDES = -I. -I$(top_srcdir) $(ZINCS)@INCLUDES = -I. -I$(top_srcdir) $(ZINCS) -I /opt64/include@g' Makefile sed -i 's@LIBS = -lz@LIBS = -L/opt64/lib -lz@g' Makefile make make install 24) 2017.11.09 Installwed expat-2.2.5 https://sourceforge.net/projects/expat/files/expat/2.1.0/ ./configure --prefix=/opt64 make -j 4 make install 25) 2017.11.09 Installed apr-1.6.2 https://archive.apache.org/dist/apr/apr-1.6.2.tar.bz2 ./configure --prefix=/opt64 \ --disable-static make -j 4 make install 26) 2017.11.09 Installed apr-util-1.6.0 https://archive.apache.org/dist/apr/apr-util-1.6.0.tar.bz2 ./configure --prefix=/opt64 \ --with-apr=/opt64 \ --with-expat=/opt64 \ --with-gdbm=/usr make -j 4 make install 27) 2017.11.09 Instaled sqlite-3.21 https://sqlite.org/2017/sqlite-autoconf-3210000.tar.gz ./configure --prefix=/opt64 --disable-static \ --enable-fts5 CFLAGS="-g -O2 \ -DSQLITE_ENABLE_FTS4=1 \ -DSQLITE_ENABLE_COLUMN_METADATA=1 \ -DSQLITE_ENABLE_UNLOCK_NOTIFY=1 \ -DSQLITE_SECURE_DELETE=1 \ -DSQLITE_ENABLE_DBSTAT_VTAB=1" make -j 4 make install 28) 2017.11.09 Installed subversion-1.9.7 https://archive.apache.org/dist/subversion/subversion-1.9.7.tar.bz2 ./configure --prefix=/opt64 \ --with-apr=/opt64 \ --with-apr-util=/opt64 \ --with-sqlite=/opt64 make -j 4 make install 29) 2017.11.09 Installed curl-7.56.1 https://curl.haxx.se/download/curl-7.56.1.tar.bz2 ./configure --prefix=/opt64 \ --disable-static \ --enable-threaded-resolver make -j 4 make install 30) 2017.11.09 Installed hdf5-1.10.1 ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.10.1.tar.bz2 setenv F77 /usr/bin/gfortran setenv FFLAGS "-fbounds-check -fno-underscoring -fPIC" ./configure --prefix=/opt64 \ --enable-fortran \ --enable-cxx \ FC=/usr/bin/gfortran \ FCFLAGS="-fbounds-check -fno-underscoring -fPIC" make -j 4 >& make.log make install >& install.log unsetenv F77 unsetenv FFLAGS 31) 2017.11.09 Installed openjpeg-2.1.0 http://downloads.sourceforge.net/openjpeg.mirror/openjpeg-2.1.0.tar.gz mkdir build; cd build cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt64 .. make -j 4 * make install 33) 2017.11.09 Installed nasm-2.13.01 http://www.nasm.us/pub/nasm/releasebuilds/2.13.01/nasm-2.13.01.tar.bz2 ./configure --prefix=/opt64 make -j 4 make install 33) 2017.11.09 Installed libjpeg-turbo-1.5.1 http://downloads.sourceforge.net/libjpeg-turbo/libjpeg-turbo-1.5.2.tar.gz ./configure --prefix=/opt64 \ --mandir=/opt64/share/man \ --with-jpeg8 \ --disable-static make -j 4 34) 2017.11.14 Installed gqview-2.1.4 http://gqview.sourceforge.net ./configure --prefix=/opt64 # sed -i "s@GTK_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype@GTK_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm@g" src/Makefile make -j 14 make install 35) 2017.10.26 Intall hdf-4.2.13 ftp://ftp.hdfgroup.org/HDF/HDF_Current/src/hdf-4.2.13.tar.bz2 setenv F77 /usr/bin/gfortran setenv FFLAGS "-fbounds-check -fno-underscoring -fPIC" setenv CFLAGS "-m64 -DHAVE_NETCDF -fPIC" ./configure \ --prefix=/opt64 \ --includedir=/opt64/include/hdf \ --disable-netcdf \ --enable-fortran \ --with-jpeg=/opt64 \ F77=/usr/bin/gfortran \ FFLAGS="-fbounds-check -fno-underscoring -fPIC" \ CFLAGS="-m64 -fPIC" \ >& configure.log find ./ -name "Makefile" -exec sed -i -e "s@ncgen dumper@dumper@g" {} \; find ./ -name "Makefile" -exec sed -i -e "s@-ljpeg -lz @-L/opt64/lib -ljpeg -lz -lm@g" {} \; make -j 4 >& make.log make install >& install.log gcc -shared -shared -Wl,--whole-archive -o /opt64/lib/libdf.so /opt64/lib/libdf.a -Wl,-no-whole-archive gcc -shared -shared -Wl,--whole-archive -o /opt64/lib/libmfhdf.so /opt64/lib/libmfhdf.a -Wl,-no-whole-archive unsetenv F77 unsetenv FFLAGS unsetenv CFLAGS unsetenv CXXFLAGS 36) 2017.11.14 Installed netcdf-4.5.0 ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.4.tar.gz http://astrogeo.org/pet_inc/netcdf_fortran_4.4.1.patch http://astrogeo.org/pet_inc/netcdf-450_jpeg.patch tar -zxvf /incoming/netcdf-4.5.0.tar.gz cd netcdf-4.5.0 patch -Np0 -i /incoming/netcdf-450_jpeg.patch ./configure --prefix=/opt64 \ --enable-shared \ --enable-netcdf-4 \ --disable-dap \ --enable-pnetcdf \ --enable-hdf4 \ --disable-dap \ --disable-pnetcdf \ CPPFLAGS="-I/opt64/include -I/opt64/include/hdf" \ CFLAGS="-I/opt64/include -I/opt64/include/hdf" \ LDFLAGS="-L/opt64/lib -lhdf5 -lmfhdf -ldf -ljpeg -lgfortran" \ F77="/usr/bin/gfortran" \ FFLAGS="-fbounds-check -fno-underscoring -DNoUnderscoreAppend -fPIC" make -j 1 >& comp.log make install >& install.log make check tar -zxvf /incoming/netcdf-fortran-4.4.4.tar.gz cd netcdf-fortran-4.4.4 patch -Np0 -i /incoming/netcdf_fortran_4.4.1.patch ./configure --prefix=/opt64 \ --enable-shared \ FC=/usr/bin/gfortran \ F90=/usr/bin/fortran \ CPPFLAGS="-DNDEBUG -DpgiFortran -DNoUnderscoreAppend -I/opt64/include" \ FFLAGS="-m64 -O3 -fPIC -fno-underscoring" \ F90FLAGS="-m64 -O3 -fPIC -fno-underscoring" \ FCFLAGS="-m64 -O3 -fPIC -fno-underscoring" \ LDFLAGS="-L/usr/lib" \ LIBS="-lgfortran" \ CC="/usr/bin/gcc" make -j 1 >& comp.log make install >& install.log 37) 2017.11.15 Installed enscrpt-1.6.6 https://ftp.gnu.org/gnu/enscript/enscript-1.6.6.tar.gz ./configure --prefix=/opt64 --with-media=Letter make -j 4 make install ............................................................................................... 30) 2017.11.09 Installed gmt-5.2.x ftp://ftp.soest.hawaii.edu/gshhg/gshhg-gmt-2.3.7.tar.gz cd /opt64/share tar -zxvf /incoming/gshhg-gmt-2.3.7.tar.gz cd /dist svn checkout svn://gmtserver.soest.hawaii.edu/gmt5/trunk gmt5-dev mv gmt5-dev gmt-5.4.2 cd gmt-5.4.2 cp cmake/ConfigUserTemplate.cmake cmake/ConfigUser.cmake sed -i 's@#set (CMAKE_INSTALL_PREFIX "prefix_path")@set (CMAKE_INSTALL_PREFIX /opt64)@g' cmake/ConfigUser.cmake sed -i 's@#set (GSHHG_ROOT "gshhg_path")@set (GSHHG_ROOT /opt64/share/gshhg-gmt-2.3.4)@g' cmake/ConfigUser.cmake sed -i 's@#set (DCW_ROOT "dcw-gmt_path")@set (DCW_ROOT /opt64/share/dcw-gmt-1.1.1)@g' cmake/ConfigUser.cmake sed -i 's@#set (FFTW3_ROOT "fftw_install_prefix")@set (FFTW3_ROOT /opt64)@g' cmake/ConfigUser.cmake sed -i 's@#set (NETCDF_ROOT "netcdf_install_prefix")@set (NETCDF_ROOT /opt64)@g' cmake/ConfigUser.cmake sed -i 's@# vim:@set (GMT_OPENMP ON)\n# vim:@g' cmake/ConfigUser.cmake mkdir build cd build cmake ../ make -j 65 wget -O ../doc/examples/ex23/example_23.ps http://media.reprojected.com/apps/gmt/ex23/example_23.ps make install ..................................................................... 40) 2017.10.26 Installed pdftk-2.022 http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk-2.02-src.zip cd pdftk-2.02_dist/pdftk cp Makefile.Redhat Makefile make -j 1 Failed: required gcj 42) 2017.10.26 difmap-2.4l patch -Np0 -i /incoming/difmap2.4l_01.patch patch -Np0 -i /incoming/difmap2.4l_02.patch ./configure linux-ia64-gcc ./makeall cp difmap /opt64/bin/ 43) 2017.10.26 Installed panoply-3.1.6 wget https://www.giss.nasa.gov/tools/panoply/download/PanoplyJ-4.8.4.tgz cat panoply.sh | sed 's@`dirname $SCRIPT`@/dist/PanoplyJ@g' > /opt64/bin/panoply chmod o+x,g+x /opt64/bin/panoply 25) 2017.10.26 Installed w3lib-2.0.6 http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/w3lib-2.0.6.tar http://astrogeo.org/pet_inc/w3lib_01.patch patch -Np0 -i /incoming/w3lib_01.patch make -j 41 /opt64/bin/gfortran -shared -Wl,--whole-archive,-soname,libw3.so.1 -o /opt64/lib/libw3.so.1 libw3.a -Wl,-no-whole-archive ln -sf /opt64/lib/libw3.so.1 /opt64/lib/libw3.so 35) 2017.10.26 Installed wgrib2-2.06c ftp://ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz.v2.0.6c mv grib2 wgrib-2.06c cp makefile makefile.orig setenv FFLAGS "-fbounds-check -fno-underscoring -DNoUnderscoreAppend -fPIC" setenv FC /opt64/bin/fortran cat makefile.orig | sed "s@USE_NETCDF4=0@USE_NETCDF4=0@g" | \ sed "s@USE_NETCDF3=1@USE_NETCDF4=0@g" | \ sed "s@USE_IPOLATES=1@USE_IPOLATES=0@g" | \ sed 's@ifeq ($(wFFLAGS),"")@wFFLAGS+=-O2\n ifeq ($(wFFLAGS),"")@g' | \ sed "s@#export CC=gcc@export CC=/opt64/bin/gcc@g" | \ sed "s@#export FC=gfortran@export FC=/opt64/bin/gfortran@g" | \ sed "s@wLDFLAGS+=-ljasper@wLDFLAGS+=-L../lib64 -ljasper@g" | \ sed "s@wLDFLAGS+=-laec@wLDFLAGS+=-L../lib64 -laec@g" | \ sed 's@${netcdf4src} ${hdf5src} ${prog} @${prog} @g' | \ sed "s@netcdf-4.4.1@netcdf-4.5.0@g" | \ sed "s@hdf5-1.8.17@hdf5-1.10.1@g" \ > makefile make cp wgrib2/wgrib2 /opt64/bin/ 36) 2017.10.26 Installed wcslib-5.17 ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-5.17.tar.bz2 http://astrogeo.org/pet_inc/wcslib_01.patch http://astrogeo.org/pet_inc/wcslib_02.patch http://astrogeo.org/pet_inc/wcslib_03.patch chmod u+rw configure.ac patch -Np0 -i /incoming/wcslib_01.patch # underscore in pgpbeg_ should have configure as well ./configure --prefix=/opt64 \ --with-cfitsiolib=/opt64/lib \ --with-cfitsioinc=/opt64/include \ --with-pgplotlib=/opt64/lib \ --with-pgplotinc=/opt64/include \ F77=/opt64/bin/gfortran \ FFLAGS="-fno-underscoring" \ LIBS="-L/opt64" patch -Np0 -i /incoming/wcslib_02.patch # should be wcsconfig_f77.h patch -Np0 -i /incoming/wcslib_03.patch make make install