Thread: Configure warnings installing XOOPIC from Berkeley Plasma Physics Group

i downloaded , unpacked sources, established dependancies linux sudo command according following readme.install.

code:

xoopic source available via www @ http://langmuir.eecs.berkeley.edu/pub/codes  if file old, here quickstart. read on if have trouble. : standard ./configure, make, make install system. : start script 'run_conf.sh' - nicer way pass arguments configure         , same xoopic , xgrafix (you need install xgrafix first) : once have edited run_conf.sh fit needs, use configure xgrafix, install it:     $> sh run_conf.sh     $> make && sudo make install # note sudo if need root privileges write destination : once completes, use _the same_ run_conf.sh configure xoopic:     $> sh run_conf.sh     $> make && cp xg/xoopic /path/to/where/i/want/xoopic  should it!  bash_completion has nice tab completion introspection of available options configure ($>./configure<tab><tab> show options)  ############################ # dependencies: ############################ building , running xgrafix/xoopic depend on following headers/libraries/programs:     x11, xpm, tcl/tk, gcc, imagemagick, bison      optional xoopic dependencies:     fortran     mpi parallel runs     hdf5 parallel or high performance dump files     libpng png diagnostics     fftw     fftw3   dependencies can installed on ubuntu (or debian based distro) command: sudo aptitude install gcc g++ gfortran build-essential automake \     tk-dev imagemagick bison libx11-dev libxpm-dev libpng-dev \     fftw-dev  libfftw3-dev h5utils hdf5-tools libhdf5-serial-*\  first 2 lines necessary, last installs optional fftw/hdf5 dependencies  on fedora, these dependencies can installed with: sudo yum install gcc gcc-gfortran gcc-c++ automake libx11-devel libxpm-devel \         imagemagick bison tk-devel libpng-devel \         hdf5 hdf5-devel  on suse, install following packages package manager:         gcc gcc-c++ gcc-fortran automake xorg-x11-devel make         tk-devel bison libpng-devel imagemagick hdf5 hdf5-devel   ################## # configure / build/ install ################## new install:  edit run_conf.sh file match system.  basic install, thing edit `prefix` - install location.  can do: sh run_conf.sh # configure build  make # build program # or, if have multiprocessor machine, can go faster with: make -j 4 #(that's 4 threads, can many or few want)  # if building xgrafix, do: make install # sudo make install if need root privileges write $prefix/{bin|lib|include}  test xgrafix build with:  ./ctest/xtest # xgrafix root dir.  once have built , installed xgrafix, can build xoopic. run_conf.sh same both xoopic , xgrafix, if configured run_conf.sh in xgrafix, use same 1 in xoopic.  process build xoopic same xgrafix, except skip 'make install' step, since need binary file in 'xg/xoopic'. can test xoopic with: ./xoopic -i input/ebeam1a.inp # xoopic root dir  once xoopic done, can install with: cp xoopic $prefix/bin/  note not need 'make install' xoopic, place binary './xoopic' anywhere in path  prefix defined in: prefix=/usr/local # install users or prefix=$home # install (assuming ~/bin in path)  ************************************** rest of file pretty old...      xoopic has been compiled on following unix systems running x11r5 or better:  os        machine     compiler    library ------------------------------------------------------------------------- hp-ux a.09.05    hp 712/80    g++2.7.2    libg++2.7.1 dec unix 3.2    dec 200/4/233    g++2.7.2    libg++2.7.1 dec unix 3.2    dec 200/4/233    cxx5.1        vendor supplied                 using dec cxx 5.1 not recommended xoopic dec unix 4.0c    pws 600au    g++2.8.0    libg++2.8.0 dec unix 4.0c    pws 600au    egcs-1.0.1    egcs libraries dec unix 4.0c    pws 600au    cxx6.0        vendor supplied. dec unix 4.0d    pws 600au    cxx6.0        vendor supplied. dec unix 4.0d    dec 8400    cxx6.0        vendor supplied. sunos 4.1.x    sparc 2        g++2.7.2    libg++2.7.1 solaris 2.5    ultrasparc    g++2.7.2     solaris 2.6    ultrasparc    sun cc 4.2    vendor supplied aix 3.2        ibm 590        g++2.7.2    libg++2.7.1 aix 3.2        ibm 590        xlc 1.00 --  had modify code,                     , turn off optimization on                     files.  furthermore, compiled                     code 1/2 fast g++. solaris 2.4    sparc 10    sun c++4.0.1                     (required few simple changes)  linux        ppro        g++2.7.2, g++2.8.0 linux/alpha    21164        g++2.7.2, g++2.8.0 freebsd        k6        g++2.7.2 -- of outdated, 2009 versions have been compiled on following: both 32/64 bit:     ubuntu linux 8.10 - 9.10, gcc 4.2-4.4, tcl/tk 8.4-8.5     mac osx 10.4.8,10.5.7,10.6.1 - using macports or fink tcl/tk     fedora core 8 (64) - gcc4.1     fedora core 11 (32) - gcc4.4      opensuse 11 (32) - gcc4.3  **************************************************************************** if possible enlist aid of system administrator compiling xoopic.  warning:  g++ 2.6.1, g++ 2.6.2, , g++ 2.6.3 broken , not  compile xoopic (on systems).  don't know previous versions.  also: g++2.7.2 on windows nt 4.0 not work. ****************************************************************************     rest of file possibly outdated: ********** compile , install xoopic, need following public domain software packages not maintain:   * g++            (/pub/gnu/gcc-2.7.2.tar.gz @ gatekeeper.dec.com) * libg++        (/pub/gnu/libg++-2.7.?.tar.gz @ gatekeeper.dec.com)  or dec cxx instead of g++ , libg++  * libtcl7.4.a (or later)     * libtk4.0.a  (or later)         * libxpm.a         * libxgrafix2.50 (or later)   (http://ptsg.eecs.berkeley.edu)  ************************************************* *** note: requirement xgrafix version *** ************************************************* update on aug. 16, 2005 h.c. kim   make version of xoopic work properly, recent version of xgrafix (later mar. 29, 2005) needs installed.  otherwise, may see "core dumped" when restoring dump file. *************************************************  once have c++ compiler, libtcl.a libtk.a libxpm.a, ready begin:  0)  sources:       http://ptsg.eecs.berkeley.edu      may have these , can omit step.  1)  unpack sources:     >tar -xvzf xoopic.tar.gz       should directory named oopic these files:     readme makefile physics/ advisor/ xg/ xgrafix/ input/ g++-fixes/ doc/     configure     physics/ contains basic physical models xoopic     advisor/ contains input file reader , input sanity checking     xgrafix/ contains graphics library used xoopic     input/ contains sample input files xoopic     g++-fixes/ contains fixes may need make g++            work     doc/ contains documentation.     bench/ benchmarks of xoopic     + other misc. files..  2)  compile , install xgrafix.     (xgrafix has own instructions)      3)  run ./configure       once have c++ compiler, libxgc250.a, libxpm.a, libtcl*.a, libtk*.a,      ready start compiling xoopic.         begin, run "configure", try find libraries      , headers needed, , accept parameters indicating      configuration options or library locations.       in directory have:      readme makefile physics/ advisor/ xg/ xgrafix/ input/            ./configure       pay attention messages configure gives.  if fails       automatically find such libxpm.a, prompt      tell find file.       configure --help       give list of configure options.       example, command cause xoopic use compiler      'cxx' instead of default 'g++':       ./configure --with-cxx=cxx       if hdf5 library not installed in systems,      need give option of '--disable-hdf5':       ./configure --disable-hdf5       depending on how idiosyncratic system installation is,      might have give complex configure comand such as:       ./configure --with-cxx=cxx --with-tclsh=/home/tcl/bin      --x-includes=/usr/x11/include --x-libraries=/sww/x11/lib     --with-xpm=/usr/local/xpm/lib --with-xgrafix-lib=/usr/local/tmp       however, should necessary if system administrator      likes install things in non-standard locations.       configure, when successful, should convert makefile.in in each of      . advisor/ physics/ , xg/ , convert them makefile.  4)   run make       make       should go each of physics/ advisor/, , xg/,      , create binary xg/xoopic you.       if compile fails, complaining of missing include files      or libraries, try editing */makefile add appropriate      includes or libraries.       if link fails missing symbols,       version of tcl/tk xoopic trying use      mismatch xgrafix library.  xgrafix must configured      use either version 7.4/4.0 of tcl/tk libraries,      or configured use version 7.5/4.1 or higher.  if       xgrafix configured wrong tcl/tk libraries,      xoopic won't link!       possible problems:  compile fails, giving errors involving      cstring.h.  g++2.7.0 problem.        fix in g++-fixes.      b) upon starting xoopic, xgrafix reports can't find      tcl/tk initialization file.      solution:  figure out file xgrafix looking is,     , fix xgrafix find it.  these in particular:     init.tcl     in tcl lib directory, (usually /usr/local/lib/tcl)     init.tk     in tk lib directory, (usually /usr/local/lib/tk)     xgsetup.tcl    in xgrafix directory      if problem finding init.tcl, , init.tk,     these libraries misinstalled.  if xgsetup.tcl not found,     didn't set xgtcl correctly when building xgrafix.     double check , recompile if necessary.  run,       xoopic -i input/dring.inp      or whatever input file appropriate you.     bugs:  email bugreports xoopic@langmuir.eecs.berkeley.edu

executing xgrafix/run_conf.sh gives following warning messages:

code:

precisiont3400@ubuntu:~/fusion/xoopic/downloads/xgrafix$ ./run_conf.sh#2 bash: ./run_conf.sh#2: permission denied precisiont3400@ubuntu:~/fusion/xoopic/downloads/xgrafix$ ./run_conf.sh#2 configuring options: --prefix=/usr/local --with-scalar=double --enable-fulloptimize --with-xgrafix-lib=/usr/local/lib --with-xgrafix-include=/usr/local/include  configure: warning: unrecognized options: --with-xgrafix-lib, --with-xgrafix-include checking bsd-compatible install... /usr/bin/install -c checking whether build environment sane... yes checking thread-safe mkdir -p... /bin/mkdir -p checking gawk... no checking mawk... mawk checking whether make sets $(make)... yes checking whether enable maintainer-specific portions of makefiles... no checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu using c++ compiler g++ using c compiler gcc checking style of include used make... gnu checking gcc... gcc checking whether c compiler works... yes checking c compiler default output file name... a.out checking suffix of executables...  checking whether cross compiling... no checking suffix of object files... o checking whether using gnu c compiler... yes checking whether gcc accepts -g... yes checking gcc option accept iso c89... none needed checking dependency style of gcc... gcc3 checking library containing strerror... none required checking whether time.h , sys/time.h may both included... yes checking bsd-compatible nm...  install-sh/usr/bin/nm -b setting flags per system , c++ compiler: g++ checking g++... /usr/bin/g++ serial c++ compiler `g++' checking g++ version... g++ configure: warning: caution: version  not known work. configure: warning: c++ compiler may generate code processor only. checking -fsquangle... no checking how build libraries... ar cr   checking gcc... /usr/bin/gcc serial c compiler `gcc' checking gcc... (cached) gcc checking whether using gnu c compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking gcc option accept iso c89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking whether using gnu c++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how run c preprocessor... gcc -e checking how run c++ preprocessor... g++ -e checking grep handles long lines , -e... /bin/grep checking egrep... /bin/grep -e checking ansi c header files... yes checking sys/types.h... yes checking sys/stat.h... yes checking stdlib.h... yes checking string.h... yes checking memory.h... yes checking strings.h... yes checking inttypes.h... yes checking stdint.h... yes checking unistd.h... yes checking size_t... yes checking whether struct tm in sys/time.h or time.h... time.h checking whether c++ compiler supports exception handling... yes checking whether c++ compiler supports typename... yes checking whether c++ compiler can explicitly instantiate templates... yes checking whether c++ compiler supports rtti... yes checking whether c++ compiler supports namespaces... yes checking whether c++ compiler has complex in namespace std... yes checking whether c++ compiler has streams in namespace std... yes checking whether c++ compiler can overload const type conversions... yes checking whether c++ compiler knows mutable... yes checking whether template friends need brackets... yes checking whether nontype template operators allowed... no checking whether static variables can declared generally... yes configure: warning: fortran libraries invalid. checking whether make sets $(make)... (cached) yes checking whether ln -s works... yes checking ranlib... ranlib checking library suffix is... .a checking how install libraries... ${install} -m 644 configure: warning: x11.m4 obsolete.  please use ac_path_x or ac_path_xtra. checking x11/xlib.h... /usr/include/x11/xlib.h checking libx11.a... no checking libx11.so... no configure: error: unable find libx11.a or libx11.so in /usr/lib32:/usr/x11r6/lib:/usr/lib:/usr/local/lib:/lib:/usr/x11/lib:/usr/openwin/lib:/usr/dt/lib:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games.  set appropriate directory using --with-x11_libdir precisiont3400@ubuntu:~/fusion/xoopic/downloads/xgrafix$

the problem seems path name of libx11.a etc. how find pathname? or how avoid final "configure: error:..." message?
advice appreciated.
dr. joel rogers, plasma physicist

look 2 first output lines: "permission denied" .so need make package executable first:

sudo chmod +x xgrafix (use exact name : case sensitive)

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