Installation on Linux troubles

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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maxwellphenderson
Posts: 22
Joined: Mon Mar 07, 2011 12:17 am

Installation on Linux troubles

Post by maxwellphenderson » Wed Apr 13, 2011 4:24 pm

I am using Andrew Davison's notes for installation for Linux. So, I downloaded the newest source files, and began running through the instructions. I ran the commands:

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$ N=`pwd`
$ tar xzf iv-17.tar.gz
$ tar xzf nrn-nn.tar.gz
$ cd iv-17
$ ./configure --prefix=`pwd`
This gives me the output:

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hendemd@lilac:~/neuron/iv$ ./configure --prefix=`pwd`
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... 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 g++ accepts -g... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for cos in -lm... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler has stringstream... yes
We are able to run a c++ program that uses streams
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking osfcn.h usability... no
checking osfcn.h presence... no
checking for osfcn.h... no
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/stat.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking stropts.h usability... yes
checking stropts.h presence... yes
checking for stropts.h... yes
checking sys/conf.h usability... no
checking sys/conf.h presence... no
checking for sys/conf.h... no
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for getpagesize... yes
checking for working mmap... yes
checking return type of signal handlers... void
checking for vprintf... yes
checking for _doprnt... no
checking for getcwd... yes
checking for gethostname... yes
checking for gettimeofday... yes
checking for regcomp... yes
checking for select... yes
checking for socket... yes
checking for strcspn... yes
checking for strerror... yes
checking for strtod... yes
checking for strtol... yes
checking for uname... yes
checking for prototype for gettimeofday... found
checking for type of signal functions... posix
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/bin/Makefile
config.status: creating src/bin/idemo/Makefile
config.status: creating src/bin/idraw/Makefile
config.status: creating src/bin/iclass/Makefile
config.status: creating src/include/Makefile
config.status: creating src/lib/Makefile
config.status: creating config.h
config.status: creating src/include/ivstream.h
config.status: src/include/ivstream.h is unchanged
Next, I run the make command. Everything seems to be OK. Then, I run make install:

Code: Select all

hendemd@lilac:~/neuron/iv$ make install
Making install in src
make[1]: Entering directory `/home/hendemd/neuron/iv/src'
Making install in lib
make[2]: Entering directory `/home/hendemd/neuron/iv/src/lib'
/bin/bash ../../mkinstalldirs /home/hendemd/neuron/iv/i686/lib 
/bin/bash ../../libtool --mode=install /usr/bin/install -c  libIVhines.la /home/hendemd/neuron/iv/i686/lib/libIVhines.la
/usr/bin/install -c .libs/libIVhines.so.3.0.3 /home/hendemd/neuron/iv/i686/lib/libIVhines.so.3.0.3
(cd /home/hendemd/neuron/iv/i686/lib && { ln -s -f libIVhines.so.3.0.3 libIVhines.so.3 || { rm -f libIVhines.so.3 && ln -s libIVhines.so.3.0.3 libIVhines.so.3; }; })
(cd /home/hendemd/neuron/iv/i686/lib && { ln -s -f libIVhines.so.3.0.3 libIVhines.so || { rm -f libIVhines.so && ln -s libIVhines.so.3.0.3 libIVhines.so; }; })
/usr/bin/install -c .libs/libIVhines.lai /home/hendemd/neuron/iv/i686/lib/libIVhines.la
PATH="$PATH:/sbin" ldconfig -n /home/hendemd/neuron/iv/i686/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/hendemd/neuron/iv/i686/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/bash ../../libtool --mode=install /usr/bin/install -c  libUnidrawhines.la /home/hendemd/neuron/iv/i686/lib/libUnidrawhines.la
/usr/bin/install -c .libs/libUnidrawhines.so.3.0.3 /home/hendemd/neuron/iv/i686/lib/libUnidrawhines.so.3.0.3
(cd /home/hendemd/neuron/iv/i686/lib && { ln -s -f libUnidrawhines.so.3.0.3 libUnidrawhines.so.3 || { rm -f libUnidrawhines.so.3 && ln -s libUnidrawhines.so.3.0.3 libUnidrawhines.so.3; }; })
(cd /home/hendemd/neuron/iv/i686/lib && { ln -s -f libUnidrawhines.so.3.0.3 libUnidrawhines.so || { rm -f libUnidrawhines.so && ln -s libUnidrawhines.so.3.0.3 libUnidrawhines.so; }; })
/usr/bin/install -c .libs/libUnidrawhines.lai /home/hendemd/neuron/iv/i686/lib/libUnidrawhines.la
PATH="$PATH:/sbin" ldconfig -n /home/hendemd/neuron/iv/i686/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/hendemd/neuron/iv/i686/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/bash ../../mkinstalldirs /home/hendemd/neuron/iv/share/app-defaults
/usr/bin/install -c app-defaults/Doc /home/hendemd/neuron/iv/share/app-defaults/Doc
/usr/bin/install -c app-defaults/InterViews /home/hendemd/neuron/iv/share/app-defaults/InterViews
/usr/bin/install -c app-defaults/Idemo /home/hendemd/neuron/iv/share/app-defaults/Idemo
make[2]: Leaving directory `/home/hendemd/neuron/iv/src/lib'
Making install in include
make[2]: Entering directory `/home/hendemd/neuron/iv/src/include'
for dir in Dispatch IV-2_6 IV-2_6/InterViews IV-X11 IV-look InterViews OS TIFF; do \
	  /bin/bash ../../mkinstalldirs /home/hendemd/neuron/iv/include/$dir; \
	  for file in $dir/*.h; do \
	    /usr/bin/install -c -m 644 $file /home/hendemd/neuron/iv/include/$file; \
	  done; \
	done
/bin/bash ../../mkinstalldirs /home/hendemd/neuron/iv/include/InterViews/Bitmaps
for file in InterViews/Bitmaps/*.bm; do \
	  /usr/bin/install -c -m 644 $file /home/hendemd/neuron/iv/include/$file; \
	done
/usr/bin/install -c -m 644 ivstream.h /home/hendemd/neuron/iv/include/ivstream.h
/usr/bin/install -c -m 644 ivstrm.h /home/hendemd/neuron/iv/include/ivstrm.h
/usr/bin/install -c -m 644 ivversion.h /home/hendemd/neuron/iv/include/ivversion.h
make[2]: Leaving directory `/home/hendemd/neuron/iv/src/include'
Making install in bin
make[2]: Entering directory `/home/hendemd/neuron/iv/src/bin'
Making install in iclass
make[3]: Entering directory `/home/hendemd/neuron/iv/src/bin/iclass'
/bin/bash ../../../mkinstalldirs /home/hendemd/neuron/iv/i686/bin
/bin/bash ../../../libtool --mode=install /usr/bin/install -c iclass /home/hendemd/neuron/iv/i686/bin/iclass
/usr/bin/install -c .libs/iclass /home/hendemd/neuron/iv/i686/bin/iclass
make[3]: Leaving directory `/home/hendemd/neuron/iv/src/bin/iclass'
Making install in idemo
make[3]: Entering directory `/home/hendemd/neuron/iv/src/bin/idemo'
/bin/bash ../../../mkinstalldirs /home/hendemd/neuron/iv/i686/bin
/bin/bash ../../../libtool --mode=install /usr/bin/install -c idemo /home/hendemd/neuron/iv/i686/bin/idemo
/usr/bin/install -c .libs/idemo /home/hendemd/neuron/iv/i686/bin/idemo
make[3]: Leaving directory `/home/hendemd/neuron/iv/src/bin/idemo'
Making install in idraw
make[3]: Entering directory `/home/hendemd/neuron/iv/src/bin/idraw'
/bin/bash ../../../mkinstalldirs /home/hendemd/neuron/iv/i686/bin
/bin/bash ../../../libtool --mode=install /usr/bin/install -c idraw /home/hendemd/neuron/iv/i686/bin/idraw
/usr/bin/install -c .libs/idraw /home/hendemd/neuron/iv/i686/bin/idraw
make[3]: Leaving directory `/home/hendemd/neuron/iv/src/bin/idraw'
make[2]: Leaving directory `/home/hendemd/neuron/iv/src/bin'
make[1]: Leaving directory `/home/hendemd/neuron/iv/src'
I execute the next few steps:

Code: Select all

cd ..
cd nrn
./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python
But now, the configuration command gives some errors:

Code: Select all

hendemd@lilac:~/neuron/nrn$ ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for style of include used by make... GNU
checking for g++... g++
checking for C++ compiler default output file name... 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 g++ accepts -g... yes
checking dependency style of g++... gcc3
Not trying to build rpms for your system (use --enable-rpm-rules to override) 
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) mawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for flex... no
checking for lex... no
checking for yywrap in -lfl... no
checking for yywrap in -ll... no
checking for bison... no
checking for byacc... no
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for cos in -lm... yes
Python binary found (/usr/bin/python)
checking nrnpython configuration... get_python_version()  '2.6'
get_python_inc(1)  '/usr/include/python2.6'
get_config_var('LIBS')  '-lpthread -ldl  -lutil'
get_config_var('LINKFORSHARED')  '-Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions'
get_config_var('LIBDIR')  '/usr/lib'
checking if python include files and libraries work... yes
configure: Use the NRNMECH_DLL_STYLE for "special"
checking for tgetent in -lncurses... no
checking for tgetent in -lcurses... no
checking for tgetent in -ltermcap... no
configure: error: cannot find one of ncurses, curses, or termcap
Any help would be much appreciated! I tried looking online for a way to download ncurses, but I am not really sure what to do with it once I get it. Thanks!

ted
Site Admin
Posts: 5566
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Installation on Linux troubles

Post by ted » Wed Apr 13, 2011 5:25 pm

Every modern Linux distribution has some kind of package manager that simplifies the process of finding, downloading, and installing software. So the relevant questions are:
1. what is your Linux's package manager
2. do you have sufficient privileges to use it
3. can you use it to search for a package that provides ncurses, curses, or termcap
4. if such a package exists, can/how do you use the package manager to download and install the package?

For example, I'm using CentOS, which offers yum (command line) and pirut (a GUI tool) as package managers, so if I lacked ncurses, curses, or termcap, I'd use yum or pirut to download and install one or more of them.

maxwellphenderson
Posts: 22
Joined: Mon Mar 07, 2011 12:17 am

Re: Installation on Linux troubles

Post by maxwellphenderson » Fri Apr 15, 2011 10:05 pm

Thanks for the help! Finally got everything installed and working properly. :)

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