VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 18 2011 - 11:14:31 CDT

susana,

>
> When I type "make" this is what appears on the screen (which is not very
> helpful):
> gfortran  -c -O2 -Wall tester.f -o tester.o
>
> "gcc -c -I/home/tomasio/plugins/include -I/home/tomasio/plugins/LINUX/  -O2
> -Wall f77_molfile.c -o f77_molfile.o
> gfortran  -o tester -L/home/tomasio/plugins/LINUX/molfile -L/usr/local/lib/
> -L/home/tomasio/local/lib/  tester.o f77_molfile.o -lmolfile_plugin -lnetcdf
> -ltcl8.5 -L/usr/share/doc -lstdc++ -ldl"

so is there a file "tester" as a result of that???
that is what is supposed to happen. and there is no indication that there isn't.

> I tried the following:
> touch empty.cxx
> g++ -v empty.cxx
>
> And the output is:
[...]

> (.text+0x18): undefined reference to `main'
> collect2: ld returned 1 exit status
>
> I think it is a problem with the -L flags but I don't know
> how to fix it.

there is nothing that needs to be fixed. the empty file is only
needed to so you can see g++ -v execute all steps of the
compilation up to the linking. and scoop up any necessary
flags in the process. it is supposed to fail at the linking stage.

axel.

> If anyone has any suggestions I'd be grateful.
>
> Thank you,
>
> Susana
>
>
>
> On Mon, Mar 14, 2011 at 11:08 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Mar 14, 2011 at 5:49 PM, Susana Tomasio <susietomasio_at_gmail.com>
>> wrote:
>> > Hi John,
>> >
>> > I see what you mean, but when I add the space between "-ltc8.5"
>> > and "-L/usr/lib/" it gives me the previous error:
>> >
>> > ld: library not found for -lstdc++
>> > collect2: ld returned 1 exit status
>>
>> so you have to find where your c++ library is located.
>>
>> i don't know much about macosx and it is doing
>> a lot of things different from other operating systems.
>> what you can try for example is to do the following:
>>
>> touch empty.cxx
>> g++ -v empty.cxx
>>
>> that will stop with an error, but thanks to the '-v' it will
>> print the full command line at each step. on my linux
>> box this is:
>>
>> Using built-in specs.
>> Target: x86_64-redhat-linux
>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
>> --infodir=/usr/share/info
>> --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
>> --enable-shared --enable-threads=posix --enable-checking=release
>> --with-system-zlib --enable-__cxa_atexit
>> --disable-libunwind-exceptions --enable-gnu-unique-object
>> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
>> --enable-java-awt=gtk --disable-dssi --enable-plugin
>> --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
>> --enable-libgcj-multifile --enable-java-maintainer-mode
>> --with-ecj-jar=/usr/share/java/eclipse-ecj.jar
>> --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic
>> --with-arch_32=i686 --build=x86_64-redhat-linux
>> Thread model: posix
>> gcc version 4.4.4 20100630 (Red Hat 4.4.4-10) (GCC)
>> COLLECT_GCC_OPTIONS='-v' '-shared-libgcc' '-mtune=generic'
>>  /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/cc1plus -quiet -v
>> -D_GNU_SOURCE empty.cxx -quiet -dumpbase empty.cxx -mtune=generic
>> -auxbase empty -version -o /tmp/cckHewnV.s
>> ignoring nonexistent directory
>> "/usr/lib/gcc/x86_64-redhat-linux/4.4.4/include-fixed"
>> ignoring nonexistent directory
>>
>> "/usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../x86_64-redhat-linux/include"
>> #include "..." search starts here:
>> #include <...> search starts here:
>>  /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../include/c++/4.4.4
>>
>>  /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../include/c++/4.4.4/x86_64-redhat-linux
>>
>>  /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../include/c++/4.4.4/backward
>>  /usr/local/include
>>  /usr/lib/gcc/x86_64-redhat-linux/4.4.4/include
>>  /usr/include
>> End of search list.
>> GNU C++ (GCC) version 4.4.4 20100630 (Red Hat 4.4.4-10)
>> (x86_64-redhat-linux)
>>        compiled by GNU C version 4.4.4 20100630 (Red Hat 4.4.4-10), GMP
>> version 4.3.1, MPFR version 2.4.1.
>> GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
>> Compiler executable checksum: 921aa223d38d78a20e67c4037f50d7c9
>> COLLECT_GCC_OPTIONS='-v' '-shared-libgcc' '-mtune=generic'
>>  as -V -Qy -o /tmp/ccY7JKAw.o /tmp/cckHewnV.s
>> GNU assembler version 2.19.51.0.14 (x86_64-redhat-linux) using BFD
>> version version 2.19.51.0.14-37.fc12 20090722
>>
>> COMPILER_PATH=/usr/libexec/gcc/x86_64-redhat-linux/4.4.4/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.4/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.4/:/usr/lib/gcc/x86_64-redhat-linux/:/usr/libexec/gcc/x86_64-redhat-linux/4.4.4/:/usr/libexec/gcc/x86_64-redhat-linux/:/usr/lib/gcc/x86_64-redhat-linux/4.4.4/:/usr/lib/gcc/x86_64-redhat-linux/
>>
>> LIBRARY_PATH=/usr/lib/gcc/x86_64-redhat-linux/4.4.4/:/usr/lib/gcc/x86_64-redhat-linux/4.4.4/:/usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../:/lib/:/usr/lib/
>> COLLECT_GCC_OPTIONS='-v' '-shared-libgcc' '-mtune=generic'
>>  /usr/libexec/gcc/x86_64-redhat-linux/4.4.4/collect2 --eh-frame-hdr
>> --build-id -m elf_x86_64 --hash-style=gnu -dynamic-linker
>> /lib64/ld-linux-x86-64.so.2
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64/crt1.o
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64/crti.o
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/crtbegin.o
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64
>> -L/lib/../lib64 -L/usr/lib/../lib64
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../.. /tmp/ccY7JKAw.o
>> -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/crtend.o
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64/crtn.o
>> /usr/lib/gcc/x86_64-redhat-linux/4.4.4/../../../../lib64/crt1.o: In
>> function `_start':
>> (.text+0x20): undefined reference to `main'
>> collect2: ld returned 1 exit status
>>
>> the last step is the linking and there you see all the -L flags that are
>> added
>> when linking a c++ code. now you can add the -v flag when linking with
>> gfortran and you can compare.
>>
>> cheers,
>>    axel.
>>
>> > Thank you,
>> >
>> > Susana
>> >
>> >
>> > On Mon, Mar 14, 2011 at 9:22 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>> >>
>> >> Susana,
>> >>  You need a space between "-ltcl8.5" and "-L/usr/lib/", they are
>> >> separate command parameters.  You may need to edit your makefile
>> >> to add spaces where necessary.
>> >>
>> >> Cheers,
>> >>  John
>> >>
>> >> On Mon, Mar 14, 2011 at 09:04:51PM +0000, Susana Tomasio wrote:
>> >> >    Hi Axel,
>> >> >
>> >> >    Thank you for your reply.
>> >> >    Your are right it doesn't complain about -lstdc++. But now it
>> >> > complains
>> >> >    about -ltcl8.5:
>> >> >
>> >> >    ld: library not found for -ltcl8.5-L/usr/lib/
>> >> >    collect2: ld returned 1 exit status
>> >> >    make: *** [tester] Error 1
>> >> >
>> >> >    Is it also related with the space between the words?
>> >> >    (Sorry I don't have experience with this sort of thing).
>> >> >
>> >> >    Thank you,
>> >> >
>> >> >    Susana
>> >> >
>> >> >    On Mon, Mar 14, 2011 at 6:43 PM, Axel Kohlmeyer
>> >> > <akohlmey_at_gmail.com>
>> >> >    wrote:
>> >> >
>> >> >      On Mon, Mar 14, 2011 at 12:52 PM, Susana Tomasio
>> >> >      <susietomasio_at_gmail.com> wrote:
>> >> >      > Hi all,
>> >> >      >
>> >> >      > I'm compiling the fortran bindings for the VMD molfile plugins
>> >> > from
>> >> >      Axel
>> >> >      > Kohlmeyer.
>> >> >      >
>> >> >      > I've compiled the molfile plugins but I am having a linkage
>> >> > problem
>> >> >      when
>> >> >      > compliling the
>> >> >      > fortran bindings. I am using a MacOSX Snow Leopard.
>> >> >
>> >> >      [...]
>> >> >      > ld: library not found for -ltcl8.5-L/usr/lib/-lstdc++
>> >> >
>> >> >      have a look at this error message.
>> >> >      it doesn't look right as a library name, or does it?
>> >> >      > collect2: ld returned 1 exit status
>> >> >      > make: *** [tester] Error 1
>> >> >      >
>> >> >      > And this is the edit section of my Makefile:
>> >> >      >
>> >> >      > ARCH           = MACOSX86-64
>> >> >      > ARCHDIR        = /Users/tomasio/plugins/MACOSXX86/molfile
>> >> >      > FC             = g77
>> >> >      > #FC             = g77
>> >> >      > #-fno-second-underscore
>> >> >      > CC             = gcc
>> >> >      > LD             = $(FC)
>> >> >      > OPT            = -O2 -Wall
>> >> >      > CPPFLAGS       = -I/Users/tomasio/plugins/include/
>> >> >      > -I/Users/tomasio/plugins/MACOSXX86 #
>> >> >      > -D_F77_F2C_UNDERSCORE
>> >> >      > CFLAGS         = -c $(CPPFLAGS) $(OPT)
>> >> >      > FFLAGS         = -c $(OPT)
>> >> >      > NETCDFLIB      =
>> >> >      >
>> >> >
>> >> >
>> >> >  -L/opt/local/var/macports/software/netcdf/4.1.1_4+dap+netcdf4/opt/local/lib/
>> >> >      > #/usr/lib64/netcdf-3
>> >> >      > NETCDFLDFLAGS  = -lnetcdf
>> >> >      > TCLLIB         =
>> >> >      /opt/local/var/macports/software/tcl/8.5.9_0/opt/local/lib/
>> >> >      > TCLLDFLAGS     = -ltcl8.5
>> >> >      > LDFLAGS        = -L$(ARCHDIR) $(TCLLIB) $(NETCDFLIB)
>> >> >      > LDLIBS         = -lmolfile_plugin $(NETCDFLDFLAGS)
>> >> >      > $(TCLLDFLAGS)-L/usr/lib/-lstdc++ -ldl
>> >> >
>> >> >      here is the problem. there have to be blanks between the
>> >> > "words",
>> >> > i.e.
>> >> >      try:
>> >> >      $(TCLLDFLAGS) -L/usr/lib/ -lstdc++ -ldl
>> >> >
>> >> >      cheers,
>> >> >          axel.
>> >> >      >
>> >> >      > I tried with gfortran and got the same error.
>> >> >      > I would be grateful if anyone could help me with this.
>> >> >      >
>> >> >      > Thank you,
>> >> >      >
>> >> >      > Susana
>> >> >      >
>> >> >
>> >> >      --
>> >> >      Dr. Axel Kohlmeyer
>> >> >      akohlmey_at_gmail.com  http://goo.gl/1wk0
>> >> >
>> >> >      Institute for Computational Molecular Science
>> >> >      Temple University, Philadelphia PA, USA.
>> >>
>> >> --
>> >> NIH Resource for Macromolecular Modeling and Bioinformatics
>> >> Beckman Institute for Advanced Science and Technology
>> >> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> >> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>> >>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.