Do I need to build this again. I had not installed GROMACS
separately , I used the command line as follows while building the
package.
./build.sh --prefix ${prefix} gromacs tools csg .
Thank You
Rakhee
On Feb 17, 3:24 pm, Christoph Junghans <[email protected]> wrote:
> Am 17. Februar 2012 13:01 schrieb rp <[email protected]>:> Thanks for the
> suggestions. I recompiled and finally ran
> > ./build.sh -DWITH_SQLITE3=OFF --prefix ${prefix} tools csg
>
> Remember that ${prefix} just puts the content of the variable prefix,
> you could more explicit run it as
> ./build.sh -DWITH_SQLITE3=OFF --prefix ~/votca tools csg
>
> > This completed with statement "done with csg"
>
> But that means building of csg was successful. tools is just a
> dependency of csg, you can not use it directly.
>
> Cheers,
>
> Christoph
>
>
>
> > Do I need to install the tools separately.
>
> > Rakhee
>
> > On Feb 15, 5:53 pm, Christoph Junghans <[email protected]> wrote:
> >> Am 15. Februar 2012 13:39 schrieb Rakhee Pani <[email protected]>:> I
> >> am getting some error message related to fftw libraries .
>
> >> > 91%] Building CXX object
> >> > src/libtools/CMakeFiles/votca_tools.dir/parsexml.cc.o
> >> > [ 95%] Building CXX object
> >> > src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
> >> > Linking CXX shared library libvotca_tools.so
> >> > /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
> >> > R_X86_64_32
> >> > against `.rodata' can not be used when making a shared object; recompile
> >> > with -fPIC
> >> > /usr/local/lib/libfftw3.a: could not read symbols: Bad value
>
> >> This is the good old shared vs. static linking issue.
> >> Search our mailing list for "R_X86_64_32" to find the details, but in
> >> short the solution is to reconfigure and recompile fftw3 with
> >> --enable-shared.
>
> >> Christoph
>
> >> > collect2: ld returned 1 exit status
> >> > make[2]: *** [src/libtools/libvotca_tools.so.3] Error 1
> >> > make[1]: *** [src/libtools/CMakeFiles/votca_tools.dir/all] Error 2
> >> > make: *** [all] Error 2
>
> >> > Thanks
> >> > Rakhee
>
> >> > On Wed, Feb 15, 2012 at 3:23 PM, Christoph Junghans <[email protected]>
> >> > wrote:
>
> >> >> Am 15. Februar 2012 12:47 schrieb Rakhee Pani <[email protected]>:
>
> >> >> > Following my previous message on installation of votca in ubuntu .I
> >> >> > fullfilled all dependencies and I still get an error message which is
> >> >> > as
> >> >> > below .Should I use the --insecure in command line .
>
> >> >> > sudo ./build.sh --prefix ${prefix} tools csg
> >> >> > This is VOTCA build.sh, version 1.8.1
> >> >> > Install prefix is '/usr/local/bin'
> >> >> > Using 5 jobs for make
> >> >> > Working on tools
> >> >> > Doing checkout for tools fromhttps://tools.votca.googlecode.com/hg/
> >> >> > (CTRL-C to stop) 5 4 3 2 1
> >> >> > abort: tools.votca.googlecode.com certificate error: certificate is
> >> >> > for
> >> >> > *.googlecode.com, *.u.googlecode.com, googlecode.com, *.codespot.com,
> >> >> > *.googlesource.com, googlesource.com (use --insecure to connect
> >> >> > insecurely)
> >> >> If have added a fix in the buildutil, please update.
>
> >> >> Christoph
>
> >> >> > Thanks All
> >> >> > Rakhee
> >> >> > On Sun, Dec 18, 2011 at 11:09 AM, Christoph Junghans
> >> >> > <[email protected]>
> >> >> > wrote:
>
> >> >> >> Am 17. Dezember 2011 17:56 schrieb rp <[email protected]>:
> >> >> >> > Below is the CMakeError.log file , as mentioned using
> >> >> >> > -DWITH_FFTW=NO
> >> >> >> > will lead to reduced functionality , will this option disable
> >> >> >> > certain
> >> >> >> > tools.Again if I try
> >> >> >> > -DFFTW3_LIBRARY='/path/to/libfftw3.so' with ./build.sh , do I need
> >> >> >> > to
> >> >> >> > replace /path/to with the place where fftw library files are
> >> >> >> > installed.
> >> >> >> Yes!
>
> >> >> >> In your last email, it said fftw was found, but some went wrong
> >> >> >> later.
> >> >> >> Please post the end of that CMakeError.log.
>
> >> >> >> Disabling fftw will only remove the ability to calculate correlation
> >> >> >> functions.
>
> >> >> >> > Determining if the function pthread_create exists in the pthreads
> >> >> >> > failed with the following output:
> >> >> >> > Change Dir: /home/rp/src/tools/CMakeFiles/CMakeTmp
>
> >> >> >> > Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
> >> >> >> > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/build
> >> >> >> > make[1]: Entering directory
> >> >> >> > `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > /usr/local/bin/cmake -E cmake_progress_report /home/rp/src/tools/
> >> >> >> > CMakeFiles/CMakeTmp/CMakeFiles 1
> >> >> >> > Building C object CMakeFiles/cmTryCompileExec.dir/
> >> >> >> > CheckFunctionExists.c.o
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/
> >> >> >> > cmake-2.8/Modules/CheckFunctionExists.c
> >> >> >> > Linking C executable cmTryCompileExec
> >> >> >> > /usr/local/bin/cmake -E cmake_link_script CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/link.txt --verbose=1
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -
> >> >> >> > rdynamic -lpthreads
> >> >> >> > /usr/bin/ld: cannot find -lpthreads
> >> >> >> > collect2: ld returned 1 exit status
> >> >> >> > make[1]: Leaving directory `/home/rakhee/src/tools/CMakeFiles/
> >> >> >> > CMakeTmp'
> >> >> >> > make[1]: *** [cmTryCompileExec] Error 1
> >> >> >> > make: *** [cmTryCompileExec/fast] Error 2
>
> >> >> >> > Determining if the function pthread_create exists in the pthreads
> >> >> >> > failed with the following output:
> >> >> >> > Change Dir: /home/rakhee/src/tools/CMakeFiles/CMakeTmp
>
> >> >> >> > Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
> >> >> >> > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/build
> >> >> >> > make[1]: Entering directory
> >> >> >> > `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > /usr/local/bin/cmake -E cmake_progress_report
> >> >> >> > /home/rakhee/src/tools/
> >> >> >> > CMakeFiles/CMakeTmp/CMakeFiles 1
> >> >> >> > Building C object CMakeFiles/cmTryCompileExec.dir/
> >> >> >> > CheckFunctionExists.c.o
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/
> >> >> >> > cmake-2.8/Modules/CheckFunctionExists.c
> >> >> >> > Linking C executable cmTryCompileExec
> >> >> >> > /usr/local/bin/cmake -E cmake_link_script CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/link.txt --verbose=1
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -
> >> >> >> > rdynamic -lpthreads
> >> >> >> > /usr/bin/ld: cannot find -lpthreads
> >> >> >> > collect2: ld returned 1 exit status
> >> >> >> > make[1]: *** [cmTryCompileExec] Error 1
> >> >> >> > make[1]: Leaving directory `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > make: *** [cmTryCompileExec/fast] Error 2
>
> >> >> >> > Determining if the function pthread_create exists in the pthreads
> >> >> >> > failed with the following output:
> >> >> >> > Change Dir: /home/rp/src/tools/CMakeFiles/CMakeTmp
>
> >> >> >> > Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
> >> >> >> > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/build
> >> >> >> > make[1]: Entering directory
> >> >> >> > `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > /usr/local/bin/cmake -E cmake_progress_report
> >> >> >> > /home/rakhee/src/tools/
> >> >> >> > CMakeFiles/CMakeTmp/CMakeFiles 1
> >> >> >> > Building C object CMakeFiles/cmTryCompileExec.dir/
> >> >> >> > CheckFunctionExists.c.o
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/
> >> >> >> > cmake-2.8/Modules/CheckFunctionExists.c
> >> >> >> > Linking C executable cmTryCompileExec
> >> >> >> > /usr/local/bin/cmake -E cmake_link_script CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/link.txt --verbose=1
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -
> >> >> >> > rdynamic -lpthreads
> >> >> >> > /usr/bin/ld: cannot find -lpthreads
> >> >> >> > collect2: ld returned 1 exit status
> >> >> >> > make[1]: *** [cmTryCompileExec] Error 1
> >> >> >> > make[1]: Leaving directory `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > make: *** [cmTryCompileExec/fast] Error 2
>
> >> >> >> > Determining if the function pthread_create exists in the pthreads
> >> >> >> > failed with the following output:
> >> >> >> > Change Dir: /home/rakhee/src/tools/CMakeFiles/CMakeTmp
>
> >> >> >> > Run Build Command:/usr/bin/make "cmTryCompileExec/fast"
> >> >> >> > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/build
> >> >> >> > make[1]: Entering directory
> >> >> >> > `/home/rp/src/tools/CMakeFiles/CMakeTmp'
> >> >> >> > /usr/local/bin/cmake -E cmake_progress_report
> >> >> >> > /home/rakhee/src/tools/
> >> >> >> > CMakeFiles/CMakeTmp/CMakeFiles 1
> >> >> >> > Building C object CMakeFiles/cmTryCompileExec.dir/
> >> >> >> > CheckFunctionExists.c.o
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -c /usr/local/share/
> >> >> >> > cmake-2.8/Modules/CheckFunctionExists.c
> >> >> >> > Linking C executable cmTryCompileExec
> >> >> >> > /usr/local/bin/cmake -E cmake_link_script CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/link.txt --verbose=1
> >> >> >> > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create
> >> >> >> > CMakeFiles/
> >> >> >> > cmTryCompileExec.dir/CheckFunctionExists.c.o -o cmTryCompileExec -
> >> >> >> > rdynamic -lpthreads
> >> >> >> > /usr/bin/ld: cannot find -lpthreads
> >> >> >> > collect2: ld returned 1 exit status
> >> >> >> > make[1]: *** [cmTryCompileExec] Error 1
> >> >> >> > make[1]: Leaving directory `/home/rakhee/src/tools/CMakeFiles/
> >> >> >> > CMakeTmp'
> >> >> >> > make: *** [cmTryCompileExec/fast] Error 2
>
> >> >> >> > Determining if the function pthread_create exists in the pthreads-
> >> >> >> > Hide quoted text -
>
> - Show quoted text -...
>
> read more »
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