Hi Christoph,
I am using the following command,
cmake -Bbuilddir -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DBUILD_CSGAPPS=ON -DBUILD_XTP=ON
-DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
-DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
-DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/
-DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a
-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_PREFIX=${prefix}
../votca
and the configuration show no problems. But when building it, I have a
problem with the linking of the libraries for gromacs, which are in this
cases static, there is not .so libraries available.
Below is the last part of the output of
cmake --build builddir --verbose
I have attached the complete output in: output_verbose_votca_19_12_2020.txt
I tried to pass the -fPIC option when compiling but I think I am doing it
wrong. How this should be done?
Best regards,
Nancy
...
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(merge_sort.c.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: nonrepresentable section on output
collect2: error: ld returned 1 exit status
csg/src/libcsg/CMakeFiles/votca_csg.dir/build.make:798: recipe for target
'csg/src/libcsg/libvotca_csg.so.6' failed
gmake[2]: *** [csg/src/libcsg/libvotca_csg.so.6] Error 1
gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir'
CMakeFiles/Makefile2:590: recipe for target
'csg/src/libcsg/CMakeFiles/votca_csg.dir/all' failed
gmake[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir'
Makefile:129: recipe for target 'all' failed
gmake: *** [all] Error 2
On Tuesday, 1 December 2020 at 15:20:46 UTC+1 nancyfor wrote:
> I think the issue with MKL is related to the gcc version, there is not
> module of MKL for gcc-8.
> When I succed, I will let you know.
> Thank you!
> Cheers
> Nancy
>
> On Tuesday, 1 December 2020 at 15:15:11 UTC+1 Christoph Junghans wrote:
>
>> On Tue, Dec 1, 2020 at 7:11 AM nancyfor <[email protected]> wrote:
>> >
>> > Hi Christoph
>> > Few minutes ago I was using,
>> >
>> > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
>> >
>> > and correctly use GNU 8.4.0
>> >
>> > However, now there is something related to the
>> 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND'
>> Try to compile without MKL for now:
>> -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, if you aren't using xtp, mkl
>> doesn't gain you much anyhow.
>>
>> Christoph
>>
>> >
>> > this is the output for cmake --build builddir
>> >
>> > Scanning dependencies of target gitversion-xtp
>> > Current git revision is 9b6bbd0
>> > [ 0%] Built target gitversion-xtp
>> > Scanning dependencies of target gitversion
>> > Current git revision is 9b6bbd0
>> > [ 0%] Built target gitversion
>> > Scanning dependencies of target votca_tools
>> > [ 1%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
>> > [ 1%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
>> > [ 1%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/calculator.cc.o
>> > [ 2%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
>> > [ 2%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
>> > [ 2%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
>> > [ 3%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
>> > [ 3%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
>> > [ 3%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/edge.cc.o
>> > [ 4%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/edgecontainer.cc.o
>> > [ 4%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/elements.cc.o
>> > [ 4%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/filesystem.cc.o
>> > [ 5%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o
>> > [ 5%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graph.cc.o
>> > [ 5%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graph_bf_visitor.cc.o
>> > [ 6%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graph_df_visitor.cc.o
>> > [ 6%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graphalgorithm.cc.o
>> > [ 6%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graphdistvisitor.cc.o
>> > [ 7%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graphnode.cc.o
>> > [ 7%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/graphvisitor.cc.o
>> > [ 8%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o
>> > [ 8%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o
>> > [ 8%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o
>> > [ 9%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o
>> > [ 9%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o
>> > [ 9%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o
>> > [ 10%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/property.cc.o
>> > [ 10%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
>> > [ 10%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
>> > [ 11%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducededge.cc.o
>> > [ 11%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/reducedgraph.cc.o
>> > [ 11%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/spline.cc.o
>> > [ 12%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/table.cc.o
>> > [ 12%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/thread.cc.o
>> > [ 12%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
>> > [ 13%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/version.cc.o
>> > gmake[2]: *** No rule to make target
>> 'MKL_ThreadingLibrary_LINK_LIBRARY-NOTFOUND', needed by
>> 'tools/src/libtools/libvotca_tools.so.6'. Stop.
>> > CMakeFiles/Makefile2:256: recipe for target
>> 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
>> > gmake[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error
>> 2
>> > Makefile:129: recipe for target 'all' failed
>> > gmake: *** [all] Error 2
>> >
>> > I have attached the output for cmake --build builddir --verbose
>> >
>> > Thanks
>> > Nancy
>> >
>> > On Tuesday, 1 December 2020 at 14:46:11 UTC+1 Christoph Junghans wrote:
>> >>
>> >> On Tue, Dec 1, 2020 at 3:00 AM nancyfor <[email protected]> wrote:
>> >> >
>> >> > Hi Christoph,
>> >> >
>> >> > I thought I was using gcc. I did not change anything on purpose. So,
>> to be a little bit more consistent, I checked again the gcc and the boost
>> version that worked together, and include the flag
>> -DCMAKE_CXX_COMPILER_ID=GNU (is this alright?) Currently I have the
>> following modules uploaded:
>> >> >
>> >> > mkl/2020.1
>> >> > gromacs/2019.4
>> >> > doxygen/1.8
>> >> > cmake/3.15
>> >> > clang/10.0
>> >> > gcc/8
>> >> > boost/1.66
>> >> > libxc/4.3.4
>> >> > fftw-serial/3.3.8
>> >> > hdf5-serial/1.8.21
>> >> >
>> >> > Un run the following with the new library paths (I have attached the
>> CMakeOutput.log and the output from "cmake -Bbuilddir ../votca"
>> output_cmake_Bbuildir.txt)
>> >> >
>> >> > cmake -Bbuilddir -DCMAKE_CXX_COMPILER_ID=GNU -DBUILD_CSGAPPS=ON
>> -DBUILD_XTP=ON
>> -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>>
>> -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>>
>> -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/include/
>>
>> -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_8-8.4.0/4.3.4/lib/libxc.a
>>
>> -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >> >
>> >> > and again when doing
>> >> > cmake --build builddir --verbose
>> >> > I get an error, different from the origina one I mentioned. The full
>> output is in cmake_verbose.txt
>> >> Thanks, the cmake log says:
>> >>
>> >> The C compiler identification is GNU 4.8.5
>> >>
>> >> GCC 4.8.5 is unfortunately too old as it misses some C++-11 features,
>> >> you mentioned a "gcc/8" in your first email, maybe you can try to use
>> >> that one instead. I guess something like "-DCMAKE_CXX_COMPILER=g++-8"
>> >>
>> >> Christoph
>> >>
>> >>
>> >> >
>> >> > Thanks
>> >> > Nancy
>> >> > On Monday, 30 November 2020 at 17:08:19 UTC+1 Christoph Junghans
>> wrote:
>> >> >>
>> >> >> Nancy,
>> >> >>
>> >> >> Are you trying to compile with gcc or icc?
>> >> >>
>> >> >> Could you attach the full output of "cmake -Bbuilddir ../votca" and
>> >> >> "cmake --build builddir --verbose" (mind the extra "--verbose"
>> here)?
>> >> >>
>> >> >> Thanks,
>> >> >>
>> >> >> Christoph
>> >> >>
>> >> >> On Mon, Nov 30, 2020 at 8:18 AM nancyfor <[email protected]>
>> wrote:
>> >> >> >
>> >> >> > Hello everybody,
>> >> >> >
>> >> >> > I am trying to install votca version 1.6.2 in a supercomputer.
>> After succesffully configure using the following modules:
>> >> >> >
>> >> >> > intel/19.1.1
>> >> >> > impi/2019.7
>> >> >> > mkl/2020.1
>> >> >> > gromacs/2019.4
>> >> >> > libxc/4.3.4
>> >> >> > doxygen/1.8
>> >> >> > cmake/3.15 (version 3.13 incompatible with doxygen 1.8)
>> >> >> > clang/10.0
>> >> >> > hdf5-serial/1.8.21
>> >> >> > fftw-serial/3.3.8
>> >> >> > boost/1.73
>> >> >> > with gcc version 9.3.0
>> >> >> >
>> >> >> > and
>> >> >> >
>> >> >> > cmake -Bbuilddir -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON
>> -DGROMACS_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/include/
>>
>> -DGROMACS_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a
>>
>> -DLIBXC_INCLUDE_DIR=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/
>>
>> -DLIBXC_LIBRARY=/mpcdf/soft/SLE_12/packages/skylake/libxc/gcc_10-10.2.0/4.3.4/lib/libxc.a
>>
>> -DCMAKE_INSTALL_PREFIX=${prefix} ../votca
>> >> >> >
>> >> >> > However when I try to run
>> >> >> >
>> >> >> > cmake --build builddir
>> >> >> >
>> >> >> > I got the following:
>> >> >> >
>> >> >> > Current git revision is 9b6bbd0
>> >> >> > [ 0%] Built target gitversion-xtp
>> >> >> > Current git revision is 9b6bbd0
>> >> >> > [ 0%] Built target gitversion
>> >> >> > [ 0%] Building CXX object
>> tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
>> >> >> > In file included from
>> /u/forero/src/votca/tools/include/votca/tools/property.h:23:0,
>> >> >> > from
>> /u/forero/src/votca/tools/include/votca/tools/application.h:21,
>> >> >> > from /u/forero/src/votca/tools/src/libtools/application.cc:19:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:107:3:
>> error: ‘unique_ptr’ in namespace ‘std’ does not name a type
>> >> >> > std::unique_ptr<boost::tokenizer<boost::char_separator<char>>>
>> tok;
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: In
>> constructor ‘votca::tools::Tokenizer::Tokenizer(const string&, const
>> char*)’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:5:
>> error: ‘tok’ was not declared in this scope
>> >> >> > tok =
>> std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:11:
>> error: ‘make_unique’ is not a member of ‘std’
>> >> >> > tok =
>> std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:50:73:
>> error: expected primary-expression before ‘>’ token
>> >> >> > tok =
>> std::make_unique<boost::tokenizer<boost::char_separator<char>>>(_str,
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:51:75:
>> warning: left operand of comma operator has no effect [-Wunused-value]
>> >> >> > sep);
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: In
>> member function ‘votca::tools::Tokenizer::iterator
>> votca::tools::Tokenizer::begin()’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:60:29:
>> error: ‘tok’ was not declared in this scope
>> >> >> > iterator begin() { return tok->begin(); }
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h: In
>> member function ‘votca::tools::Tokenizer::iterator
>> votca::tools::Tokenizer::end()’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/tokenizer.h:65:27:
>> error: ‘tok’ was not declared in this scope
>> >> >> > iterator end() { return tok->end(); }
>> >> >> > ^
>> >> >> > In file included from
>> /u/forero/src/votca/tools/include/votca/tools/application.h:21:0,
>> >> >> > from /u/forero/src/votca/tools/src/libtools/application.cc:19:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: In
>> constructor ‘votca::tools::Property::Property(const string&, const string&,
>> const string&)’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
>> >> >> > : _name(name), _value(value), _path(path) {}
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:59:7:
>> warning: declaration of ‘name’ shadows a member of 'this' [-Wshadow]
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: In
>> member function ‘votca::tools::Property& votca::tools::Property::set(const
>> string&, const string&)’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:248:56:
>> warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
>> >> >> > const std::string &value) {
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: In
>> member function ‘votca::tools::Property& votca::tools::Property::add(const
>> string&, const string&)’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:255:56:
>> warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
>> >> >> > const std::string &value) {
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:256:15:
>> warning: declaration of ‘path’ shadows a member of 'this' [-Wshadow]
>> >> >> > std::string path = _path;
>> >> >> > ^
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h: In
>> member function ‘void votca::tools::Property::setAttribute(const string&,
>> const T&)’:
>> >> >> > /u/forero/src/votca/tools/include/votca/tools/property.h:420:50:
>> warning: declaration of ‘value’ shadows a member of 'this' [-Wshadow]
>> >> >> > const T &value) {
>> >> >> > ^
>> >> >> > tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:75:
>> recipe for target
>> 'tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o' failed
>> >> >> > gmake[2]: ***
>> [tools/src/libtools/CMakeFiles/votca_tools.dir/application.cc.o] Error 1
>> >> >> > CMakeFiles/Makefile2:256: recipe for target
>> 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed
>> >> >> > gmake[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all]
>> Error 2
>> >> >> > Makefile:129: recipe for target 'all' failed
>> >> >> > gmake: *** [all] Error 2
>> >> >> >
>> >> >> > Does anyone have an idea of what might be the problem. I tried
>> different combinations of the gcc version and the boost without success.
>> >> >> >
>> >> >> > Best regards,
>> >> >> > Nancy
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> >> > ---
>> >> >> > You received this message because you are subscribed to the
>> Google Groups "votca" group.
>> >> >> > To unsubscribe from this group and stop receiving emails from it,
>> send an email to [email protected].
>> >> >> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/41e71c8f-bef2-4df9-85ae-dcdc81474176n%40googlegroups.com.
>>
>>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
>> >> > --
>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
>> >> > ---
>> >> > You received this message because you are subscribed to the Google
>> Groups "votca" group.
>> >> > To unsubscribe from this group and stop receiving emails from it,
>> send an email to [email protected].
>> >> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/27db68be-a714-4e69-92e0-a990dc90014en%40googlegroups.com.
>>
>>
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
>> > --
>> > Join us on Slack: https://join.slack.com/t/votca/signup
>> > ---
>> > You received this message because you are subscribed to the Google
>> Groups "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an email to [email protected].
>> > To view this discussion on the web visit
>> https://groups.google.com/d/msgid/votca/6815a3c7-fefc-4d92-b3f5-7703a3e8cbc4n%40googlegroups.com.
>>
>>
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>
--
Join us on Slack: https://join.slack.com/t/votca/signup
---
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To unsubscribe from this group and stop receiving emails from it, send an email
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forero@cobra01:~/src/votca> cmake --build builddir --verbose
/u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake
-S/u/forero/src/votca -B/u/forero/src/votca/builddir --check-build-system
CMakeFiles/Makefile.cmake 0
/u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E
cmake_progress_start /u/forero/src/votca/builddir/CMakeFiles
/u/forero/src/votca/builddir/CMakeFiles/progress.marks
/usr/bin/gmake -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/cobra/u/forero/src/votca/builddir'
/usr/bin/gmake -f xtp/src/libxtp/CMakeFiles/gitversion-xtp.dir/build.make
xtp/src/libxtp/CMakeFiles/gitversion-xtp.dir/depend
gmake[2]: Entering directory '/cobra/u/forero/src/votca/builddir'
cd /u/forero/src/votca/builddir &&
/u/system/soft/SLE_12/packages/x86_64/cmake/3.15.2/bin/cmake -E cmake_depends
"Unix Makefiles" /u/forero/src/votca /u/forero/src/votca/xtp/src/libxtp
/u/forero/src/votca/builddir /u/forero/src/votca/builddir/xtp/src/libxtp
/u/forero/src/votca/builddir/xtp/src/libxtp/CMakeFiles/gitversion-xtp.dir/DependInfo.cmake
--color=
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relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(forcefieldparameters.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z8pr_titleP8_IO_FILEiPKc' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(idef.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(mtop_util.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z11init_blockaP8t_blocka' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(symtab.cpp.o):
relocation R_X86_64_PC32 against symbol
`_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm@@GLIBCXX_3.4.21'
can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(topsort.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(alignedallocator.cpp.o):
relocation R_X86_64_PC32 against symbol `posix_memalign@@GLIBC_2.2.5' can not
be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(cstringutil.cpp.o):
relocation R_X86_64_PC32 against symbol `strlen@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(datafilefinder.cpp.o):
relocation R_X86_64_PC32 against symbol `_ZN3gmx17getProgramContextEv' can not
be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(directoryenumerator.cpp.o):
relocation R_X86_64_PC32 against symbol
`_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm@@GLIBCXX_3.4.21'
can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(errorcodes.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(errorformat.cpp.o):
relocation R_X86_64_PC32 against symbol `_ZN3gmx17getProgramContextEv' can not
be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(exceptions.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(filestream.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(gmxassert.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(keyvaluetreeserializer.cpp.o):
relocation R_X86_64_PC32 against symbol `_Znwm@@GLIBCXX_3.4' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(checkpoint.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(filetypes.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(g96io.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z6fgets2PciP8_IO_FILE' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(gmxfio-xdr.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(gmxfio.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z9gmx_fseekP8_IO_FILEli' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(groio.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(libxdrf.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z9gmx_ftellP8_IO_FILE' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(md5.cpp.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(pdbio.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(readinp.cpp.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(timecontrol.cpp.o):
relocation R_X86_64_32 against `.bss' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(tngio.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(trrio.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(warninp.cpp.o):
relocation R_X86_64_PC32 against symbol `strlen@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(xdrd.cpp.o):
relocation R_X86_64_PC32 against symbol `xdr_int@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(pull.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z8pbc_dx_dPK5t_pbcPKdS3_Pd' can not
be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(pullutil.cpp.o):
relocation R_X86_64_PC32 against symbol `_ZNK3gmx12LocalAtomSet10localIndexEv'
can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(awh.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(bias.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(biasparams.cpp.o):
relocation R_X86_64_PC32 against symbol `pow@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(biassharing.cpp.o):
relocation R_X86_64_PC32 against symbol `_Znwm@@GLIBCXX_3.4' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(biasstate.cpp.o):
relocation R_X86_64_PC32 against symbol `exp@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(biaswriter.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(coordstate.cpp.o):
relocation R_X86_64_PC32 against symbol `_ZNK3gmx4Grid12nearestIndexEPKd' can
not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(correlationgrid.cpp.o):
relocation R_X86_64_PC32 against symbol `_ZN3gmx17CorrelationTensorC1Eiid' can
not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(correlationhistory.cpp.o):
relocation R_X86_64_PC32 against symbol
`_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm@@GLIBCXX_3.4.21'
can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(correlationtensor.cpp.o):
relocation R_X86_64_PC32 against symbol `sqrt@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(grid.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(histogramsize.cpp.o):
relocation R_X86_64_PC32 against symbol `memset@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(pointstate.cpp.o):
relocation R_X86_64_PC32 against symbol `exp@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(network.cpp.o):
relocation R_X86_64_PC32 against symbol `strlen@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(gmx_omp_nthreads.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(tng_io.c.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(md5.c.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(compress.c.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(deflate.c.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(trees.c.o):
relocation R_X86_64_32S against symbol `_length_code' can not be used when
making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(uncompr.c.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(zutil.c.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(filenm.cpp.o):
relocation R_X86_64_PC32 against symbol `strcmp@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(localatomsetmanager.cpp.o):
relocation R_X86_64_PC32 against symbol `_Znwm@@GLIBCXX_3.4' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(df_history.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(wallcycle.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(atomprop.cpp.o):
relocation R_X86_64_PC32 against symbol
`_Z26gmx_residuetype_is_proteinP17gmx_residuetype_tPKc' can not be used when
making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(exclusionblocks.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(residuetypes.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(basenetwork.cpp.o):
relocation R_X86_64_PC32 against symbol `debug' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(binaryinformation.cpp.o):
relocation R_X86_64_PC32 against symbol `_Z11gmx_versionv' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(coolstuff.cpp.o):
relocation R_X86_64_PC32 against symbol
`_ZNSt13random_device7_M_initERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@@GLIBCXX_3.4.21'
can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(int64_to_int.cpp.o):
relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(logger.cpp.o):
relocation R_X86_64_PC32 against symbol
`_ZN3gmx13formatStringVB5cxx11EPKcP13__va_list_tag' can not be used when making
a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(niceheader.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(pleasecite.cpp.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(strdb.cpp.o):
relocation R_X86_64_PC32 against symbol `fgets@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(sysinfo.cpp.o):
relocation R_X86_64_PC32 against symbol `gethostname@@GLIBC_2.2.5' can not be
used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(textreader.cpp.o):
relocation R_X86_64_PC32 against symbol `_Znwm@@GLIBCXX_3.4' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(enxio.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(xvgr.cpp.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(tng_compress.c.o):
relocation R_X86_64_PC32 against symbol `Ptngc_coder_init' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(crc32.c.o):
relocation R_X86_64_32 against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(inflate.c.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(inftrees.c.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(localatomsetdata.cpp.o):
relocation R_X86_64_PC32 against symbol `_Znwm@@GLIBCXX_3.4' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(coder.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(warnmalloc.c.o):
relocation R_X86_64_PC32 against symbol `malloc@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(xtc2.c.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(xtc3.c.o):
relocation R_X86_64_PC32 against symbol `memset@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(inffast.c.o):
relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(bwlzh.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(bwt.c.o):
relocation R_X86_64_PC32 against symbol `Ptngc_bwt_merge_sort_inner' can not
be used when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(huffmem.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(lz77.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(mtf.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(widemuldiv.c.o):
relocation R_X86_64_PC32 against symbol `memset@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(dict.c.o):
relocation R_X86_64_PC32 against symbol `memset@@GLIBC_2.2.5' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(huffman.c.o):
relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a
shared object; recompile with -fPIC
/usr/bin/ld:
/mpcdf/soft/SLE_12/packages/skylake/gromacs/gcc_8-8.4.0-impi_2019.7-2019.7.217/2019.4/lib64/libgromacs.a(merge_sort.c.o):
relocation R_X86_64_PC32 against symbol `memcpy@@GLIBC_2.14' can not be used
when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: nonrepresentable section on output
collect2: error: ld returned 1 exit status
csg/src/libcsg/CMakeFiles/votca_csg.dir/build.make:798: recipe for target
'csg/src/libcsg/libvotca_csg.so.6' failed
gmake[2]: *** [csg/src/libcsg/libvotca_csg.so.6] Error 1
gmake[2]: Leaving directory '/cobra/u/forero/src/votca/builddir'
CMakeFiles/Makefile2:590: recipe for target
'csg/src/libcsg/CMakeFiles/votca_csg.dir/all' failed
gmake[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2
gmake[1]: Leaving directory '/cobra/u/forero/src/votca/builddir'
Makefile:129: recipe for target 'all' failed
gmake: *** [all] Error 2
