Installation fails, recipe for target 'all' failed

[Arash Elahi]

Hi All

I'm trying to install VOTCA, but I'm facing errors I couldn't resolve after days of struggling with this error in the title.

My OS version: Ubuntu 16.04

My local Gromcas: 2019.3

I appreciate your helps regarding this issue very much

VOTCA_install$ cmake -Bbuilddir -DBUILD_XTP=OFF -DBUILD_OWN_LIBINT=ON -DCMAKE_INSTALL_PREFIX=${prefix} ENABLE_TESTING=ON votca

-- MKL: Thread Layer(Intel OpenMP) Interface(4-byte Integer)

-- Found Boost: /usr/include (found suitable version "1.58.0", minimum required is "1.53.0") found components: program_options filesystem system 

-- MKL: Thread Layer(Intel OpenMP) Interface(4-byte Integer)

-- Found Eigen3: /usr/lib/cmake/eigen3

-- Found Boost: /usr/include (found suitable version "1.58.0", minimum required is "1.53.0") found components: program_options filesystem system regex 

-- Found Eigen3: /usr/lib/cmake/eigen3

-- Found VOTCA_TOOLS: 

-- Checking for module 'libgromacs_d'

--   No package 'libgromacs_d' found

-- Found HDF5: $HOME/anaconda3/lib/libhdf5_cpp.so;$HOME/anaconda3/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so;$HOME/anaconda3/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.17") found components: CXX 

-- Could NOT find LMP (missing: LMP_EXECUTABLE) 

-- Could NOT find CLANG_FORMAT: Found unsuitable version "6.0.1", but required is at least "11" (found /opt/moose/llvm-6.0.1/bin/clang-format)

-- The following features have been enabled:

 * BUILD_OWN_LIBINT, Build an internal version of libint

 * BUILD_MANPAGES, Build manpages (disable for cross-compile)

 * INSTALL_RC_FILES, Install votca rc files (VOTCARC.bash etc.)

-- The following OPTIONAL packages have been found:

 * Git

   Generated version for development version

 * OpenMP

 * MKL

   Enables accelerated performance with MKL

 * TXT2TAGS

   Used to build manpages

 * UnixCommands

   Used to build manpages

 * Python (required version >= 3)

   Used to build documentation files

 * Doxygen

   Needed to build API documentation

-- The following RECOMMENDED packages have been found:

 * PkgConfig

   Used to detect gromacs package

 * GROMACS (required version >= 2018)

   Used to read/write gromacs data files

 * HDF5

   Used to read h5md data files

-- The following REQUIRED packages have been found:

 * EXPAT

   Used for XML parsing

 * Boost (required version >= 1.53.0)

   Extended C++ libraries

 * Eigen3 (required version >= 3.3.0)

   C++ vector data structures

 * Threads

   Used for thread parallelization

-- The following features have been disabled:

 * BUILD_XTP, Build xtp module

 * ENABLE_TESTING, Enable unit tests

 * ENABLE_RPATH_INJECT, Inject rpath into executables

 * BUILD_OWN_GROMACS, Build an internal version of gromacs

 * BUILD_CSGAPPS, Install extra app using csg

 * ENABLE_REGRESSION_TESTING, Enable regression tests

-- The following OPTIONAL packages have not been found:

 * CLANG_FORMAT (required version >= 11)

-- Configuring done

-- Generating done

-- Build files have been written to: VOTCA_install/builddir

VOTCA_install$ cmake --build builddir/ --parallel 12

/usr/bin/ld: $HOME/Downloads/amber20_src/build/AmberTools/src/boost/stage/lib/libboost_program_options.a(cmdline.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC

$HOME/Downloads/amber20_src/build/AmberTools/src/boost/stage/lib/libboost_program_options.a: error adding symbols: Bad value

collect2: error: ld returned 1 exit status

tools/src/libtools/CMakeFiles/votca_tools.dir/build.make:681: recipe for target 'tools/src/libtools/libvotca_tools.so.2021' failed

make[2]: *** [tools/src/libtools/libvotca_tools.so.2021] Error 1

CMakeFiles/Makefile2:682: recipe for target 'tools/src/libtools/CMakeFiles/votca_tools.dir/all' failed

make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

checking target system type... x86_64-pc-linux-gnu

Using standard ordering of cartesian Gaussians

Using standard ordering of solid harmonic Gaussians

Will generate standard shell quartet sets

Will generate composite evaluators for multiple integral types

Shell sets will be unrolled up to size 100

Will generate single evaluator type

Will not generate FMA instructions

Will copy integrals to the buffer

FLOP counter will not be supported

Profiling instrumentation disabled

Will support contracted integrals

checking whether make sets $(MAKE)... yes

checking whether ln -s works... yes

checking for a BSD-compatible install... /usr/bin/install -c

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether mpicxx accepts -g... yes

checking how to run the C++ preprocessor... mpicxx -E

checking for ar... ar

checking for perl... perl

checking for gnutar... no

checking for tar... tar

checking for python... python

checking for doxygen... /opt/moose/doxygen-1.8.14/bin/doxygen

checking for pdflatex... no

checking for pslatex... no

checking for dvips... no

checking for latex... no

checking for latex2html... no

checking for bibtex... no

configure: WARNING: C++ optimization options are not given! For optimum performance give CXXGENFLAGS or use --with-cxxgen-optflags configure option

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -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 limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking for stdint.h... (cached) yes

checking for posix_memalign... yes

checking CXX for general C++11 support... yes

checking CXX for shared_ptr... yes

checking CXX for std::make_shared and std::allocate_shared... yes

checking CXX for type_traits... yes

checking CXX for array... yes

checking CXXGEN for general C++11 support... yes

checking gmpxx.h usability... no

checking gmpxx.h presence... no

checking for gmpxx.h... no

configure: error: cannot link against GMP C++ library. Please get the latest GMP with support for C++. It can be obtained at gmplib.org .

CMakeFiles/Libint_build.dir/build.make:91: recipe for target 'libint/src/Libint_build-stamp/Libint_build-configure' failed

make[2]: *** [libint/src/Libint_build-stamp/Libint_build-configure] Error 1

CMakeFiles/Makefile2:561: recipe for target 'CMakeFiles/Libint_build.dir/all' failed

make[1]: *** [CMakeFiles/Libint_build.dir/all] Error 2

Makefile:135: recipe for target 'all' failed

make: *** [all] Error 2

[Christoph Junghans]

On Fri, May 21, 2021 at 3:51 PM Arash Elahi <ael...@uic.edu> wrote:
>
> Hi All
> I'm trying to install VOTCA, but I'm facing errors I couldn't resolve after days of struggling with this error in the title.
> My OS version: Ubuntu 16.04
> My local Gromcas: 2019.3
> I appreciate your helps regarding this issue very much
> VOTCA_install$ cmake -Bbuilddir -DBUILD_XTP=OFF -DBUILD_OWN_LIBINT=ON -DCMAKE_INSTALL_PREFIX=${prefix} ENABLE_TESTING=ON votca

If you don't need xtp, you also don't need to build libint.

The error message basically says it, you need a shared (or version
compiled with -fPIC) of the boost library.

If you don't want to compile boost yourself, just try to use spack
instead, https://github.com/votca/votca/blob/master/share/doc/INSTALL.rst#spack

Christoph

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--
Christoph Junghans
Web: http://www.compphys.de

[Arash Elahi]

Thank you dear Christoph for your reply.

Spack was very helpful for the installation, but there's hdf5 inconsistency when I use smack, when I want to run the csg executables, let's say csg_map. installing hdf5 locally did not make it work out yet. Is it what I needed to do?

Thanks

Best

HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:

  #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:

  #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:

  #000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:

.....

[Christoph Junghans]

On Tue, Jun 1, 2021 at 11:10 AM Arash Elahi <ael...@uic.edu> wrote:
>
> Thank you dear Christoph for your reply.
> Spack was very helpful for the installation, but there's hdf5 inconsistency when I use smack, when I want to run the csg executables, let's say csg_map. installing hdf5 locally did not make it work out yet. Is it what I needed to do?

We already know about this issue:
https://github.com/votca/csg/issues/684, but haven't fixed it yet, as
it is only a warning, so please ignore it for now.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/4875b995-8512-4140-a81a-34798f089022n%40googlegroups.com.