Hi.Could you please help me with installation abinit under kubuntu. I'm a newbie both in linux and in abinit so I'd appreciate any help. Here is the problem.
I've downloaded abinit-5.8.4, unpacked it and moved to it's folder. Then i typed
sudo ./configure
and after I've entered my password everything was done OK (at least there were no err messages in output). The last line in the outptut was
Configuration complete.
You may now type "make" to build ABINIT.
(or "make mj4", "make multi" or "make multi_alt" on a SMP machine)
So I've typed
sudo make
and here is what I've got
make all-recursive
make[1]: Entering directory `/home/rs/abinit-5.8.4'
Making all in prereqs
make[2]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
Making all in linalg
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
make[2]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
Making all in plugins
make[2]: Entering directory `/home/rs/abinit-5.8.4/plugins'
Making all in netcdf
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/netcdf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/netcdf'
Making all in etsf_io
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
Making all in libxc
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/libxc'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/libxc'
Making all in bigdft
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make -f ../../plugins/bigdft/bigdft.mk
make[4]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
gzip -cd /home/rs/.abinit/tarballs/bigdft-1.2.0.2.tar.gz | tar xf -
cd bigdft-1.2.0.2 && patch -p1 < /home/rs/abinit-5.8.4/plugins/bigdft/bigdft-1.2.0.2-0001.patch
/bin/sh: patch: not found
make[4]: *** [uncompress-stamp] Error 127
make[4]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rs/abinit-5.8.4/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rs/abinit-5.8.4'
make: *** [all] Error 2
So could you please tell me what's wrong.
Thank you in advance!
[SOLVED] Need help with abinit installation under kubuntu
Moderators: fgoudreault, mcote
Forum rules
Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Please have a look at ~abinit/doc/config/build-config.ac in the source package for detailed and up-to-date information about the configuration of Abinit 8 builds.
For a video explanation on how to build Abinit 7.x for Linux, please go to: http://www.youtube.com/watch?v=DppLQ-KQA68.
IMPORTANT: when an answer solves your problem, please check the little green V-like button on its upper-right corner to accept it.
Re: Need help with abinit installation under kubuntu
The configure script should never be run with sudo, since it may damage your system in a totally unpredictible way and because then the files will belong to root, not to you anymore.
I suggest you run a "sudo chown -R <username>:<username> ." (where <username> is your login) in your source tree before restarting the whole process.
I suggest you run a "sudo chown -R <username>:<username> ." (where <username> is your login) in your source tree before restarting the whole process.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
Simune Atomistics
Donostia-San Sebastián, Spain
Re: Need help with abinit installation under kubuntu
So as I have understood I just have to become owner of "abinit-5.8.4" folder and all the files in it and then run "configure" without sudo. I thought I'm it's owner already as I've downloaded and unzipped it running under my account. Somehow or other I'll try what you adviced. Thanks for the help!
Re: Need help with abinit installation under kubuntu
I've just done as you suggested. Unfortunately result is the same 
What should I do now? Here is copy-paste from bash (just in case).
rs@LinuxPC:~/abinit-5.8.4$ sudo chown -R rs:rs .
rs@LinuxPC:~/abinit-5.8.4$ ./configure
==============================================================================
=== Overall startup ===
==============================================================================
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) mawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
==============================================================================
=== Build-system information ===
==============================================================================
configure: ABINIT version: 5.8.4
configure: M4 010411 - Autoconf 026200 - Automake 011001 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-macroave is available
configure: * new option --enable-gsl is available
configure: * new option --with-gsl-includes is available
configure: * new option --with-gsl-libs is available
configure: * new option --enable-exports is available
configure: * new option --with-ar-dbgflags is available
configure: * new option --with-cpp-dbgflags is available
configure: * new option --with-cc-dbgflags is available
configure: * new option --with-cc-ld-dbgflags is available
configure: * new option --with-cc-ld-dbglibs is available
configure: * new option --with-cxx-dbgflags is available
configure: * new option --with-cxx-ld-dbgflags is available
configure: * new option --with-cxx-ld-dbglibs is available
configure: * new option --with-fc-dbgflags is available
configure: * new option --with-fc-ld-dbgflags is available
configure: * new option --with-fc-ld-dbglibs is available
configure: * new option --enable-env-file is available
configure: * new option --enable-mpi-io-buggy is available
configure: * new option --enable-papi is available
configure: * new option --with-papi-includes is available
configure: * new option --with-papi-libs is available
configure: * --with-fc-vendor has a new meaning
configure: please check that with-fc-vendor="" is OK for you
configure: * new option --with-fc-version is available
configure: * --enable-etsf-xc renamed --enable-libxc
configure: * --with-etsf-xc-includes renamed --with-libxc-includes
configure: * --with-etsf-xc-libs renamed --with-libxc-libs
==============================================================================
=== Option consistency checking ===
==============================================================================
configure: checking consistency of MPI options
configure: |---> all OK
configure:
configure: checking consistency of external prerequisite options
configure: |---> all OK
configure:
configure: checking consistency of plug-in options
configure: |---> all OK
configure:
configure: parsing command-line options
==============================================================================
=== MPI startup ===
==============================================================================
checking for MPI support requested... no
+--------------------------------------------------------------+
| IMPORTANT NOTE |
+--------------------------------------------------------------+
| MPI support is disabled by default because it makes the |
| configure script abort when the build environment is not |
| properly set-up. |
| |
| You may activate it using the --enable-mpi="yes" |
| option, provided that the PATH and LD_LIBRARY_PATH |
| environment variables are properly set-up. If this is not |
| the case, the configure script will abort with the following |
| error message: |
| |
| configure: error: cannot run C compiled programs. |
| If you meant to cross compile, use `--host'. |
| See `config.log' for more details. |
+--------------------------------------------------------------+
==============================================================================
=== Utilities ===
==============================================================================
checking for sh... /bin/sh
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for mv... /bin/mv
checking for tar... /bin/tar
checking for latex... /bin/false
checking for dvips... /bin/false
checking for dvipdf... /usr/bin/dvipdf
checking for ps2pdf... /usr/bin/ps2pdf
checking for markdown... no
checking for wget... /usr/bin/wget
configure: using internal version of MarkDown
==============================================================================
=== Preprocessing ===
==============================================================================
checking for style of include used by make... GNU
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for the true C preprocessor... /lib/cpp
checking for C preprocessor options... -P -std=c89
==============================================================================
=== C support ===
==============================================================================
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking which type of compiler we have... gnu gcc
configure: applying C compiler tricks (type: gnu, version: gcc)
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 whether byte ordering is bigendian... no
==============================================================================
=== C++ support ===
==============================================================================
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
checking which type of C++ compiler we have... generic 0.0
configure: applying C++ compiler tricks (type: generic, version: 0.0)
==============================================================================
=== Fortran support ===
==============================================================================
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.4
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts gamma()... yes
configure: applying Fortran compiler tricks (type: gnu, version: 4.4)
checking whether to use C clock for timings... no
==============================================================================
=== Python support ===
==============================================================================
checking for python... python
checking for python-config... no
checking for python2.6-config... no
checking for python2.5-config... no
checking for python2.4-config... no
checking for Python CPPFLAGS...
checking for bzr... no
==============================================================================
=== Libraries and linking ===
==============================================================================
checking for ar... /usr/bin/ar
checking for ranlib... ranlib
==============================================================================
=== 64-bit support ===
==============================================================================
configure: this section is still under development
checking for a 64-bit architecture... no
==============================================================================
=== Optimizations and debugging ===
==============================================================================
checking for optimization level... standard
configure: loading optimizations for cc: gnu/all/amd_athlon
configure: loading optimizations for cxx: generic/all/all
configure: loading optimizations for fc: gnu/all/amd_athlon
configure: setting C debug flags to '-g'
configure: setting Fortran debug flags to '-g'
==============================================================================
=== MPI support ===
==============================================================================
checking whether MPI is usable... no
checking whether to build parallel code... no
==============================================================================
=== External prerequisites ===
==============================================================================
checking whether to use the FFTW library... no
checking whether to use the GNU Scientific Library... no
configure: applying linear algebra tricks (type: abinit)
checking whether to build the LINALG library... yes
checking whether to activate ScaLAPACK support... no
checking whether to use the PAPI library... no
==============================================================================
=== Plug-ins ===
==============================================================================
configure: using tarball repository /home/rs/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking for a source tarball of NETCDF... yes
configure: applying NetCDF tricks (vendor: gnu, version: 4.4)
checking whether to enable the NETCDF plug-in... yes
checking whether to build the NETCDF plug-in... yes
checking for a source tarball of ETSF_IO... yes
configure: applying ETSF_IO tricks (vendor: gnu, version: 4.4)
checking whether to enable the ETSF_IO plug-in... yes
checking whether to build the ETSF_IO plug-in... yes
checking for a source tarball of LIBXC... yes
configure: applying LIBXC tricks (not needed yet)
checking whether to enable the LIBXC plug-in... yes
checking whether to build the LIBXC plug-in... yes
checking for a source tarball of BIGDFT... yes
configure: applying BigDFT tricks (vendor: gnu, version: 4.4)
checking whether to enable the BIGDFT plug-in... yes
checking whether to build the BIGDFT plug-in... yes
checking whether to enable the XMLF90 plug-in... no
checking whether to build the XMLF90 plug-in... no
checking for a source tarball of WANNIER90... yes
configure: applying Wannier90 tricks (vendor: gnu, version: 4.4)
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes
==============================================================================
=== Nightly builds ===
==============================================================================
checking whether to build Nightly code... no
==============================================================================
=== Experimental developments ===
==============================================================================
checking whether to enable bindings... no
checking whether to enable error handlers... no
checking whether to build exports... no
checking whether to enable GW double-precision calculations... no
checking whether to use macroave... yes
==============================================================================
=== Output ===
==============================================================================
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.py
config.status: creating config.sh
config.status: creating config.dump
config.status: creating config/wrappers/wrap-fc
config.status: creating plugins/xmlf90/build.mk
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating tests/tests.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/interfaces/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/32_contract/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/42_geometry/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/47_papi_counters/Makefile
config.status: creating src/50_abitypes_defs/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_bader/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/67_recursion/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/68_gw/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/72_geomoptim/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/93_rdm/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating src/nightly/Makefile
config.status: creating prereqs/Makefile
config.status: creating prereqs/linalg/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/fox/Makefile
config.status: creating plugins/netcdf/Makefile
config.status: creating plugins/etsf_io/Makefile
config.status: creating plugins/libxc/Makefile
config.status: creating plugins/bigdft/Makefile
config.status: creating plugins/wannier90/Makefile
config.status: creating plugins/xmlf90/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating doc/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing script-perms commands
Configuration complete.
You may now type "make" to build ABINIT.
(or "make mj4", "make multi" or "make multi_alt" on a SMP machine)
rs@LinuxPC:~/abinit-5.8.4$ make
make all-recursive
make[1]: Entering directory `/home/rs/abinit-5.8.4'
Making all in prereqs
make[2]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
Making all in linalg
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
make[2]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
Making all in plugins
make[2]: Entering directory `/home/rs/abinit-5.8.4/plugins'
Making all in netcdf
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/netcdf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/netcdf'
Making all in etsf_io
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
Making all in libxc
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/libxc'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/libxc'
Making all in bigdft
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make -f ../../plugins/bigdft/bigdft.mk
make[4]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
gzip -cd /home/rs/.abinit/tarballs/bigdft-1.2.0.2.tar.gz | tar xf -
cd bigdft-1.2.0.2 && patch -p1 < /home/rs/abinit-5.8.4/plugins/bigdft/bigdft-1.2.0.2-0001.patch
/bin/sh: patch: not found
make[4]: *** [uncompress-stamp] Error 127
make[4]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rs/abinit-5.8.4/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rs/abinit-5.8.4'
make: *** [all] Error 2
rs@LinuxPC:~/abinit-5.8.4$
What should I do now? Here is copy-paste from bash (just in case).rs@LinuxPC:~/abinit-5.8.4$ sudo chown -R rs:rs .
rs@LinuxPC:~/abinit-5.8.4$ ./configure
==============================================================================
=== Overall startup ===
==============================================================================
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) mawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
==============================================================================
=== Build-system information ===
==============================================================================
configure: ABINIT version: 5.8.4
configure: M4 010411 - Autoconf 026200 - Automake 011001 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-macroave is available
configure: * new option --enable-gsl is available
configure: * new option --with-gsl-includes is available
configure: * new option --with-gsl-libs is available
configure: * new option --enable-exports is available
configure: * new option --with-ar-dbgflags is available
configure: * new option --with-cpp-dbgflags is available
configure: * new option --with-cc-dbgflags is available
configure: * new option --with-cc-ld-dbgflags is available
configure: * new option --with-cc-ld-dbglibs is available
configure: * new option --with-cxx-dbgflags is available
configure: * new option --with-cxx-ld-dbgflags is available
configure: * new option --with-cxx-ld-dbglibs is available
configure: * new option --with-fc-dbgflags is available
configure: * new option --with-fc-ld-dbgflags is available
configure: * new option --with-fc-ld-dbglibs is available
configure: * new option --enable-env-file is available
configure: * new option --enable-mpi-io-buggy is available
configure: * new option --enable-papi is available
configure: * new option --with-papi-includes is available
configure: * new option --with-papi-libs is available
configure: * --with-fc-vendor has a new meaning
configure: please check that with-fc-vendor="" is OK for you
configure: * new option --with-fc-version is available
configure: * --enable-etsf-xc renamed --enable-libxc
configure: * --with-etsf-xc-includes renamed --with-libxc-includes
configure: * --with-etsf-xc-libs renamed --with-libxc-libs
==============================================================================
=== Option consistency checking ===
==============================================================================
configure: checking consistency of MPI options
configure: |---> all OK
configure:
configure: checking consistency of external prerequisite options
configure: |---> all OK
configure:
configure: checking consistency of plug-in options
configure: |---> all OK
configure:
configure: parsing command-line options
==============================================================================
=== MPI startup ===
==============================================================================
checking for MPI support requested... no
+--------------------------------------------------------------+
| IMPORTANT NOTE |
+--------------------------------------------------------------+
| MPI support is disabled by default because it makes the |
| configure script abort when the build environment is not |
| properly set-up. |
| |
| You may activate it using the --enable-mpi="yes" |
| option, provided that the PATH and LD_LIBRARY_PATH |
| environment variables are properly set-up. If this is not |
| the case, the configure script will abort with the following |
| error message: |
| |
| configure: error: cannot run C compiled programs. |
| If you meant to cross compile, use `--host'. |
| See `config.log' for more details. |
+--------------------------------------------------------------+
==============================================================================
=== Utilities ===
==============================================================================
checking for sh... /bin/sh
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for mv... /bin/mv
checking for tar... /bin/tar
checking for latex... /bin/false
checking for dvips... /bin/false
checking for dvipdf... /usr/bin/dvipdf
checking for ps2pdf... /usr/bin/ps2pdf
checking for markdown... no
checking for wget... /usr/bin/wget
configure: using internal version of MarkDown
==============================================================================
=== Preprocessing ===
==============================================================================
checking for style of include used by make... GNU
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for the true C preprocessor... /lib/cpp
checking for C preprocessor options... -P -std=c89
==============================================================================
=== C support ===
==============================================================================
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking which type of compiler we have... gnu gcc
configure: applying C compiler tricks (type: gnu, version: gcc)
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 whether byte ordering is bigendian... no
==============================================================================
=== C++ support ===
==============================================================================
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
checking which type of C++ compiler we have... generic 0.0
configure: applying C++ compiler tricks (type: generic, version: 0.0)
==============================================================================
=== Fortran support ===
==============================================================================
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.4
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts gamma()... yes
configure: applying Fortran compiler tricks (type: gnu, version: 4.4)
checking whether to use C clock for timings... no
==============================================================================
=== Python support ===
==============================================================================
checking for python... python
checking for python-config... no
checking for python2.6-config... no
checking for python2.5-config... no
checking for python2.4-config... no
checking for Python CPPFLAGS...
checking for bzr... no
==============================================================================
=== Libraries and linking ===
==============================================================================
checking for ar... /usr/bin/ar
checking for ranlib... ranlib
==============================================================================
=== 64-bit support ===
==============================================================================
configure: this section is still under development
checking for a 64-bit architecture... no
==============================================================================
=== Optimizations and debugging ===
==============================================================================
checking for optimization level... standard
configure: loading optimizations for cc: gnu/all/amd_athlon
configure: loading optimizations for cxx: generic/all/all
configure: loading optimizations for fc: gnu/all/amd_athlon
configure: setting C debug flags to '-g'
configure: setting Fortran debug flags to '-g'
==============================================================================
=== MPI support ===
==============================================================================
checking whether MPI is usable... no
checking whether to build parallel code... no
==============================================================================
=== External prerequisites ===
==============================================================================
checking whether to use the FFTW library... no
checking whether to use the GNU Scientific Library... no
configure: applying linear algebra tricks (type: abinit)
checking whether to build the LINALG library... yes
checking whether to activate ScaLAPACK support... no
checking whether to use the PAPI library... no
==============================================================================
=== Plug-ins ===
==============================================================================
configure: using tarball repository /home/rs/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking for a source tarball of NETCDF... yes
configure: applying NetCDF tricks (vendor: gnu, version: 4.4)
checking whether to enable the NETCDF plug-in... yes
checking whether to build the NETCDF plug-in... yes
checking for a source tarball of ETSF_IO... yes
configure: applying ETSF_IO tricks (vendor: gnu, version: 4.4)
checking whether to enable the ETSF_IO plug-in... yes
checking whether to build the ETSF_IO plug-in... yes
checking for a source tarball of LIBXC... yes
configure: applying LIBXC tricks (not needed yet)
checking whether to enable the LIBXC plug-in... yes
checking whether to build the LIBXC plug-in... yes
checking for a source tarball of BIGDFT... yes
configure: applying BigDFT tricks (vendor: gnu, version: 4.4)
checking whether to enable the BIGDFT plug-in... yes
checking whether to build the BIGDFT plug-in... yes
checking whether to enable the XMLF90 plug-in... no
checking whether to build the XMLF90 plug-in... no
checking for a source tarball of WANNIER90... yes
configure: applying Wannier90 tricks (vendor: gnu, version: 4.4)
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes
==============================================================================
=== Nightly builds ===
==============================================================================
checking whether to build Nightly code... no
==============================================================================
=== Experimental developments ===
==============================================================================
checking whether to enable bindings... no
checking whether to enable error handlers... no
checking whether to build exports... no
checking whether to enable GW double-precision calculations... no
checking whether to use macroave... yes
==============================================================================
=== Output ===
==============================================================================
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.py
config.status: creating config.sh
config.status: creating config.dump
config.status: creating config/wrappers/wrap-fc
config.status: creating plugins/xmlf90/build.mk
config.status: creating src/16_hideleave/m_build_info.F90
config.status: creating tests/tests.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/10_defs/Makefile
config.status: creating src/interfaces/Makefile
config.status: creating src/01_gsl_ext/Makefile
config.status: creating src/01_macroavnew_ext/Makefile
config.status: creating src/12_hide_mpi/Makefile
config.status: creating src/14_hidewrite/Makefile
config.status: creating src/16_hideleave/Makefile
config.status: creating src/18_timing/Makefile
config.status: creating src/27_toolbox_oop/Makefile
config.status: creating src/28_numeric_noabirule/Makefile
config.status: creating src/32_util/Makefile
config.status: creating src/32_contract/Makefile
config.status: creating src/42_parser/Makefile
config.status: creating src/42_geometry/Makefile
config.status: creating src/42_nlstrain/Makefile
config.status: creating src/47_xml/Makefile
config.status: creating src/47_papi_counters/Makefile
config.status: creating src/50_abitypes_defs/Makefile
config.status: creating src/51_manage_mpi/Makefile
config.status: creating src/52_fft_mpi_noabirule/Makefile
config.status: creating src/53_abiutil/Makefile
config.status: creating src/53_spacepar/Makefile
config.status: creating src/53_ffts/Makefile
config.status: creating src/56_xc/Makefile
config.status: creating src/56_recipspace/Makefile
config.status: creating src/57_iovars/Makefile
config.status: creating src/59_io_mpi/Makefile
config.status: creating src/61_ionetcdf/Makefile
config.status: creating src/62_cg_noabirule/Makefile
config.status: creating src/62_poisson/Makefile
config.status: creating src/62_wvl_wfs/Makefile
config.status: creating src/62_iowfdenpot/Makefile
config.status: creating src/62_bader/Makefile
config.status: creating src/62_occeig/Makefile
config.status: creating src/65_nonlocal/Makefile
config.status: creating src/65_psp/Makefile
config.status: creating src/66_wfs/Makefile
config.status: creating src/66_paw/Makefile
config.status: creating src/67_recursion/Makefile
config.status: creating src/67_common/Makefile
config.status: creating src/68_rsprc/Makefile
config.status: creating src/68_gw/Makefile
config.status: creating src/72_response/Makefile
config.status: creating src/72_geomoptim/Makefile
config.status: creating src/77_suscep/Makefile
config.status: creating src/77_lwf/Makefile
config.status: creating src/77_ddb/Makefile
config.status: creating src/79_seqpar_mpi/Makefile
config.status: creating src/83_cut3d/Makefile
config.status: creating src/93_rdm/Makefile
config.status: creating src/95_drive/Makefile
config.status: creating src/98_main/Makefile
config.status: creating src/libs/Makefile
config.status: creating src/nightly/Makefile
config.status: creating prereqs/Makefile
config.status: creating prereqs/linalg/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/fox/Makefile
config.status: creating plugins/netcdf/Makefile
config.status: creating plugins/etsf_io/Makefile
config.status: creating plugins/libxc/Makefile
config.status: creating plugins/bigdft/Makefile
config.status: creating plugins/wannier90/Makefile
config.status: creating plugins/xmlf90/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating doc/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing script-perms commands
Configuration complete.
You may now type "make" to build ABINIT.
(or "make mj4", "make multi" or "make multi_alt" on a SMP machine)
rs@LinuxPC:~/abinit-5.8.4$ make
make all-recursive
make[1]: Entering directory `/home/rs/abinit-5.8.4'
Making all in prereqs
make[2]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
Making all in linalg
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs/linalg'
make[3]: Entering directory `/home/rs/abinit-5.8.4/prereqs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
make[2]: Leaving directory `/home/rs/abinit-5.8.4/prereqs'
Making all in plugins
make[2]: Entering directory `/home/rs/abinit-5.8.4/plugins'
Making all in netcdf
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/netcdf'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/netcdf'
Making all in etsf_io
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/etsf_io'
Making all in libxc
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/libxc'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/libxc'
Making all in bigdft
make[3]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make -f ../../plugins/bigdft/bigdft.mk
make[4]: Entering directory `/home/rs/abinit-5.8.4/plugins/bigdft'
gzip -cd /home/rs/.abinit/tarballs/bigdft-1.2.0.2.tar.gz | tar xf -
cd bigdft-1.2.0.2 && patch -p1 < /home/rs/abinit-5.8.4/plugins/bigdft/bigdft-1.2.0.2-0001.patch
/bin/sh: patch: not found
make[4]: *** [uncompress-stamp] Error 127
make[4]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[3]: *** [package-ready] Error 2
make[3]: Leaving directory `/home/rs/abinit-5.8.4/plugins/bigdft'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rs/abinit-5.8.4/plugins'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rs/abinit-5.8.4'
make: *** [all] Error 2
rs@LinuxPC:~/abinit-5.8.4$
Re: Need help with abinit installation under kubuntu
Your development enviornment is incomplete. You need to install some packages first:
This should solve your problem.
Code: Select all
sudo aptitude --with-recommends install devscriptsThis should solve your problem.
Yann Pouillon
Simune Atomistics
Donostia-San Sebastián, Spain
Simune Atomistics
Donostia-San Sebastián, Spain
Re: Need help with abinit installation under kubuntu
Hello, pouillon. I've performed all in the way you told and had a success! I've also run my first abinit job following tutorial's 1st chapter.
Learning abinit is exciting, in spite of I've only just started! Many many thanks for the help! I wouldn't cope myself.
Learning abinit is exciting, in spite of I've only just started! Many many thanks for the help! I wouldn't cope myself.
Re: [SOLVED] Need help with abinit installation under kubuntu
I'm really sorry for disturbing you again, but I have a problem. I've decided to install the software on the second PC and it works OK when I run configure script. But when I run make install after that I get a lot of output and at the end it says
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
make[2]: *** [abinis] Error 1
make[2]: Leaving directory `/home/nvsaharov/abinit-5.8.4/src/98_main'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/nvsaharov/abinit-5.8.4/src'
make: *** [install-recursive] Error 1
I've missed the most of the output because it's too much I think to paste it here. I've previously run
sudo aptitude --with-recommends install devscripts
before running configure script to install devscripts package and not to have troubles I had first time. So tell me please what should I do now? Probably I have to download some additional packages? Thank you in advance.
P.S. When I run configure script first time it told me it does not find fortran compiler, so I think I've installed it running sudo aptitude install gfortran. After that I've run configure script again and it went OK, and after all I've had difficulties with make install, I've just described. Probably this will help you.
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
make[2]: *** [abinis] Error 1
make[2]: Leaving directory `/home/nvsaharov/abinit-5.8.4/src/98_main'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/nvsaharov/abinit-5.8.4/src'
make: *** [install-recursive] Error 1
I've missed the most of the output because it's too much I think to paste it here. I've previously run
sudo aptitude --with-recommends install devscripts
before running configure script to install devscripts package and not to have troubles I had first time. So tell me please what should I do now? Probably I have to download some additional packages? Thank you in advance.
P.S. When I run configure script first time it told me it does not find fortran compiler, so I think I've installed it running sudo aptitude install gfortran. After that I've run configure script again and it went OK, and after all I've had difficulties with make install, I've just described. Probably this will help you.
Re: [SOLVED] Need help with abinit installation under kubuntu
I'm sorry, force alarm. Everything OK now.