The ABINIT Users Mailing List ( CLOSED )

[Alain Jacques <ajs.jacques@gmail.com>]

Hello Myrta, hello Aaron,

There should be no problem building and installing Abinit as a plain user.
Reading the log, it seems that a working fortran compiler cannot be found. May I do the following suggestions:

1) there i no need to invoque makemake. It is also a good practice to build abinit in its own directory. So untar the distribution file, cd abinit-5.6.4, mkdir tmp-build (as an example), cd tmp-build and invoque ../configure directly. And if anything goes wrong during the make part, you can restart with a clean setup with a "make clean" from here.

2) your LD_LIBRARY_PATH is getting a bit too complicated, making it easy to mix incompatible libraries. Try with a simpler export LD_LIBRARY_PATH=/home/opt/intel//fce/10.1.015/lib. Same story for PATH; check that it starts with /home/opt/intel//fce/10.1.015/bin. I assume that the Intel C compiler is also on your system. Add the corresponding libpath to LD_LIBRARY_PATH and execpath to PATH. Check that "ifort -v" and "icc -v" both work.

3) let try a simple config:
../configure --enable-64bit-flags CC=icc LDFLAGS="-L/home/opt/inte
l/cce/10.1.015/lib -L/home/opt/intel//fce/10.1.015/lib -L/usr/lib64" CXX=icpc FC=ifort CPPFLAGS="-I/home/opt/intel/cce/10.1.015/include -I/home/opt/intel/fce/10.1.015/include"
Check that there is no space between the -I or -L and the paths. If it goes up to the end, try a make ... have a cup of coffee. At the end, you should have ./src/main/abinis. what does it say?

All the plugins should be working. I suggest to rebuild with optimization on. Beeing on a cluster, you'll probably want openmpi or similar.

Kind regards,

Alain


阿火 wrote:

4101f9fe0812250330u23342f2bxaec89c1cebc7a3aa@mail.gmail.com" type="cite">hallo Myrta,

    Thank you for your advice.  I have tried reconfiguring with --disable-netcdf, and I have checked with ./configure --help that the key is correct.  Disappointing that the key had no effect on the problem.  Errors appeared just like before.

    Could it be related to authority?  I don't have root power.  The compilation was done in my own directory.

2008/12/25 Myrta Grüning <Myrta.Gruning@uclouvain.be>

Hallo Aaron,

the "About Intel Fortran Compiler" is indeed a message/warning that
appears every time you choose ifort and it does not imply that the
configure process failed.
It seems however that you have problem with the netcdf libraries.
NETCDF support is very useful, but at the moment not essential.
You can try to reconfigure abinit disabling netcdf (--disable-netcdf or
--enable-netcdf=no, check with ./configure --help if those keys are
correct). Then try again make to see if it works. I hope it does.

m

On Thu, December 25, 2008 5:14 am, Aaron wrote:
> Dear abinit users:
>
>      I have been trying to install abinit in a Fedora cluster, but have
> encountered a installation problem.  After unpacking abinit-5.6.4.tar.gz
> successfully, I executed commands in directory abinit-5.6.4/ in accordance
> with
> the following sequence:
> ./config/scripts/makemake
> everything was fine in this step, and then:
> ./configure FC=ifort
> configuration completed without error, except a warning like this:
>       +--------------------------------------------------------------+
>       | About the Intel Fortran compiler                             |
>       +--------------------------------------------------------------+
>       | Your compiler will work properly only if the LD_LIBRARY_PATH |
>       | and INTEL_LICENSE_FILE environment variables are correctly   |
>       | set-up. Please make sure that this is the case before        |
>       | building ABINIT.                                             |
>       |                                                              |
>       | In most cases it means sourcing a script in the Intel        |
>       | compiler install directory, e.g.:                            |
>       |                                                              |
>       | . /opt/intel/fc/9.1/bin/ifortvars.sh                         |
>       |                                                              |
>       | for a Bourne-like shell (do not forget the leading dot), or  |
>       |                                                              |
>       | source /opt/intel/fc/9.1/bin/ifortvars.csh                   |
>       |                                                              |
>       | for a C-like shell.                                          |
>       |                                                              |
>       | If you do not know what this is all about, please refer to   |
>       | the Intel documentation or ask your system administrator.    |
>       |                                                              |
>       | Please note that the same holds for the Intel C and C++      |
>       | compilers.                                                   |
>       +--------------------------------------------------------------+
> I don't know if the LD_LIBRARY_PATH and INTEL_LICENSE_FILE environment
> variables are correctly  set-up in my system, though I have checked
> environment
> variables and found these:
> *************************************************************
> declare -x
> INTEL_LICENSE_FILE="/home/opt/intel/licenses:/home/opt/intel//fce/10.1.015/licenses:/opt/intel/licenses:/home/mfeng/intel/licenses:/Users/Shared/Library/Application
> Support/Intel/Licenses"
> declare -x
> LD_LIBRARY_PATH="/home/opt/acml/4.0.0/pathscale64/lib:/home/opt/pathscale/lib/3.0:/home/opt/pathscale/lib/3.0/32:/home/opt/intel/impi/3.1/lib64:/home/opt/intel/mkl/10.0.3.020/lib/em64t:/home/opt/intel//fce/10.1.015/lib"
> *************************************************************
> So I continued to execute command:
> make
> then errors appeared as following:
> **************************************************************
> checking for C compiler default output file name...
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
> make[4]: *** [configure-stamp] Error 77
> make[4]: Leaving directory
> `/home/mfeng/abinit/abinit-5.6.4/plugins/netcdf'
> make[3]: *** [package-ready] Error 2
> make[3]: Leaving directory
> `/home/mfeng/abinit/abinit-5.6.4/plugins/netcdf'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/mfeng/abinit/abinit-5.6.4/plugins'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/mfeng/abinit/abinit-5.6.4'
> make: *** [all] Error 2
> **************************************************************
> I looked into config.log where I found these:
> **************************************************************
> conftest.c:16:28: error: ac_nonexistent.h: No such file or directory
> configure:9254: $? = 1
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "ABINIT"
> | #define PACKAGE_TARNAME "abinit"
> | #define PACKAGE_VERSION "5.6.4"
> | #define PACKAGE_STRING "ABINIT 5.6.4"
> | #define PACKAGE_BUGREPORT "https://bugs.launchpad.net/abinit/"
> | #define PACKAGE "abinit"
> | #define VERSION "5.6.4"
> | #define ABINIT_VERSION "5.6.4"
> | #define ABINIT_VERSION_MAJOR "5"
> | #define ABINIT_VERSION_MINOR "6"
> | #define ABINIT_VERSION_MICRO "4"
> | #define ABINIT_VERSION_BUILD "20081225"
> | #define ABINIT_VERSION_BASE "5.6"
> | /* end confdefs.h.  */
> .........
> conftest.c: In function 'main':
> conftest.c:34: error: 'not' undeclared (first use in this function)
> conftest.c:34: error: (Each undeclared identifier is reported only once
> conftest.c:34: error: for each function it appears in.)
> conftest.c:34: error: expected ';' before 'big'
> configure:11056: $? = 1
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME "ABINIT"
> | #define PACKAGE_TARNAME "abinit"
> | #define PACKAGE_VERSION "5.6.4"
> | #define PACKAGE_STRING "ABINIT 5.6.4"
> | #define PACKAGE_BUGREPORT "https://bugs.launchpad.net/abinit/"
> | #define PACKAGE "abinit"
> | #define VERSION "5.6.4"
> | #define ABINIT_VERSION "5.6.4"
> | #define ABINIT_VERSION_MAJOR "5"
> | #define ABINIT_VERSION_MINOR "6"
> | #define ABINIT_VERSION_MICRO "4"
> | #define ABINIT_VERSION_BUILD "20081225"
> | #define ABINIT_VERSION_BASE "5.6"
> | #define GCC_CC 1
> | #define STDC_HEADERS 1
> | #define HAVE_SYS_TYPES_H 1
> | #define HAVE_SYS_STAT_H 1
> | #define HAVE_STDLIB_H 1
> | #define HAVE_STRING_H 1
> | #define HAVE_MEMORY_H 1
> | #define HAVE_STRINGS_H 1
> | #define HAVE_INTTYPES_H 1
> | #define HAVE_STDINT_H 1
> | #define HAVE_UNISTD_H 1
> | /* end confdefs.h.  */
> | #include <sys/types.h>
> | #include <sys/param.h>
> |
> | int
> | main ()
> | {
> | #if BYTE_ORDER != BIG_ENDIAN
> |  not big endian
> | #endif
> |
> |   ;
> ............
> configure:12443: checking whether we are using the GNU Fortran compiler
> configure:12462: ifort -c   conftest.F >&5
> fortcom: Error: conftest.F, line 3: Syntax error, found END-OF-STATEMENT
> when
> expecting one of: => = . ( : %
>        choke me
> ---------------^
> fortcom: Error: conftest.F, line 3: This statement is positioned
> incorrectly
> and/or has syntax errors.
>        choke me
> ---------------^
> compilation aborted for conftest.F (code 1)
> configure:12468: $? = 1
> configure: failed program was:
> |     program main
> | #ifndef __GNUC__
> |      choke me
> | #endif
> |
> |     end
> **********************************************************************
> As I continued to execute command:
> make install
> compilation aborted with following errors:
> ***********************************************************************
> ifort -DHAVE_CONFIG_H -I. -I../.. -I../../src/defs -I../../src/defs
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/netcdf
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/etsf_io
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/bigdft   -g -O3 -arch pn4 -tune
> pn4
> -xT -extend_source -vec-report0 -c -o chkdpr.o chkdpr.F90
> ifort -DHAVE_CONFIG_H -I. -I../.. -I../../src/defs -I../../src/defs
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/netcdf
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/etsf_io
> -I/home/mfeng/abinit/abinit-5.6.4/plugins/bigdft   -g -O3 -arch pn4 -tune
> pn4
> -xT -extend_source -vec-report0 -c -o chkinp.o chkinp.F90
> fortcom: Error: chkinp.F90, line 50: Error in opening the compiled module
> file.
>  Check INCLUDE paths. [ETSF_IO]
>  use etsf_io
> -----^
> compilation aborted for chkinp.F90 (code 1)
> make[2]: *** [chkinp.o] Error 1
> make[2]: Leaving directory `/home/mfeng/abinit/abinit-5.6.4/src/13iovars'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/home/mfeng/abinit/abinit-5.6.4/src'
> make: *** [install-recursive] Error 1
> ***************************************************************************
>     I hope the problem would not be a serious one and someone could give
> me
> some suggestions.  Any advice is welcome.
>
> Best regards,
> Aaron
>

****************************************************
Dr. Myrta Gruning
Université Catholique de Louvain
SE/FSA/MAPR/PCPM
Pl. Croix du Sud 1
1348 - Louvain-la-Neuve (Belgium)

tel  : +32 (0)10/47 3568
fax  : +32 (0)10/47 3452
email: myrta.gruning@uclouvain.be
url  : http://www.myrta.eu