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Fwd: [Help-gsl] GSL not detected


From: Francesco Pietra
Subject: Fwd: [Help-gsl] GSL not detected
Date: Sat, 24 Oct 2009 07:15:15 +0200

I forgot to add that, in the attempts you have seen at gls-help, I
used LAM as provided by Debian in the meta-package  GROMACS. Unsure if
all headers were comprised, I have installed a new version, 1.3.3 of
openmpi, compiled gfortran, as OCTOPUS needs all libraries compiled
with the same compiler (Debian libraries are compiled with gfortran).
This is aside another installation of openmpi (1.2.6), Intel compiled.


---------- Forwarded message ----------
From: Francesco Pietra <address@hidden>
Date: Sat, Oct 24, 2009 at 7:08 AM
Subject: Re: [Help-gsl] GSL not detected
To: Francesco Pietra <address@hidden>, address@hidden
Cc: address@hidden


The thread can be found at <address@hidden>. To speed up, I
report here below, between ========, the new thread with the last
attempts of mine. It should be detailed enough to answer your
requests.

The OS is Debian Linux amd64 lenny and, until the problems are solved,
I am "experimenting" on a small machine, with two dual Opterons,
shared memory 8GB.
thanks
francesco

=======================================
In my .bashrc:

#For openmpi-1.2.6 Intel compiler

if [ "$LD_LIBRARY_PATH" ] ; then
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
else
 export LD_LIBRARY_PATH="/usr/local/lib"
fi

#For openmpi-1.3.3 gnu (gfortran) compiled

if [ "$LD_LIBRARY_PATH" ] ; then
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/lib"
else
 export LD_LIBRARY_PATH="/opt/lib"
fi


if [ "$PATH" ] ; then
 export PATH="$PATH:/opt/bin"
else
 export PATH="/opt/bin"
fi

(while "export PATH=.... does not work here)

now

address@hidden:~$ $PATH
bash: 
/opt/etsf/bin:/usr/local/delphi_4.1.1:/opt/intel/cce/10.1.015/bin:/opt/intel/fce/10.1.015/bin:/usr/local/bin/vmd:/usr/local/chimera/bin:/opt/etsf/bin:/usr/local/delphi_4.1.1:/opt/intel/cce/10.1.015/bin:/opt/intel/fce/10.1.015/bin:/usr/local/bin/vmd:/usr/local/chimera/bin:/opt/etsf/bin:/usr/local/delphi_4.1.1:/opt/intel/cce/10.1.015/bin:/opt/intel/fce/10.1.015/bin:/usr/local/bin/vmd:/usr/local/chimera/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/home/francesco/hole2/exe:/opt/bin:/usr/local/amber10/exe:/usr/local/dock6/bin:/home/francesco/hole2/exe:/opt/bin:/usr/local/amber10/exe:/usr/local/dock6/bin:/home/francesco/hole2/exe:/opt/bin:/usr/local/amber10/exe:/usr/local/dock6/bin:
No such file or directory
address@hidden:~$

To get info, I have to command

$ /opt/bin/ompi_info
which reports correctly.

$ ompi_info
reports about previous installation of 1.2.6 version (intel).
====================================================

address@hidden:~/octopus/octopus-3.1.0$ export FC=/opt/bin/mpif90

address@hidden:~/octopus/octopus-3.1.0$ export CC=/opt/bin/mpicc

address@hidden:~/octopus/octopus-3.1.0$ export FCFLAGS="-O3
-funroll-loops -ffast-math -ffree-line-length-none
-fsecond-underscore"

address@hidden:~/octopus/octopus-3.1.0$ ./configure --enable-mpi
--with-lapack='-L/opt/acml4.2.0/gfortran64_mp_int64/lib -llapack'
--with-blas='-L/opt/acml4.2.0/gfortran64_mp_int64/lib -lblas'

screen output:
**********************************************
***   octopus_mpi  will be generated
**********************************************
checking for sgemm in -L/opt/acml4.2.0/gfortran64_mp_int64/lib
-lblas... yes (-L/opt/acml4.2.0/gfortran64_mp_int64/lib -lblas)
checking for cheev in -L/opt/acml4.2.0/gfortran64_mp_int64/lib
-llapack... yes (-L/opt/acml4.2.0/gfortran64_mp_int64/lib -llapack)
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.9... no
*** Could not run GSL test program, checking why...
*** The test program failed to compile or link. See the file config.log for the
*** exact error that occured. This usually means GSL was incorrectly installed
*** or that you have moved GSL since it was installed. In the latter case, you
*** may want to edit the gsl-config script: /usr/bin/gsl-config
configure: error: could not find required gsl library
address@hidden:~/octopus/octopus-3.1.0$

Errors in config.log (config.log.no.gls.stated for my reference) are of type:

configure:5371: /opt/bin/mpicc -E  conftest.c
conftest.c:13:28: error: ac_nonexistent.h: No such file or directory

configure:6626: /opt/bin/mpicc -c -g -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:77: error: expected expression before ')' token

configure:8504: /opt/bin/mpicc -c -g -O2  conftest.c >&5
conftest.c: In function 'main':
conftest.c:84: error: too many arguments to function 'getpgrp'

/* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */

configure:8992: checking for strerror
configure:9048: /opt/bin/mpicc -o conftest -g -O2   conftest.c  >&5
configure:9055: $? = 0
configure:9077: result: yes

#define HAVE_STRERROR 1

configure:8992: checking for perror
configure:9048: /opt/bin/mpicc -o conftest -g -O2   conftest.c  >&5
configure:9055: $? = 0
configure:9077: result: yes


#define HAVE_PERROR 1

| #ifdef FC_DUMMY_MAIN
| #ifndef FC_DUMMY_MAIN_EQ_F77
| #  ifdef __cplusplus
|      extern "C"
| #  endif
|    int FC_DUMMY_MAIN() { return 1; }
| #endif
| #endif
| int
| main ()
| {
|  return 0;
|   ;
|   return 0;
| }
configure:13829: error: could not find required gsl library

ac_cv_func_perror=yes

ac_cv_func_strerror=yes

===========
Assuming that these are not fatal errors, "$ make" returned a variety
of undefined references:

atomic_oct.f90:(.text+0x5919): undefined reference to `xc_f90_gga_init__'
atomic_oct.f90:(.text+0x5942): undefined reference to `xc_f90_gga_init__'
../../src/species/libspecies.a(ps_hgh.o): In function
`__ps_hgh_m_MOD_vlocalr_scalar':
.................
root_solver_oct.f90:(.text+0xdc9): undefined reference to `oct_parse_int__'
root_solver_oct.f90:(.text+0xdf6): undefined reference to `oct_parse_int__'
../../src/math/libmath.a(solvers.o): In function
`__solvers_m_MOD_zqmr_sym_gen_dotp':
solvers_oct.f90:(.text+0x6789): undefined reference to `oct_progress_bar__'
solvers_oct.f90:(.text+0x6bee): undefined reference to `oct_progress_bar__'
../../src/math/libmath.a(solvers.o): In function
`__solvers_m_MOD_zqmr_gen_dotp':
...........................
splines_oct.f90:(.text+0x12af): undefined reference to `oct_spline_y__'
splines_oct.f90:(.text+0x12de): undefined reference to `oct_spline_eval__'
........................................
../../src/math/libmath.a(splines.o): In function
`__splines_m_MOD_spline_eval8_array':
............................
fft_oct.f90:(.text+0x7ea): undefined reference to `oct_fft_optimize__'
fft_oct.f90:(.text+0x856): undefined reference to `oct_fft_optimize__'
..........................
tdfunction_oct.f90:(.text+0x1318): undefined reference to
`oct_parse_block_int__'
tdfunction_oct.f90:(.text+0x1364): undefined reference to
`oct_parse_block_end__'
..............................
`__ode_solver_m_MOD_zode_solver_init':
ode_solver_oct.f90:(.text+0x3360): undefined reference to `oct_parse_int__'
................................
loct_oct.f90:(.text+0x9dad): undefined reference to `oct_rm__'
...............................
string_oct.f90:(.text+0x1360): undefined reference to `break_c_string__'
string_oct.f90:(.text+0x14b8): undefined reference to `break_c_string__'
../../src/basic/libbasic.a(varinfo.o): In function
`__varinfo_m_MOD_varinfo_print':
varinfo_oct.f90:(.text+0x2d): undefined reference to `varinfo_getvar__'
varinfo_oct.f90:(.text+0x82): undefined reference to `varinfo_getinfo__'
4): undefined reference to `varinfo_getopt__'
../../src/basic/libbasic.a(varinfo.o): In function

global_oct.f90:(.text+0x1d): undefined reference to `oct_gettimeofday__'
global_oct.f90:(.text+0x3b): undefined reference to `oct_getenv__'

loct_parser_oct.f90:(.text+0x31): undefined reference to `oct_parse_init__'
loct_parser_oct.f90:(.text+0xca): undefined reference to `oct_parse_input__'

loct_parser_oct.f90:(.text+0x5be): undefined reference to
`oct_parse_block_int__'
../../src/basic/libbasic.a(loct_parser.o): In function
`__loct_parser_m_MOD_oct_parse_putsym_double4':

`__loct_parser_m_MOD_oct_parse_complex4':
loct_parser_oct.f90:(.text+0x66b): undefined reference to `oct_parse_complex__'
../../src/basic/libbasic.a(loct_parser.o): In function
`__loct_parser_m_MOD_oct_parse_block_double4':

`__datasets_m_MOD_datasets_init':
datasets_oct.f90:(.text+0x95): undefined reference to `oct_parse_block_cols__'
datasets_oct.f90:(.text+0x260): undefined reference to `oct_parse_block_n__'
...........................
messages_oct.f90:(.text+0x4fc): undefined reference to `oct_mkdir__'
../../src/basic/libbasic.a(messages.o): In function `push_sub_write.1217':
messages_oct.f90:(.text+0x4b12): undefined reference to `oct_clock__'
............................
../../src/basic/libbasic.a(io.o): In function `__io_m_MOD_io_init':
io_oct.f90:(.text+0x1aa): undefined reference to `oct_parse_string__'
io_oct.f90:(.text+0x236): undefined reference to `oct_parse_string__'

units_oct.f90:(.text+0x6ef): undefined reference to `oct_parse_isdef__'
units_oct.f90:(.text+0x72b): undefined reference to `oct_parse_int__'
........................
profiling_oct.f90:(.text+0x1417): undefined reference to `oct_parse_int__'
.................
multicomm_oct.f90:(.text+0x3c28): undefined reference to `oct_parse_block_int__'
../../src/basic/libbasic.a(multicomm.o):multicomm_oct.f90:(.text+0x3c5d):
more undefined references to `oct_parse_block_int__' follow
/usr/lib/libmpi.so: undefined reference to `orte_data_value_t_class'
/usr/lib/libmpi.so: undefined reference to `opal_progress_event_increment'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_conversion_fn_null__'
/usr/lib/libmpi.so: undefined reference to `opal_progress_events'
/usr/lib/libmpi.so: undefined reference to `orte_hash_table_set_proc'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_conversion_fn_null'
/usr/lib/libmpi.so: undefined reference to `orte_gpr'
/usr/lib/libmpi.so: undefined reference to `orte_init_stage2'
/usr/lib/libmpi.so: undefined reference to `orte_schema'
/usr/lib/libmpi.so: undefined reference to `orte_gpr_trigger_t_class'
/usr/lib/libmpi_f77.so: undefined reference to `MPI_CONVERSION_FN_NULL'
/usr/lib/libmpi.so: undefined reference to `orte_ns'
/usr/lib/libmpi_f77.so: undefined reference to `ompi_registered_datareps'
/usr/lib/libmpi_f77.so: undefined reference to `mpi_conversion_fn_null_'
/usr/lib/libmpi.so: undefined reference to `opal_progress_mpi_init'
/usr/lib/libmpi.so: undefined reference to `orte_gpr_base_selected_component'
/usr/lib/libmpi.so: undefined reference to `orte_smr'
/usr/lib/libmpi.so: undefined reference to `opal_progress_mpi_disable'
/usr/lib/libmpi.so: undefined reference to `orte_app_context_map_t_class'
/usr/lib/libmpi.so: undefined reference to `orte_ns_name_wildcard'
/usr/lib/libmpi.so: undefined reference to `orte_system_info'
/usr/lib/libmpi.so: undefined reference to `orte_buffer_t_class'
/usr/lib/libmpi.so: undefined reference to `orte_rmgr'
/usr/lib/libmpi.so: undefined reference to `opal_progress_event_decrement'
/usr/lib/libmpi.so: undefined reference to `orte_hash_table_get_proc'
/usr/lib/libmpi.so: undefined reference to `orte_init_stage1'
/usr/lib/libmpi.so: undefined reference to `orte_dss'
/usr/lib/libmpi.so: undefined reference to `orte_gpr_subscription_t_class'
/usr/lib/libmpi.so: undefined reference to `opal_progress_mpi_enable'
make[3]: *** [octopus_mpi] Error 1
make[3]: Leaving directory `/home/francesco/octopus/octopus-3.1.0/src/main'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/francesco/octopus/octopus-3.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/francesco/octopus/octopus-3.1.0'
make: *** [all] Error 2
address@hidden:~/octopus/octopus-3.1.0$

========================================================================================

ON THE OTHER HAND, with

0$ ./configure --enable-mpi
--with-lapack='-L/opt/acml4.2.0/gfortran64_mp_int64/lib -llapack'
--with-blas='-L/opt/acml4.2.0/gfortran64_mp_int64/lib -lblas'
--with-gsl-prefix=/usr

the screen output is identical. The config.log
(config,log.with-gsl-prefix=usr for my reference), as far as gsl is
concerned;

configure:13552: checking for gsl-config
configure:13583: result: /usr/bin/gsl-config
configure:13592: checking for GSL - version >= 1.9
configure:13702: /opt/bin/mpicc -o conftest -g -O2 -I/usr/include
conftest.c -lnuma  -L/usr/lib -lgsl -lgslcblas -lm >&5

 system ("touch conf.gsltest");

===
$ make
returned the same errors as above.

 {
|       printf("\n*** 'gsl-config --version' returned %d.%d.%d, but
the minimum version\n", 1, 11, 0);
|       printf("*** of GSL required is %d.%d.%d. If gsl-config is
correct, then it is\n", major, minor, micro);
|       printf("*** best to upgrade to the required version.\n");
|       printf("*** If gsl-config was wrong, set the environment
variable GSL_CONFIG\n");
|       printf("*** to point to the correct copy of gsl-config, and
remove the file\n");
|       printf("*** config.cache before re-running configure\n");
|       exit(1);
|     }
| }
|
|
configure:13741: result: no
configure:13786: /opt/bin/mpicc -o conftest -g -O2 -I/usr/include
conftest.c -lnuma  -L/usr/lib -lgsl -lgslcblas -lm >&5

configure:13829: error: could not find required gsl library

ac_cv_path_GSL_CONFIG=/usr/bin/gsl-config

GREP='/bin/grep'
GSL_CFLAGS='-I/usr/include'
GSL_CONFIG='/usr/bin/gsl-config'
GSL_LIBS='-L/usr/lib -lgsl -lgslcblas -lm'
==================

Using "--with-gsl-exec-prefix=/usr/bin" triggered an incorrect vsearch
in search in "/usr/bin/bin".

Finally, /usr/bin/gsl-config initial part reads:

#! /bin/sh

prefix=/usr
exec_prefix=${prefix}
includedir=${prefix}/include
===============================================


On Fri, Oct 23, 2009 at 10:23 PM, Marco Maggi <address@hidden> wrote:
> "Francesco Pietra" wrote:
>> In  the  parallel  compilation  of software  OCTOPUS  with
>> gfortran  on   Debian  Linux  amd64  lenny,   gsl  is  not
>> seen.
>
> Interested people can find tarballs at:
>
> <http://www.tddft.org/programs/octopus/download/3.1.0/>
>
> disclaimer: I am no Octopus user.  I cannot try it because I
> do not have installed all the prerequisite packages.
>
>> As  the problem  was not  yet solved  through  the OCTOPUS
>> mailing list, I am asking help here.
>
> Can you  post a link to the  thread, so that we  can see how
> far did you go?
>
>> configure:13552: checking for gsl-config
>> configure:13570: found /usr/bin/gsl-config
>> configure:13583: result: /usr/bin/gsl-config
>> configure:13592: checking for GSL - version >= 1.9
>> configure:13702: /usr/lib/lam/bin/mpicc -o conftest -g -O2
>> -I/usr/include   conftest.c -lnuma  -L/usr/lib -lgsl -lgslcblas -lm >&5
>
> This  seems to  indicate that  gsl-config is  found  and run
> correctly.
>
>> /usr/lib/libmpi.so: undefined reference to `orte_init_stage2'
>> [...]
>> /usr/lib/libmpi.so: undefined reference to `opal_progress_mpi_init'
>
> This  seems  to indicate  that,  while  linking  the test  C
> program, the  libraries exporting the  "orte_*" and "opal_*"
> functions were not included on the command line.
>
>  I dunno where  they come from... from a  quick search they
> seem to be  OpenMPI stuff; is "mpicc" supposed  to link them
> in automatically?
>
>> configure:13706: $? = 1
>> configure: program exited with status 1
>
> This has nothing to do  with the GSL; the displayed error is
> about GSL-not-found  because the failed test program purpose
> was  to find  the GSL;  "configure" scripts  have no  way to
> distinguish the cause of the failure.
>
>  My  guess is that  Octopus' "configure.ac"  does something
> wrong around these lines:
>
> AC_LANG_PUSH(C)
> LIBS="${acx_save_libs}"
>
> maybe some more libraries should have been included in LIBS'
> value.  I see that a previous execution of "mpif90" included:
>
>  -lmpi -lopen-rte -lopen-pal
>
> maybe these are required by "mpicc", too.
>
> HTH
> --
> Marco Maggi
>
>




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