Hi, Nick
That works perfectly.
Thanks!
At 2014/11/3 16:58, Nick Papior Andersen wrote:
MPI_SIESTA should not be compiled for many of the utilities in the
Util directory.
In your case the Gen-basis/Makefile has a bug (it has been corrected
in later versions).
Change the lines:
DEFS:=$(DEFS_PREFIX)-UMPI $(DEFS)
FPPFLAGS:=$(DEFS_PREFIX)-UMPI $(FPPFLAGS)
to
DEFS:=$(DEFS) $(DEFS_PREFIX)-UMPI
FPPFLAGS:= $(FPPFLAGS) $(DEFS_PREFIX)-UMPI
and re-compile (remember "make clean").
2014-11-03 7:31 GMT+01:00 Bing Huang <[email protected]
<mailto:[email protected]>>:
In fact, i've noticed that mpi_siesta.mod exists under the
directory siesta/Obj/, by copying it to the Util/Gen-basis/, the
previous error dissapears. Unfortunately, new error message poped
up, as shown below. Any ideas?
######################################################################
############################## Error Message #########################
gen-basis.o: In function `gen_basis':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/gen-basis.F:68:
undefined reference to `mpi_init_'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/gen-basis.F:69:
undefined reference to `mpi_comm_rank_'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/gen-basis.F:70:
undefined reference to `mpi_comm_size_'
alloc.o: In function `print_report':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:1705:
undefined reference to `__mpi__r8_s_MOD_mpi_reduce_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:1707:
undefined reference to `__mpi__r8_v_MOD_mpi_reduce_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:1711:
undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:1723:
undefined reference to `__mpi__r8_s_MOD_mpi_recv_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:1718:
undefined reference to `__mpi__r8_s_MOD_mpi_send_t'
alloc.o: In function `__alloc_MOD_alloc_report':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:318:
undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:319:
undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/alloc.F90:320:
undefined reference to `__mpi__character_s_MOD_mpi_bcast_t'
xcmod.o: In function `__xcmod_MOD_setxc':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/xcmod.F:136:
undefined reference to `__mpi__integer_s_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/xcmod.F:138:
undefined reference to `__mpi__character_v_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/xcmod.F:140:
undefined reference to `__mpi__character_v_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/xcmod.F:142:
undefined reference to `__mpi__r8_v_MOD_mpi_bcast_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/xcmod.F:144:
undefined reference to `__mpi__r8_v_MOD_mpi_bcast_t'
memory.o: In function `printmemory_':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/memory.F:144:
undefined reference to `__mpi__integer_s_MOD_mpi_allreduce_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/memory.F:167:
undefined reference to `__mpi__integer_sv_MOD_mpi_gather_t'
atom_options.o: In function `__atom_options_MOD_get_atom_options':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/atom_options.F90:26:
undefined reference to `mpi_comm_rank_'
sys.o: In function `__sys_MOD_bye':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/sys.F:105:
undefined reference to `mpi_finalize_'
sys.o: In function `__sys_MOD_die':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/sys.F:69:
undefined reference to `mpi_abort_'
timer.o: In function `timer1_':
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/timer.F:117:
undefined reference to `__mpi__r8_s_MOD_mpi_allreduce_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/timer.F:164:
undefined reference to `__mpi__r8_v_MOD_mpi_reduce_t'
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/timer.F:139:
undefined reference to `__mpi__r8_v_MOD_mpi_reduce_t'
collect2: error: ld returned 1 exit status
make: *** [gen-basis] Error 1
######################################################################
############################## Error Message #########################
At 2014/11/3 14:00, Bing Huang wrote:
Hi, siesta users,
i've got an error (see the last part of this message) when
compiling the Gen-basis utility. Everything was just fine when
compling the main program (MPI version) of siesta and its
dependencies.
As suggested in the Makefile (whose absolute path is
`siesta-3.2/Util/Gen-basis/Makefile), i.e.,define an FC_SERIAL
symbol in my top arch.make, to avoid linking in the mpi libraries
even if we explicitly undefine MPI below.
I've followed exactly the suggestion by insert one line with
content "FC_SERIAL=gfortran" in top arch.make file and modified
the related lines in `siesta-3.2/Util/Gen-basis/Makefile
#+++++++++++++++++++++++++++++++++++++++++++++++++++
#FC_DEFAULT:=$(FC)
#FC_SERIAL?=$(FC_DEFAULT)
FC:=$(FC_SERIAL) # Make it non-recursive
#+++++++++++++++++++++++++++++++++++++++++++++++++++
the error still exists. Any suggestions?
Best regards,
Bing
######################################################################
############################## *Error Message*
#########################
bhuang@ubuntu:~/src/siesta-3.2/Util/Gen-basis$
<mailto:bhuang@ubuntu:%7E/src/siesta-3.2/Util/Gen-basis$> make
(cd fdf ; make -f
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/makefile
"FC=gfortran "
"VPATH=/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf"
\
"ARCH_MAKE=../../../Obj/arch.make" \
"INCFLAGS=-I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include " "FFLAGS=-g -O2" module)
make[1]: Entering directory
`/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/fdf'
In fdf, INCFLAGS is: -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
gfortran -c -g -O2 -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/fdf.f
Assembler messages:
Fatal error: can't create fdf.o: Permission denied
make[1]: *** [fdf.o] Error 1
make[1]: Leaving directory
`/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/fdf'
make: *** [libfdf.a] Error 2
bhuang@ubuntu:~/src/trash/siesta-3.2/Util/Gen-basis$
<mailto:bhuang@ubuntu:%7E/src/trash/siesta-3.2/Util/Gen-basis$>
sudo make
(cd fdf ; make -f
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/makefile
"FC=gfortran "
"VPATH=/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf"
\
"ARCH_MAKE=../../../Obj/arch.make" \
"INCFLAGS=-I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include " "FFLAGS=-g -O2" module)
make[1]: Entering directory
`/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/fdf'
In fdf, INCFLAGS is: -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
gfortran -c -g -O2 -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/fdf.f
gfortran -c -g -O2 -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/parse.f
gfortran -c -g -O2 -I
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf
-I/home/bhuang/netcdf/include
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/fdf/fdf_mod.f
ar cru libfdf.a fdf.o fdf_mod.o parse.o
ranlib libfdf.a
cp libfdf.a ..
make[1]: Leaving directory
`/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/fdf'
gfortran -c -g -O2 -I/home/bhuang/netcdf/include
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/parallel.f
gfortran -c -g -O2 -I/home/bhuang/netcdf/include -UMPI
-DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/precision.F
gfortran -c -g -O2 -I/home/bhuang/netcdf/include -UMPI
-DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/sys.F
/home/bhuang/src/trash/siesta-3.2/Util/Gen-basis/../../Src/sys.F:23.9:
use mpi_siesta
1
Fatal Error: Can't open module file 'mpi_siesta.mod' for reading
at (1): No such file or directory
make: *** [sys.o] Error 1
######################################################################
############################## *Error Message*
#########################
--
Kind regards Nick
